//**********************************************************************************************************************
vector<string> AlignCommand::setParameters(){
try {
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate);
- CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch);
- CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
- CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
- CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
- CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
- CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
- CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
- CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
- CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none","fasta-alignreport-accnos",false,true,true); parameters.push_back(pcandidate);
+ CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "","",false,false,true); parameters.push_back(psearch);
+ CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
+ CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
+ CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false,true); parameters.push_back(palign);
+ CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+ CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
+ CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pflip);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
+ CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string AlignCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string tag = "";
- map<string, vector<string> >::iterator it;
+string AlignCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { tag = "align"; }
- else if (type == "alignreport") { tag = "align.report"; }
- else if (type == "accnos") { tag = "flip.accnos"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return tag;
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "getOutputFileName");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],align"; } //makes file like: amazon.align
+ else if (type == "alignreport") { pattern = "[filename],align.report"; }
+ else if (type == "accnos") { pattern = "[filename],flip.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
AlignCommand::AlignCommand(){
try {
m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); }
- string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("fasta");
- string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("alignreport");
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("accnos");
+ map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s]));
+ string alignFileName = getOutputFileName("fasta", variables);
+ string reportFileName = getOutputFileName("alignreport", variables);
+ string accnosFileName = getOutputFileName("accnos", variables);
+
bool hasAccnos = true;
int numFastaSeqs = 0;
vector<string> setParameters();
string getCommandName() { return "align.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-9.\nSchloss PD (2009). A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.\nSchloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.\nhttp://www.mothur.org/wiki/Align.seqs http://www.mothur.org/wiki/Align.seqs"; }
string getDescription() { return "align sequences"; }
//**********************************************************************************************************************
vector<string> AmovaCommand::setParameters(){
try {
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
- CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(palpha);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","amova",false,true,true); parameters.push_back(pdesign);
+ CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","amova",false,true,true); parameters.push_back(pphylip);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string AmovaCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string tag = "";
- map<string, vector<string> >::iterator it;
+string AmovaCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "amova") { tag = "amova"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file.\n"); }
- }
- return tag;
- }
- catch(exception& e) {
- m->errorOut(e, "AmovaCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "amova") { pattern = "[filename],amova"; } //makes file like: amazon.align
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AmovaCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
AmovaCommand::AmovaCommand(){
//create a new filename
ofstream AMOVAFile;
- string AMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("amova");
+ map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
+ string AMOVAFileName = getOutputFileName("amova", variables);
+
m->openOutputFile(AMOVAFileName, AMOVAFile);
outputNames.push_back(AMOVAFileName); outputTypes["amova"].push_back(AMOVAFileName);
vector<string> setParameters();
string getCommandName() { return "amova"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
- string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
+ string getOutputPattern(string);
+ string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
string getDescription() { return "analysis of molecular variance"; }
int execute();
//**********************************************************************************************************************
vector<string> AnosimCommand::setParameters(){
try {
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(palpha);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","anosim",false,true,true); parameters.push_back(pdesign);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","anosim",false,true,true); parameters.push_back(pphylip);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string AnosimCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string AnosimCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "anosim") { outputFileName = "anosim"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "AnosimCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "anosim") { pattern = "[filename],anosim"; } //makes file like: amazon.align
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AnosimCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
AnosimCommand::AnosimCommand(){
//create a new filename
ofstream ANOSIMFile;
- string ANOSIMFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("anosim");
+ map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
+ string ANOSIMFileName = getOutputFileName("anosim", variables);
+
m->openOutputFile(ANOSIMFileName, ANOSIMFile);
outputNames.push_back(ANOSIMFileName); outputTypes["anosim"].push_back(ANOSIMFileName);
m->mothurOut("\ncomparison\tR-value\tP-value\n");
vector<string> setParameters();
string getCommandName() { return "anosim"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
string getDescription() { return "analysis of similarity"; }
//**********************************************************************************************************************
vector<string> BinSeqCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plist);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string BinSeqCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string BinSeqCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "fasta"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "BinSeqCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],[distance],fasta"; } //makes file like: amazon.0.03.fasta
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
BinSeqCommand::BinSeqCommand(){
if (groupfile != "") { delete groupMap; }
if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //set align file as new current fastafile
+ string currentFasta = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
//return 1 if error, 0 otherwise
int BinSeqCommand::process(ListVector* list) {
try {
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + "." + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = list->getLabel();
+ string outputFileName = getOutputFileName("fasta", variables);
+
m->openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
vector<string> setParameters();
string getCommandName() { return "bin.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
string getDescription() { return "maps sequences to otus"; }
//**********************************************************************************************************************
vector<string> CatchAllCommand::setParameters(){
try {
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
//can choose shared or sabund not both, so put them in the same chooseOnlyOneGroup
- CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(pshared);
- CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(psabund);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none","analysis-bestanalysis-models-bubble-summary",false,false,true); parameters.push_back(pshared);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none","analysis-bestanalysis-models-bubble-summary",false,false,true); parameters.push_back(psabund);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string CatchAllCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string CatchAllCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "csv") { outputFileName = "csv"; }
- else if (type == "summary") { outputFileName = "catchall.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "CatchAllCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "analysis") { pattern = "[filename],_Analysis.csv"; }
+ else if (type == "bestanalysis") { pattern = "[filename],_BestModelsAnalysis.csv"; }
+ else if (type == "models") { pattern = "[filename],_BestModelsAnalysis.csv"; }
+ else if (type == "bubble") { pattern = "[filename],_BubblePlot.csv"; }
+ else if (type == "summary") { pattern = "[filename],catchall.summary"; }
+ else if (type == "sabund") { pattern = "[filename],[distance],csv"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CatchAllCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
CatchAllCommand::CatchAllCommand(){
setParameters();
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["csv"] = tempOutNames;
+ outputTypes["analysis"] = tempOutNames;
+ outputTypes["bestanalysis"] = tempOutNames;
+ outputTypes["models"] = tempOutNames;
+ outputTypes["bubble"] = tempOutNames;
outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["csv"] = tempOutNames;
- outputTypes["summary"] = tempOutNames;
+ outputTypes["analysis"] = tempOutNames;
+ outputTypes["bestanalysis"] = tempOutNames;
+ outputTypes["models"] = tempOutNames;
+ outputTypes["bubble"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
set<string> processedLabels;
set<string> userLabels = labels;
- string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+ string summaryfilename = getOutputFileName("summary", variables);
summaryfilename = m->getFullPathName(summaryfilename);
if (m->debug) { m->mothurOut("[DEBUG]: Input File = " + inputFileNames[p] + ".\n[DEBUG]: inputdata address = " + toString(&input) + ".\n[DEBUG]: sabund address = " + toString(&sabund) + ".\n"); }
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
#else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
- catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
- //wrap entire string in ""
- catchAllCommand = "\"" + catchAllCommand + "\"";
+ //removes extra '\\' catchall doesnt like that
+ vector<string> tempNames;
+ string tempFilename = filename;
+ m->splitAtDash(tempFilename, tempNames);
+ tempFilename = tempNames[0];
+ tempNames.clear();
+ string tempOutputPath = outputPath;
+ m->splitAtDash(tempOutputPath, tempNames);
+ tempOutputPath = tempNames[0];
+ if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \"" + tempOutputPath + "\" 1";
+ catchAllCommand = "\"" + catchAllCommand + "\"";
#endif
if (m->debug) { m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
- outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
- outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
- outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
- outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv"));
+ variables["[filename]"] = filename;
+ outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables));
+ outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables));
+ outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables));
+ outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables));
if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
#else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
- catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
+ //removes extra '\\' catchall doesnt like that
+ vector<string> tempNames;
+ string tempFilename = filename;
+ m->splitAtDash(tempFilename, tempNames);
+ tempFilename = tempNames[0];
+ tempNames.clear();
+ string tempOutputPath = outputPath;
+ m->splitAtDash(tempOutputPath, tempNames);
+ tempOutputPath = tempNames[0];
+ if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \"" + tempOutputPath + "\" 1";
catchAllCommand = "\"" + catchAllCommand + "\"";
#endif
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
- outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
- outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
- outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
- outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv"));
+ variables["[filename]"] = filename;
+ outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables));
+ outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables));
+ outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables));
+ outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables));
if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
#else
- if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
- catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1";
- catchAllCommand = "\"" + catchAllCommand + "\"";
+ //removes extra '\\' catchall doesnt like that
+ vector<string> tempNames;
+ string tempFilename = filename;
+ m->splitAtDash(tempFilename, tempNames);
+ tempFilename = tempNames[0];
+ tempNames.clear();
+ string tempOutputPath = outputPath;
+ m->splitAtDash(tempOutputPath, tempNames);
+ tempOutputPath = tempNames[0];
+ if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); }
+ catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \"" + tempOutputPath + "\" 1";
+ catchAllCommand = "\"" + catchAllCommand + "\"";
#endif
if (m->debug) { m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
- outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
- outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
- outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
- outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
+ variables["[filename]"] = filename;
+ outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables));
+ outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables));
+ outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables));
+ outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables));
+ if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
//**********************************************************************************************************************
string CatchAllCommand::process(SAbundVector* sabund, string file1) {
try {
- string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + sabund->getLabel() + ".csv";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(file1));
+ variables["[distance]"] = sabund->getLabel();
+ string filename = getOutputFileName("sabund", variables);
filename = m->getFullPathName(filename);
ofstream out;
try {
ofstream out;
- string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ string combineFileName = getOutputFileName("summary", variables);
//open combined file
m->openOutputFile(combineFileName, out);
vector<string> setParameters();
string getCommandName() { return "catchall"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Bunge J, Woodard L, Bohning D, Foster JA, Connolly S, Allen HK (2012). Estimating population diversity with CatchAll. Bioinformatics 28:1045.\nhttp://www.northeastern.edu/catchall/index.html\nhttp://www.mothur.org/wiki/Catchall"; }
string getDescription() { return "estimate number of species"; }
//**********************************************************************************************************************
vector<string> ChimeraBellerophonCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none","none","none",false,true); parameters.push_back(pfasta);
- CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
- CommandParameter pcorrection("correction", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcorrection);
- CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
- CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none","none","none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
+ CommandParameter pcorrection("correction", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcorrection);
+ CommandParameter pwindow("window", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pwindow);
+ CommandParameter pincrement("increment", "Number", "", "25", "", "", "","",false,false); parameters.push_back(pincrement);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ChimeraBellerophonCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ChimeraBellerophonCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "chimera") { outputFileName = "bellerophon.chimeras"; }
- else if (type == "accnos") { outputFileName = "bellerophon.accnos"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraBellerophonCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "chimera") { pattern = "[filename],bellerophon.chimeras"; }
+ else if (type == "accnos") { pattern = "[filename],bellerophon.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraBellerophonCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);
- if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera");
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("accnos");
+ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]));
+ string outputFileName = getOutputFileName("chimera", variables);
+ string accnosFileName = getOutputFileName("accnos", variables);
chimera->getChimeras();
vector<string> setParameters();
string getCommandName() { return "chimera.bellerophon"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Huber T, Faulkner G, Hugenholtz P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-9. \nhttp://www.mothur.org/wiki/Chimera.bellerophon"; }
string getDescription() { return "detect chimeric sequences"; }
//**********************************************************************************************************************
vector<string> ChimeraCcodeCommand::setParameters(){
try {
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
- CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
- CommandParameter pnumwanted("numwanted", "Number", "", "20", "", "", "",false,false); parameters.push_back(pnumwanted);
- CommandParameter pmask("mask", "String", "", "", "", "", "",false,false); parameters.push_back(pmask);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-mapinfo-accnos",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
+ CommandParameter pwindow("window", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pwindow);
+ CommandParameter pnumwanted("numwanted", "Number", "", "20", "", "", "","",false,false); parameters.push_back(pnumwanted);
+ CommandParameter pmask("mask", "String", "", "", "", "", "","",false,false); parameters.push_back(pmask);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ChimeraCcodeCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ChimeraCcodeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "chimera") { outputFileName = "ccode.chimeras"; }
- else if (type == "mapinfo") { outputFileName = "mapinfo"; }
- else if (type == "accnos") { outputFileName = "ccode.accnos"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraCcodeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "chimera") { pattern = "[filename],[tag],ccode.chimeras-[filename],ccode.chimeras"; }
+ else if (type == "accnos") { pattern = "[filename],[tag],ccode.accnos-[filename],ccode.accnos"; }
+ else if (type == "mapinfo") { pattern = "[filename],mapinfo"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ChimeraCcodeCommand::ChimeraCcodeCommand(){
outputTypes["chimera"] = tempOutNames;
outputTypes["mapinfo"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
+
}
catch(exception& e) {
m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
outputTypes["chimera"] = tempOutNames;
outputTypes["mapinfo"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
string outputFileName, accnosFileName;
- if (maskfile != "") {
- outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + getOutputFileNameTag("chimera");
- accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + getOutputFileNameTag("accnos");
- }else {
- outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
- accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
-
- }
-
- string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("mapinfo");
-
-
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ string mapInfo = getOutputFileName("mapinfo", variables);
+ if (maskfile != "") { variables["[tag]"] = maskfile; }
+ outputFileName = getOutputFileName("chimera", variables);
+ accnosFileName = getOutputFileName("accnos", variables);
+
if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); return 0; }
#ifdef USE_MPI
vector<string> setParameters();
string getCommandName() { return "chimera.ccode"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
string getDescription() { return "detect chimeric sequences"; }
//**********************************************************************************************************************
vector<string> ChimeraCheckCommand::setParameters(){
try {
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter psvg("svg", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psvg);
- CommandParameter pincrement("increment", "Number", "", "10", "", "", "",false,false); parameters.push_back(pincrement);
- CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter psvg("svg", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psvg);
+ CommandParameter pincrement("increment", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pincrement);
+ CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ChimeraCheckCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ChimeraCheckCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "chimera") { outputFileName = "chimeracheck.chimeras"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraCcodeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "chimera") { pattern = "[filename],chimeracheck.chimeras"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCheckCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ChimeraCheckCommand::ChimeraCheckCommand(){
if (m->control_pressed) { delete chimera; return 0; }
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]));
+ string outputFileName = getOutputFileName("chimera", variables);
outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
#ifdef USE_MPI
vector<string> setParameters();
string getCommandName() { return "chimera.check"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
string getDescription() { return "detect chimeric sequences"; }
//**********************************************************************************************************************
vector<string> ChimeraPerseusCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "NameCount", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "NameCount", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter pcutoff("cutoff", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter palpha("alpha", "Number", "", "-5.54", "", "", "",false,false); parameters.push_back(palpha);
- CommandParameter pbeta("beta", "Number", "", "0.33", "", "", "",false,false); parameters.push_back(pbeta);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "NameCount", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "NameCount", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter pcutoff("cutoff", "Number", "", "0.5", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter palpha("alpha", "Number", "", "-5.54", "", "", "","",false,false); parameters.push_back(palpha);
+ CommandParameter pbeta("beta", "Number", "", "0.33", "", "", "","",false,false); parameters.push_back(pbeta);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ChimeraPerseusCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ChimeraPerseusCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "chimera") { outputFileName = "perseus.chimeras"; }
- else if (type == "accnos") { outputFileName = "perseus.accnos"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraPerseusCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "chimera") { pattern = "[filename],perseus.chimeras"; }
+ else if (type == "accnos") { pattern = "[filename],perseus.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ChimeraPerseusCommand::ChimeraPerseusCommand(){
m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
int start = time(NULL);
- if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
+ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ string outputFileName = getOutputFileName("chimera", variables);
+ string accnosFileName = getOutputFileName("accnos", variables);
//string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
it = counts.find(thisGroupsSeqs[i].getName());
if (it == counts.end()) { error = true; m->mothurOut("[ERROR]: " + thisGroupsSeqs[i].getName() + " is in your fasta file and not in your count file, please correct."); m->mothurOutEndLine(); }
else {
+ thisGroupsSeqs[i].setAligned(removeNs(thisGroupsSeqs[i].getUnaligned()));
sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), it->second));
if (thisGroupsSeqs[i].getUnaligned().length() > alignLength) { alignLength = thisGroupsSeqs[i].getUnaligned().length(); }
}
if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + thisGroupsSeqs[i].getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
else {
int num = m->getNumNames(it->second);
+ thisGroupsSeqs[i].setAligned(removeNs(thisGroupsSeqs[i].getUnaligned()));
sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), num));
if (thisGroupsSeqs[i].getUnaligned().length() > alignLength) { alignLength = thisGroupsSeqs[i].getUnaligned().length(); }
}
it = nameMap.find(temp.getName());
if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + temp.getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
else {
+ temp.setAligned(removeNs(temp.getUnaligned()));
sequences.push_back(seqData(temp.getName(), temp.getUnaligned(), it->second));
if (temp.getUnaligned().length() > alignLength) { alignLength = temp.getUnaligned().length(); }
}
}
}
//**********************************************************************************************************************
+string ChimeraPerseusCommand::removeNs(string seq){
+ try {
+ string newSeq = "";
+ for (int i = 0; i < seq.length(); i++) {
+ if (seq[i] != 'N') { newSeq += seq[i]; }
+ }
+ return newSeq;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPerseusCommand", "removeNs");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
vector<seqData> ChimeraPerseusCommand::readFiles(string inputFile, CountTable* ct){
try {
//read fasta file and create sequenceData structure - checking for file mismatches
int count = ct->getNumSeqs(temp.getName());
if (m->control_pressed) { break; }
else {
+ temp.setAligned(removeNs(temp.getUnaligned()));
sequences.push_back(seqData(temp.getName(), temp.getUnaligned(), count));
if (temp.getUnaligned().length() > alignLength) { alignLength = temp.getUnaligned().length(); }
}
vector<string> setParameters();
string getCommandName() { return "chimera.perseus"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38.\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194.\nhttp://www.mothur.org/wiki/Chimera.perseus\n"; }
string getDescription() { return "detect chimeric sequences"; }
int deconvoluteResults(map<string, string>&, string, string);
int driverGroups(string, string, int, int, vector<string>);
int createProcessesGroups(string, string, vector<string>, string, string, string);
+ string removeNs(string);
};
/**************************************************************************************************/
int totalSeqs = 0;
int numChimeras = 0;
- for (int i = pDataArray->start; i < pDataArray->end; i++) {
+ for (int u = pDataArray->start; u < pDataArray->end; u++) {
int start = time(NULL); if (pDataArray->m->control_pressed) { if (pDataArray->hasCount) { delete cparser; } { delete parser; } pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
- pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Checking sequences from group " + pDataArray->groups[i] + "..."); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Checking sequences from group " + pDataArray->groups[u] + "..."); pDataArray->m->mothurOutEndLine();
//vector<seqData> sequences = loadSequences(parser, groups[i]); - same function below
////////////////////////////////////////////////////////////////////////////////////////
int alignLength = 0;
vector<seqData> sequences;
if (pDataArray->hasCount) {
- vector<Sequence> thisGroupsSeqs = cparser->getSeqs(pDataArray->groups[i]);
- map<string, int> counts = cparser->getCountTable(pDataArray->groups[i]);
+ vector<Sequence> thisGroupsSeqs = cparser->getSeqs(pDataArray->groups[u]);
+ map<string, int> counts = cparser->getCountTable(pDataArray->groups[u]);
map<string, int>::iterator it;
for (int i = 0; i < thisGroupsSeqs.size(); i++) {
it = counts.find(thisGroupsSeqs[i].getName());
if (it == counts.end()) { error = true; pDataArray->m->mothurOut("[ERROR]: " + thisGroupsSeqs[i].getName() + " is in your fasta file and not in your count file, please correct."); pDataArray->m->mothurOutEndLine(); }
else {
+ string newSeq = "";
+ string tempSeq = thisGroupsSeqs[i].getUnaligned();
+ for (int j = 0; j < tempSeq.length(); j++) { if (tempSeq[j] != 'N') { newSeq += tempSeq[j]; } }
+ thisGroupsSeqs[i].setAligned(newSeq);
+
sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), it->second));
if (thisGroupsSeqs[i].getUnaligned().length() > alignLength) { alignLength = thisGroupsSeqs[i].getUnaligned().length(); }
}
}
}else{
- vector<Sequence> thisGroupsSeqs = parser->getSeqs(pDataArray->groups[i]);
- map<string, string> nameMap = parser->getNameMap(pDataArray->groups[i]);
+ vector<Sequence> thisGroupsSeqs = parser->getSeqs(pDataArray->groups[u]);
+ map<string, string> nameMap = parser->getNameMap(pDataArray->groups[u]);
map<string, string>::iterator it;
for (int i = 0; i < thisGroupsSeqs.size(); i++) {
if (it == nameMap.end()) { error = true; pDataArray->m->mothurOut("[ERROR]: " + thisGroupsSeqs[i].getName() + " is in your fasta file and not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); }
else {
int num = pDataArray->m->getNumNames(it->second);
+ string newSeq = "";
+ string tempSeq = thisGroupsSeqs[i].getUnaligned();
+ for (int j = 0; j < tempSeq.length(); j++) { if (tempSeq[j] != 'N') { newSeq += tempSeq[j]; } }
+ thisGroupsSeqs[i].setAligned(newSeq);
+
sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), num));
if (thisGroupsSeqs[i].getUnaligned().length() > alignLength) { alignLength = thisGroupsSeqs[i].getUnaligned().length(); }
}
//int numSeqs = driver((outputFName + groups[i]), sequences, (accnos+groups[i]), numChimeras); - same function below
////////////////////////////////////////////////////////////////////////////////////////
- string chimeraFileName = pDataArray->outputFName+pDataArray->groups[i];
- string accnosFileName = pDataArray->accnos+pDataArray->groups[i];
+ string chimeraFileName = pDataArray->outputFName+pDataArray->groups[u];
+ string accnosFileName = pDataArray->accnos+pDataArray->groups[u];
vector<vector<double> > correctModel(4); //could be an option in the future to input own model matrix
for(int j=0;j<4;j++){ correctModel[j].resize(4); }
//append files
pDataArray->m->appendFiles(chimeraFileName, pDataArray->outputFName); pDataArray->m->mothurRemove(chimeraFileName);
pDataArray->m->appendFiles(accnosFileName, pDataArray->accnos); pDataArray->m->mothurRemove(accnosFileName);
- pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + pDataArray->groups[i] + "."); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + pDataArray->groups[u] + "."); pDataArray->m->mothurOutEndLine();
if (pDataArray->m->control_pressed) { if (pDataArray->hasCount) { delete cparser; } { delete parser; } pDataArray->m->mothurRemove(pDataArray->outputFName); pDataArray->m->mothurRemove(pDataArray->accnos); return 0; }
}
//**********************************************************************************************************************
vector<string> ChimeraPintailCommand::setParameters(){
try {
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pconservation("conservation", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pconservation);
- CommandParameter pquantile("quantile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pquantile);
- CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
- CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
- CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement);
- CommandParameter pmask("mask", "String", "", "", "", "", "",false,false); parameters.push_back(pmask);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pconservation("conservation", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconservation);
+ CommandParameter pquantile("quantile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pquantile);
+ CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
+ CommandParameter pwindow("window", "Number", "", "0", "", "", "","","",false,false); parameters.push_back(pwindow);
+ CommandParameter pincrement("increment", "Number", "", "25", "", "", "","",false,false); parameters.push_back(pincrement);
+ CommandParameter pmask("mask", "String", "", "", "", "", "","",false,false); parameters.push_back(pmask);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ChimeraPintailCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ChimeraPintailCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "chimera") { outputFileName = "pintail.chimeras"; }
- else if (type == "accnos") { outputFileName = "pintail.accnos"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraPintailCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "chimera") { pattern = "[filename],[tag],pintail.chimeras-[filename],pintail.chimeras"; }
+ else if (type == "accnos") { pattern = "[filename],[tag],pintail.accnos-[filename],pintail.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraPintailCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ChimeraPintailCommand::ChimeraPintailCommand(){
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
+
}
catch(exception& e) {
m->errorOut(e, "ChimeraPintailCommand", "ChimeraPintailCommand");
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
inputDir = validParameter.validFile(parameters, "inputdir", false);
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
string outputFileName, accnosFileName;
- if (maskfile != "") {
- outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + getOutputFileNameTag("chimera");
- accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + getOutputFileNameTag("accnos");
- }else {
- outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
- accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
- }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ if (maskfile != "") { variables["[tag]"] = m->getSimpleName(m->getRootName(maskfile)); }
+ outputFileName = getOutputFileName("chimera", variables);
+ accnosFileName = getOutputFileName("accnos", variables);
+
if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
vector<string> setParameters();
string getCommandName() { return "chimera.pintail"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-36. \nAshelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-41. \nhttp://www.mothur.org/wiki/Chimera.pintail"; }
string getDescription() { return "detect chimeric sequences"; }
//**********************************************************************************************************************
vector<string> ChimeraSlayerCommand::setParameters(){
try {
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pwindow("window", "Number", "", "50", "", "", "",false,false); parameters.push_back(pwindow);
- CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
- CommandParameter pmatch("match", "Number", "", "5.0", "", "", "",false,false); parameters.push_back(pmatch);
- CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "",false,false); parameters.push_back(pmismatch);
- CommandParameter pminsim("minsim", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminsim);
- CommandParameter pmincov("mincov", "Number", "", "70", "", "", "",false,false); parameters.push_back(pmincov);
- CommandParameter pminsnp("minsnp", "Number", "", "10", "", "", "",false,false); parameters.push_back(pminsnp);
- CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs);
- CommandParameter psearch("search", "Multiple", "kmer-blast", "blast", "", "", "",false,false); parameters.push_back(psearch);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter prealign("realign", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(prealign);
- CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim);
- CommandParameter psplit("split", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psplit);
- CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "",false,false); parameters.push_back(pnumwanted);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "",false,false); parameters.push_back(pdivergence);
- CommandParameter pparents("parents", "Number", "", "3", "", "", "",false,false); parameters.push_back(pparents);
- CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement);
- CommandParameter pblastlocation("blastlocation", "String", "", "", "", "", "",false,false); parameters.push_back(pblastlocation);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pwindow("window", "Number", "", "50", "", "", "","",false,false); parameters.push_back(pwindow);
+ CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
+ CommandParameter pmatch("match", "Number", "", "5.0", "", "", "","",false,false); parameters.push_back(pmatch);
+ CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+ CommandParameter pminsim("minsim", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pminsim);
+ CommandParameter pmincov("mincov", "Number", "", "70", "", "", "","",false,false); parameters.push_back(pmincov);
+ CommandParameter pminsnp("minsnp", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pminsnp);
+ CommandParameter pminbs("minbs", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pminbs);
+ CommandParameter psearch("search", "Multiple", "kmer-blast", "blast", "", "", "","",false,false); parameters.push_back(psearch);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter prealign("realign", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(prealign);
+ CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "","fasta",false,false); parameters.push_back(ptrim);
+ CommandParameter psplit("split", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psplit);
+ CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "","",false,false); parameters.push_back(pnumwanted);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "","",false,false); parameters.push_back(pdivergence);
+ CommandParameter pparents("parents", "Number", "", "3", "", "", "","",false,false); parameters.push_back(pparents);
+ CommandParameter pincrement("increment", "Number", "", "5", "", "", "","",false,false); parameters.push_back(pincrement);
+ CommandParameter pblastlocation("blastlocation", "String", "", "", "", "", "","",false,false); parameters.push_back(pblastlocation);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ChimeraSlayerCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ChimeraSlayerCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "chimera") { outputFileName = "slayer.chimeras"; }
- else if (type == "accnos") { outputFileName = "slayer.accnos"; }
- else if (type == "fasta") { outputFileName = "slayer.fasta"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "chimera") { pattern = "[filename],slayer.chimeras"; }
+ else if (type == "accnos") { pattern = "[filename],slayer.accnos"; }
+ else if (type == "fasta") { pattern = "[filename],slayer.fasta"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ChimeraSlayerCommand::ChimeraSlayerCommand(){
m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
int start = time(NULL);
- if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
- string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("fasta");
+ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ string outputFileName = getOutputFileName("chimera", variables);
+ string accnosFileName = getOutputFileName("accnos", variables);
+ string trimFastaFileName = getOutputFileName("fasta", variables);
//clears files
ofstream out, out1, out2;
vector<string> setParameters();
string getCommandName() { return "chimera.slayer"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494.\nhttp://www.mothur.org/wiki/Chimera.slayer"; }
string getDescription() { return "detect chimeric sequences"; }
//**********************************************************************************************************************
vector<string> ChimeraUchimeCommand::setParameters(){
try {
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter pabskew("abskew", "Number", "", "1.9", "", "", "",false,false); parameters.push_back(pabskew);
- CommandParameter pchimealns("chimealns", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pchimealns);
- CommandParameter pminh("minh", "Number", "", "0.3", "", "", "",false,false); parameters.push_back(pminh);
- CommandParameter pmindiv("mindiv", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pmindiv);
- CommandParameter pxn("xn", "Number", "", "8.0", "", "", "",false,false); parameters.push_back(pxn);
- CommandParameter pdn("dn", "Number", "", "1.4", "", "", "",false,false); parameters.push_back(pdn);
- CommandParameter pxa("xa", "Number", "", "1", "", "", "",false,false); parameters.push_back(pxa);
- CommandParameter pchunks("chunks", "Number", "", "4", "", "", "",false,false); parameters.push_back(pchunks);
- CommandParameter pminchunk("minchunk", "Number", "", "64", "", "", "",false,false); parameters.push_back(pminchunk);
- CommandParameter pidsmoothwindow("idsmoothwindow", "Number", "", "32", "", "", "",false,false); parameters.push_back(pidsmoothwindow);
- CommandParameter pdups("dereplicate", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdups);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter pabskew("abskew", "Number", "", "1.9", "", "", "","",false,false); parameters.push_back(pabskew);
+ CommandParameter pchimealns("chimealns", "Boolean", "", "F", "", "", "","alns",false,false); parameters.push_back(pchimealns);
+ CommandParameter pminh("minh", "Number", "", "0.3", "", "", "","",false,false); parameters.push_back(pminh);
+ CommandParameter pmindiv("mindiv", "Number", "", "0.5", "", "", "","",false,false); parameters.push_back(pmindiv);
+ CommandParameter pxn("xn", "Number", "", "8.0", "", "", "","",false,false); parameters.push_back(pxn);
+ CommandParameter pdn("dn", "Number", "", "1.4", "", "", "","",false,false); parameters.push_back(pdn);
+ CommandParameter pxa("xa", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pxa);
+ CommandParameter pchunks("chunks", "Number", "", "4", "", "", "","",false,false); parameters.push_back(pchunks);
+ CommandParameter pminchunk("minchunk", "Number", "", "64", "", "", "","",false,false); parameters.push_back(pminchunk);
+ CommandParameter pidsmoothwindow("idsmoothwindow", "Number", "", "32", "", "", "","",false,false); parameters.push_back(pidsmoothwindow);
+ CommandParameter pdups("dereplicate", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdups);
//CommandParameter pminsmoothid("minsmoothid", "Number", "", "0.95", "", "", "",false,false); parameters.push_back(pminsmoothid);
- CommandParameter pmaxp("maxp", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmaxp);
- CommandParameter pskipgaps("skipgaps", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pskipgaps);
- CommandParameter pskipgaps2("skipgaps2", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pskipgaps2);
- CommandParameter pminlen("minlen", "Number", "", "10", "", "", "",false,false); parameters.push_back(pminlen);
- CommandParameter pmaxlen("maxlen", "Number", "", "10000", "", "", "",false,false); parameters.push_back(pmaxlen);
- CommandParameter pucl("ucl", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pucl);
- CommandParameter pqueryfract("queryfract", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pqueryfract);
+ CommandParameter pmaxp("maxp", "Number", "", "2", "", "", "","",false,false); parameters.push_back(pmaxp);
+ CommandParameter pskipgaps("skipgaps", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pskipgaps);
+ CommandParameter pskipgaps2("skipgaps2", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pskipgaps2);
+ CommandParameter pminlen("minlen", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pminlen);
+ CommandParameter pmaxlen("maxlen", "Number", "", "10000", "", "", "","",false,false); parameters.push_back(pmaxlen);
+ CommandParameter pucl("ucl", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pucl);
+ CommandParameter pqueryfract("queryfract", "Number", "", "0.5", "", "", "","",false,false); parameters.push_back(pqueryfract);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ChimeraUchimeCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ChimeraUchimeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "chimera") { outputFileName = "uchime.chimeras"; }
- else if (type == "accnos") { outputFileName = "uchime.accnos"; }
- else if (type == "alns") { outputFileName = "uchime.alns"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraUchimeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "chimera") { pattern = "[filename],uchime.chimeras"; }
+ else if (type == "accnos") { pattern = "[filename],uchime.accnos"; }
+ else if (type == "alns") { pattern = "[filename],uchime.alns"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraUchimeCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ChimeraUchimeCommand::ChimeraUchimeCommand(){
int start = time(NULL);
string nameFile = "";
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
- string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("alns");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ string outputFileName = getOutputFileName("chimera", variables);
+ string accnosFileName = getOutputFileName("accnos", variables);
+ string alnsFileName = getOutputFileName("alns", variables);
string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
//you provided a groupfile
vector<string> setParameters();
string getCommandName() { return "chimera.uchime"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code was donated to the public domain.\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194.\nhttp://www.mothur.org/wiki/Chimera.uchime\n"; }
string getDescription() { return "detect chimeric sequences"; }
//**********************************************************************************************************************
vector<string> ChopSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnumbases);
- CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcountgaps);
- CommandParameter pshort("short", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshort);
- CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "",false,false); parameters.push_back(pkeep);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "","",false,true,true); parameters.push_back(pnumbases);
+ CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcountgaps);
+ CommandParameter pshort("short", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshort);
+ CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "","",false,false); parameters.push_back(pkeep);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ChopSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ChopSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "chop.fasta"; }
- else if (type == "accnos") { outputFileName = "chop.accnos"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],chop.fasta"; }
+ else if (type == "accnos") { pattern = "[filename],chop.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ChopSeqsCommand::ChopSeqsCommand(){
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
- string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
-
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileName = getOutputFileName("fasta", variables);
+ string outputFileNameAccnos = getOutputFileName("accnos", variables);
vector<unsigned long long> positions;
vector<linePair> lines;
vector<string> setParameters();
string getCommandName() { return "chop.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
string getDescription() { return "trim sequence length"; }
//**********************************************************************************************************************
vector<string> ClassifyOtuCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(preftaxonomy);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pbasis("basis", "Multiple", "otu-sequence", "otu", "", "", "",false,false); parameters.push_back(pbasis);
- CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "",false,true); parameters.push_back(pcutoff);
- CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pprobs);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","constaxonomy",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(preftaxonomy);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppersample);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pbasis("basis", "Multiple", "otu-sequence", "otu", "", "", "","",false,false); parameters.push_back(pbasis);
+ CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "","",false,true); parameters.push_back(pcutoff);
+ CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pprobs);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ClassifyOtuCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ClassifyOtuCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "constaxonomy") { outputFileName = "cons.taxonomy"; }
- else if (type == "taxsummary") { outputFileName = "cons.tax.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ClassifyOtuCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "constaxonomy") { pattern = "[filename],[distance],cons.taxonomy"; }
+ else if (type == "taxsummary") { pattern = "[filename],[distance],cons.tax.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyOtuCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ClassifyOtuCommand::ClassifyOtuCommand(){
if (outputDir == "") { outputDir += m->hasPath(listfile); }
ofstream out;
- string outputFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." +getOutputFileNameTag("constaxonomy");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = processList->getLabel();
+ string outputFile = getOutputFileName("constaxonomy", variables);
m->openOutputFile(outputFile, out);
outputNames.push_back(outputFile); outputTypes["constaxonomy"].push_back(outputFile);
ofstream outSum;
- string outputSumFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." +getOutputFileNameTag("taxsummary");
+ string outputSumFile = getOutputFileName("taxsummary", variables);
m->openOutputFile(outputSumFile, outSum);
outputNames.push_back(outputSumFile); outputTypes["taxsummary"].push_back(outputSumFile);
for (int i = 0; i < groups.size(); i++) {
groupIndex[groups[i]] = i;
ofstream* temp = new ofstream();
- string outputFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + groups[i] + "." +getOutputFileNameTag("constaxonomy");
+ variables["[distance]"] = processList->getLabel() + "." + groups[i];
+ string outputFile = getOutputFileName("constaxonomy", variables);
m->openOutputFile(outputFile, *temp);
(*temp) << "OTU\tSize\tTaxonomy" << endl;
outs.push_back(temp);
outputNames.push_back(outputFile); outputTypes["constaxonomy"].push_back(outputFile);
ofstream* tempSum = new ofstream();
- string outputSumFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + groups[i] + "." +getOutputFileNameTag("taxsummary");
+ string outputSumFile = getOutputFileName("taxsummary", variables);
m->openOutputFile(outputSumFile, *tempSum);
outSums.push_back(tempSum);
outputNames.push_back(outputSumFile); outputTypes["taxsummary"].push_back(outputSumFile);
vector<string> setParameters();
string getCommandName() { return "classify.otu"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nhttp://www.mothur.org/wiki/Classify.otu"; }
string getDescription() { return "find the concensus taxonomy for each OTU"; }
//**********************************************************************************************************************
vector<string> ClassifySeqsCommand::setParameters(){
try {
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","taxonomy",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
- CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance-align", "kmer", "", "", "",false,false); parameters.push_back(psearch);
- CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
- CommandParameter pmethod("method", "Multiple", "wang-knn-zap", "wang", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
- CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
- CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
- CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
- //CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
- CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
- CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pprobs);
- CommandParameter piters("iters", "Number", "", "100", "", "", "",false,true); parameters.push_back(piters);
- CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
- CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshortcuts);
- CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "",false,true); parameters.push_back(pnumwanted);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance-align", "kmer", "", "", "","",false,false); parameters.push_back(psearch);
+ CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
+ CommandParameter pmethod("method", "Multiple", "wang-knn-zap", "wang", "", "", "","",false,false); parameters.push_back(pmethod);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
+ CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+ CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
+ CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
+ CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "","",false,true); parameters.push_back(pcutoff);
+ CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pprobs);
+ CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,true); parameters.push_back(piters);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
+ CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshortcuts);
+ CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "","",false,true); parameters.push_back(pnumwanted);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ClassifySeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ClassifySeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "taxonomy") { outputFileName = "taxonomy"; }
- else if (type == "accnos") { outputFileName = "flip.accnos"; }
- else if (type == "taxsummary") { outputFileName = "tax.summary"; }
- else if (type == "matchdist") { outputFileName = "match.dist"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ClassifySeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "taxonomy") { pattern = "[filename],[tag],[tag2],taxonomy"; }
+ else if (type == "taxsummary") { pattern = "[filename],[tag],[tag2],tax.summary"; }
+ else if (type == "accnos") { pattern = "[filename],[tag],[tag2],flip.accnos"; }
+ else if (type == "matchdist") { pattern = "[filename],[tag],[tag2],match.dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ClassifySeqsCommand::ClassifySeqsCommand(){
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
}
-
- it = parameters.find("group");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["group"] = inputDir + it->second; }
- }
-
- it = parameters.find("count");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["count"] = inputDir + it->second; }
- }
- }
+ }
fastaFileName = validParameter.validFile(parameters, "fasta", false);
if (fastaFileName == "not found") {
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < groupfileNames.size(); i++) {
- if (inputDir != "") {
- string path = m->hasPath(groupfileNames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { groupfileNames[i] = inputDir + groupfileNames[i]; }
- }
- int ableToOpen;
- ifstream in;
- ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
- m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- groupfileNames[i] = tryPath;
+ bool ignore = false;
+ if (groupfileNames[i] == "current") {
+ groupfileNames[i] = m->getGroupFile();
+ if (groupfileNames[i] != "") { m->mothurOut("Using " + groupfileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current group file, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ groupfileNames.erase(groupfileNames.begin()+i);
+ i--;
}
}
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
- m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- groupfileNames[i] = tryPath;
+ if (!ignore) {
+
+ if (inputDir != "") {
+ string path = m->hasPath(groupfileNames[i]);
+ cout << path << '\t' << inputDir << endl;
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { groupfileNames[i] = inputDir + groupfileNames[i]; }
+ }
+
+ int ableToOpen;
+
+ ifstream in;
+ ableToOpen = m->openInputFile(groupfileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
+ m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ groupfileNames[i] = tryPath;
+ }
+ }
+
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
+ m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ groupfileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ groupfileNames.erase(groupfileNames.begin()+i);
+ i--;
+ }else {
+ m->setGroupFile(groupfileNames[i]);
}
}
- in.close();
-
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
- //erase from file list
- groupfileNames.erase(groupfileNames.begin()+i);
- i--;
- }else {
- m->setGroupFile(groupfileNames[i]);
- }
}
}
else if (foundDot && (baseTName[i] == '.')) { break; }
else if (!foundDot && (baseTName[i] == '.')) { foundDot = true; }
}
- if (RippedTaxName != "") { RippedTaxName += "."; }
+ //if (RippedTaxName != "") { RippedTaxName += "."; }
if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
- string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + outputMethodTag + getOutputFileNameTag("taxonomy");
- string newaccnosFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + outputMethodTag +getOutputFileNameTag("accnos");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ variables["[tag]"] = RippedTaxName;
+ variables["[tag2]"] = outputMethodTag;
+ string newTaxonomyFile = getOutputFileName("taxonomy", variables);
+ string newaccnosFile = getOutputFileName("accnos", variables);
string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
- string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + outputMethodTag + getOutputFileNameTag("taxsummary");
+ string taxSummary = getOutputFileName("taxsummary", variables);
if ((method == "knn") && (search == "distance")) {
- string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("matchdist");
+ string DistName = getOutputFileName("matchdist", variables);
classify->setDistName(DistName); outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName);
}
vector<string> setParameters();
string getCommandName() { return "classify.seqs"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
string getDescription() { return "classify sequences"; }
vector<string> ClassifySharedCommand::setParameters(){
try {
//CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
- CommandParameter potupersplit("otupersplit", "Multiple", "log2-squareroot", "log2", "", "", "",false,false); parameters.push_back(potupersplit);
- CommandParameter psplitcriteria("splitcriteria", "Multiple", "gainratio-infogain", "gainratio", "", "", "",false,false); parameters.push_back(psplitcriteria);
- CommandParameter pnumtrees("numtrees", "Number", "", "100", "", "", "",false,false); parameters.push_back(pnumtrees);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+ CommandParameter potupersplit("otupersplit", "Multiple", "log2-squareroot", "log2", "", "", "","",false,false); parameters.push_back(potupersplit);
+ CommandParameter psplitcriteria("splitcriteria", "Multiple", "gainratio-infogain", "gainratio", "", "", "","",false,false); parameters.push_back(psplitcriteria);
+ CommandParameter pnumtrees("numtrees", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pnumtrees);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ClassifySharedCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string tag = "";
- map<string, vector<string> >::iterator it;
+string ClassifySharedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "summary") { tag = "summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return tag;
- }
- catch(exception& e) {
- m->errorOut(e, "ClassifySharedCommand", "getOutputFileName");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],[distance],summary"; } //makes file like: amazon.0.03.fasta
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySharedCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
randomForest.populateDecisionTrees();
randomForest.calcForrestErrorRate();
- string filename = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = lookup[0]->getLabel();
+ string filename = getOutputFileName("summary", variables);
outputNames.push_back(filename); outputTypes["summary"].push_back(filename);
randomForest.calcForrestVariableImportance(filename);
vector<string> setParameters();
string getCommandName() { return "classify.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
- string getHelpString();
+
+ string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Classify.shared\n"; }
string getDescription() { return "description"; }
int execute();
//**********************************************************************************************************************
vector<string> ClassifyTreeCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "", "", "none",false,true); parameters.push_back(ptree);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "", "", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "",false,true); parameters.push_back(pcutoff);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "", "", "none","tree-summary",false,true,true); parameters.push_back(ptree);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "", "", "none","",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "","",false,true); parameters.push_back(pcutoff);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ClassifyTreeCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ClassifyTreeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "tree") { outputFileName = "taxonomy.tre"; }
- else if (type == "summary") { outputFileName = "taxonomy.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ClassifyTreeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],taxonomy.summary"; } //makes file like: amazon.0.03.fasta
+ else if (type == "tree") { pattern = "[filename],taxonomy.tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifyTreeCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ClassifyTreeCommand::ClassifyTreeCommand(){
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(treefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(treefile));
+ string outputFileName = getOutputFileName("summary", variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
string treeOutputDir = outputDir;
if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
- string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
+ variables["[filename]"] = treeOutputDir + m->getRootName(m->getSimpleName(treefile));
+ string outputTreeFileName = getOutputFileName("tree", variables);
//create a map from tree node index to names of descendants, save time later
map<int, map<string, set<string> > > nodeToDescendants; //node# -> (groupName -> groupMembers)
vector<string> setParameters();
string getCommandName() { return "classify.tree"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Classify.tree"; }
string getDescription() { return "Find the consensus taxonomy for the descendant of each tree node"; }
//**********************************************************************************************************************
vector<string> ClearcutCommand::setParameters(){
try {
- CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pverbose);
- CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pquiet);
- CommandParameter pversion("version", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pversion);
- CommandParameter pseed("seed", "String", "", "", "*", "", "",false,false); parameters.push_back(pseed);
- CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnorandom);
- CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshuffle);
- CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pneighbor);
- CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpblen);
- CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpdist);
- CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pDNA);
- CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pprotein);
- CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pjukes);
- CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkimura);
- CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pstdout);
- CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "",false,false); parameters.push_back(pntrees);
- CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "",false,false); parameters.push_back(pmatrixout);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pphylip);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pverbose);
+ CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pquiet);
+ CommandParameter pversion("version", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pversion);
+ CommandParameter pseed("seed", "String", "", "", "*", "", "","",false,false); parameters.push_back(pseed);
+ CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnorandom);
+ CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshuffle);
+ CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pneighbor);
+ CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpblen);
+ CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpdist);
+ CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pDNA);
+ CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pprotein);
+ CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pjukes);
+ CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkimura);
+ CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pstdout);
+ CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pntrees);
+ CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "","",false,false); parameters.push_back(pmatrixout);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ClearcutCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ClearcutCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "tree") { outputFileName = "tre"; }
- else if (type == "matrixout") { outputFileName = ""; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ClearcutCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "matrixout") { pattern = "[filename],"; }
+ else if (type == "tree") { pattern = "[filename],tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ClearcutCommand::ClearcutCommand(){
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//prepare filename
- string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + getOutputFileNameTag("tree");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFile));
+ string outputName = getOutputFileName("tree", variables);
outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
vector<char*> cPara;
vector<string> setParameters();
string getCommandName() { return "clearcut"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Sheneman L, Evans J, Foster JA (2006). Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22: 2823-4. \nhttp://www.mothur.org/wiki/Clearcut"; }
string getDescription() { return "create a tree from a fasta or phylip file"; }
}
}
//**********************************************************************************************************************
-string ClearMemoryCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
-
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ClearMemoryCommand", "getOutputFileNameTag");
- exit(1);
- }
-}
-//**********************************************************************************************************************
string ClearMemoryCommand::getHelpString(){
try {
string helpString = "";
vector<string> setParameters();
string getCommandName() { return "clear.memory"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Clear.memory"; }
string getDescription() { return "remove saved references from memory"; }
//**********************************************************************************************************************
vector<string> ClusterCommand::setParameters(){
try {
- CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
- CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
- CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);
- CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","list",false,false,true); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list",false,false,true); parameters.push_back(pcolumn);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false,true); parameters.push_back(pmethod);
+ CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund);
+ CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
+ CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ClusterCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ClusterCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "list") { outputFileName = "list"; }
- else if (type == "rabund") { outputFileName = "rabund"; }
- else if (type == "sabund") { outputFileName = "sabund"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; }
+ else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; }
+ else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ClusterCommand::ClusterCommand(){
if (outputDir == "") { outputDir += m->hasPath(distfile); }
fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
- string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
- string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
- string listFileName = fileroot+ tag + ".";
- if (countfile != "") { listFileName += "unique_"; }
- listFileName += getOutputFileNameTag("list");
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ if (countfile != "") { variables["[tag2]"] = "unique_list"; }
+ variables["[clustertag]"] = tag;
+ string sabundFileName = getOutputFileName("sabund", variables);
+ string rabundFileName = getOutputFileName("rabund", variables);
+ string listFileName = getOutputFileName("list", variables);
if (countfile == "") {
m->openOutputFile(sabundFileName, sabundFile);
vector<string> setParameters();
string getCommandName() { return "cluster"; }
string getCommandCategory() { return "Clustering"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster"; }
string getDescription() { return "cluster your sequences into OTUs using a distance matrix"; }
//**********************************************************************************************************************
vector<string> ClusterDoturCommand::setParameters(){
try {
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
- CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","rabund-sabund",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false); parameters.push_back(pmethod);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
+ CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ClusterDoturCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ClusterDoturCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "list") { outputFileName = "list"; }
- else if (type == "rabund") { outputFileName = "rabund"; }
- else if (type == "sabund") { outputFileName = "sabund"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterDoturCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; }
+ else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; }
+ else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterDoturCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ClusterDoturCommand::ClusterDoturCommand(){
if (outputDir == "") { outputDir += m->hasPath(phylipfile); }
fileroot = outputDir + m->getRootName(m->getSimpleName(phylipfile));
- string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
- string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
- string listFileName = fileroot+ tag + ".";
- if (countfile != "") { listFileName += "unique_"; }
- listFileName += getOutputFileNameTag("list");
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ if (countfile != "") { variables["[tag2]"] = "unique_list"; }
+ variables["[clustertag]"] = tag;
+ string sabundFileName = getOutputFileName("sabund", variables);
+ string rabundFileName = getOutputFileName("rabund", variables);
+ string listFileName = getOutputFileName("list", variables);
if (countfile == "") {
m->openOutputFile(sabundFileName, sabundFile);
vector<string> setParameters();
string getCommandName() { return "cluster.classic"; }
string getCommandCategory() { return "Clustering"; }
- string getOutputFileNameTag(string, string);
- string getHelpString();
+
+ string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster.classic\n";}
string getDescription() { return "cluster your sequences into OTUs using DOTUR’s method"; }
//**********************************************************************************************************************
vector<string> ClusterFragmentsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
- CommandParameter ppercent("percent", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppercent);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pdiffs);
+ CommandParameter ppercent("percent", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppercent);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ClusterFragmentsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ClusterFragmentsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "fragclust.fasta"; }
- else if (type == "name") { outputFileName = "fragclust.names"; }
- else if (type == "count") { outputFileName = "fragclust.count_table"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterFragmentsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],fragclust.fasta"; }
+ else if (type == "name") { pattern = "[filename],fragclust.names"; }
+ else if (type == "count") { pattern = "[filename],fragclust.count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
ClusterFragmentsCommand::ClusterFragmentsCommand(){
try {
string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
-
- string newFastaFile = fileroot + getOutputFileNameTag("fasta");
- string newNamesFile = fileroot + getOutputFileNameTag("name");
- if (countfile != "") { newNamesFile = fileroot + getOutputFileNameTag("count"); }
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ string newFastaFile = getOutputFileName("fasta", variables);
+ string newNamesFile = getOutputFileName("name", variables);
+ if (countfile != "") { newNamesFile = getOutputFileName("count", variables); }
if (m->control_pressed) { return 0; }
vector<string> setParameters();
string getCommandName() { return "cluster.fragments"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Cluster.fragments"; }
string getDescription() { return "creates a namesfile with sequences that are a fragment of a larger sequence"; }
//**********************************************************************************************************************
vector<string> ClusterSplitCommand::setParameters(){
try {
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FastaTaxName",false,false); parameters.push_back(ptaxonomy);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "FastaTaxName",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName-FastaTaxName",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "",false,false); parameters.push_back(pcount);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "ColumnName",false,false); parameters.push_back(pcolumn);
- CommandParameter ptaxlevel("taxlevel", "Number", "", "3", "", "", "",false,false); parameters.push_back(ptaxlevel);
- CommandParameter psplitmethod("splitmethod", "Multiple", "classify-fasta-distance", "distance", "", "", "",false,false); parameters.push_back(psplitmethod);
- CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
- CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
- CommandParameter pcluster("cluster", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcluster);
- CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pcutoff("cutoff", "Number", "", "0.25", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
- CommandParameter pclassic("classic", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pclassic);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FastaTaxName","",false,false,true); parameters.push_back(ptaxonomy);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "none","list",false,false,true); parameters.push_back(pphylip);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "FastaTaxName","list",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName-FastaTaxName","rabund-sabund",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "ColumnName","list",false,false,true); parameters.push_back(pcolumn);
+ CommandParameter ptaxlevel("taxlevel", "Number", "", "3", "", "", "","",false,false,true); parameters.push_back(ptaxlevel);
+ CommandParameter psplitmethod("splitmethod", "Multiple", "classify-fasta-distance", "distance", "", "", "","",false,false,true); parameters.push_back(psplitmethod);
+ CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
+ CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund);
+ CommandParameter pcluster("cluster", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcluster);
+ CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pcutoff("cutoff", "Number", "", "0.25", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false); parameters.push_back(pmethod);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
+ CommandParameter pclassic("classic", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pclassic);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ClusterSplitCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ClusterSplitCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "list") { outputFileName = "list"; }
- else if (type == "rabund") { outputFileName = "rabund"; }
- else if (type == "sabund") { outputFileName = "sabund"; }
- else if (type == "column") { outputFileName = "dist"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterSplitCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; }
+ else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; }
+ else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; }
+ else if (type == "column") { pattern = "[filename],dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterSplitCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ClusterSplitCommand::ClusterSplitCommand(){
if (outputDir == "") { outputDir += m->hasPath(distfile); }
fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
- string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
- string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
- string listFileName = fileroot+ tag + ".";
- if (countfile != "") { listFileName += "unique_"; }
- listFileName += getOutputFileNameTag("list");
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ if (countfile != "") { variables["[tag2]"] = "unique_list"; }
+ variables["[clustertag]"] = tag;
+ string sabundFileName = getOutputFileName("sabund", variables);
+ string rabundFileName = getOutputFileName("rabund", variables);
+ string listFileName = getOutputFileName("list", variables);
if (countfile == "") {
m->openOutputFile(sabundFileName, outSabund);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir = m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("column");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileName = getOutputFileName("column", variables);
m->mothurRemove(outputFileName);
vector<string> setParameters();
string getCommandName() { return "cluster.split"; }
string getCommandCategory() { return "Clustering"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219. \nhttp://www.mothur.org/wiki/Cluster.split"; }
string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
//**********************************************************************************************************************
vector<string> CollectCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
- CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(psabund);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+ CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psize);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string CollectCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string CollectCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "sobs") { outputFileName = "sobs"; }
- else if (type == "chao") { outputFileName = "chao"; }
- else if (type == "nseqs") { outputFileName = "nseqs"; }
- else if (type == "coverage") { outputFileName = "coverage"; }
- else if (type == "ace") { outputFileName = "ace"; }
- else if (type == "jack") { outputFileName = "jack"; }
- else if (type == "shannon") { outputFileName = "shannon"; }
- else if (type == "shannoneven") { outputFileName = "shannoneven"; }
- else if (type == "npshannon") { outputFileName = "npshannon"; }
- else if (type == "heip") { outputFileName = "heip"; }
- else if (type == "smithwilson") { outputFileName = "smithwilson"; }
- else if (type == "simpson") { outputFileName = "simpson"; }
- else if (type == "simpsoneven") { outputFileName = "simpsoneven"; }
- else if (type == "invsimpson") { outputFileName = "invsimpson"; }
- else if (type == "bootstrap") { outputFileName = "bootstrap"; }
- else if (type == "geometric") { outputFileName = "geometric"; }
- else if (type == "qstat") { outputFileName = "qstat"; }
- else if (type == "logseries") { outputFileName = "logseries"; }
- else if (type == "bergerparker") { outputFileName = "bergerparker"; }
- else if (type == "bstick") { outputFileName = "bstick"; }
- else if (type == "goodscoverage") { outputFileName = "goodscoverage"; }
- else if (type == "efron") { outputFileName = "efron"; }
- else if (type == "boneh") { outputFileName = "boneh"; }
- else if (type == "solow") { outputFileName = "solow"; }
- else if (type == "shen") { outputFileName = "shen"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "CollectCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "sobs") { pattern = "[filename],sobs"; }
+ else if (type == "chao") { pattern = "[filename],chao"; }
+ else if (type == "nseqs") { pattern = "[filename],nseqs"; }
+ else if (type == "coverage") { pattern = "[filename],coverage"; }
+ else if (type == "ace") { pattern = "[filename],ace"; }
+ else if (type == "jack") { pattern = "[filename],jack"; }
+ else if (type == "shannon") { pattern = "[filename],shannon"; }
+ else if (type == "shannoneven") { pattern = "[filename],shannoneven"; }
+ else if (type == "npshannon") { pattern = "[filename],npshannon"; }
+ else if (type == "heip") { pattern = "[filename],heip"; }
+ else if (type == "smithwilson") { pattern = "[filename],smithwilson"; }
+ else if (type == "simpson") { pattern = "[filename],simpson"; }
+ else if (type == "simpsoneven") { pattern = "[filename],simpsoneven"; }
+ else if (type == "invsimpson") { pattern = "[filename],invsimpson"; }
+ else if (type == "bootstrap") { pattern = "[filename],bootstrap"; }
+ else if (type == "geometric") { pattern = "[filename],geometric"; }
+ else if (type == "qstat") { pattern = "[filename],qstat"; }
+ else if (type == "logseries") { pattern = "[filename],logseries"; }
+ else if (type == "bergerparker") { pattern = "[filename],bergerparker"; }
+ else if (type == "bstick") { pattern = "[filename],bstick"; }
+ else if (type == "goodscoverage") { pattern = "[filename],goodscoverage"; }
+ else if (type == "efron") { pattern = "[filename],efron"; }
+ else if (type == "boneh") { pattern = "[filename],boneh"; }
+ else if (type == "solow") { pattern = "[filename],solow"; }
+ else if (type == "shen") { pattern = "[filename],shen"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
CollectCommand::CollectCommand(){
if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
//globaldata->inputFileName = inputFileNames[p];
if (inputFileNames.size() > 1) {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("single", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
- cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("sobs"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sobs")); outputTypes["sobs"].push_back(fileNameRoot+getOutputFileNameTag("sobs"));
+ cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(getOutputFileName("sobs", variables))));
+ outputNames.push_back(getOutputFileName("sobs", variables)); outputTypes["sobs"].push_back(getOutputFileName("sobs", variables));
}else if (Estimators[i] == "chao") {
- cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("chao"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("chao")); outputTypes["chao"].push_back(fileNameRoot+getOutputFileNameTag("chao"));
+ cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("chao", variables))));
+ outputNames.push_back(getOutputFileName("chao", variables)); outputTypes["chao"].push_back(getOutputFileName("chao", variables));
}else if (Estimators[i] == "nseqs") {
- cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("nseqs"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("nseqs")); outputTypes["nseqs"].push_back(fileNameRoot+getOutputFileNameTag("nseqs"));
+ cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(getOutputFileName("nseqs", variables))));
+ outputNames.push_back(getOutputFileName("nseqs", variables)); outputTypes["nseqs"].push_back(getOutputFileName("nseqs", variables));
}else if (Estimators[i] == "coverage") {
- cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("coverage"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("coverage")); outputTypes["coverage"].push_back(fileNameRoot+getOutputFileNameTag("coverage"));
+ cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(getOutputFileName("coverage", variables))));
+ outputNames.push_back(getOutputFileName("coverage", variables)); outputTypes["coverage"].push_back(getOutputFileName("coverage", variables));
}else if (Estimators[i] == "ace") {
- cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("ace"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("ace")); outputTypes["ace"].push_back(fileNameRoot+getOutputFileNameTag("ace"));
+ cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("ace", variables))));
+ outputNames.push_back(getOutputFileName("ace", variables)); outputTypes["ace"].push_back(getOutputFileName("ace", variables));
}else if (Estimators[i] == "jack") {
- cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("jack"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("jack")); outputTypes["jack"].push_back(fileNameRoot+getOutputFileNameTag("jack"));
+ cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("jack", variables))));
+ outputNames.push_back(getOutputFileName("jack", variables)); outputTypes["jack"].push_back(getOutputFileName("jack", variables));
}else if (Estimators[i] == "shannon") {
- cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("shannon"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("shannon")); outputTypes["shannon"].push_back(fileNameRoot+getOutputFileNameTag("shannon"));
+ cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("shannon", variables))));
+ outputNames.push_back(getOutputFileName("shannon", variables)); outputTypes["shannon"].push_back(getOutputFileName("shannon", variables));
}else if (Estimators[i] == "shannoneven") {
- cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("shannoneven"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("shannoneven")); outputTypes["shannoneven"].push_back(fileNameRoot+getOutputFileNameTag("shannoneven"));
+ cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(getOutputFileName("shannoneven", variables))));
+ outputNames.push_back(getOutputFileName("shannoneven", variables)); outputTypes["shannoneven"].push_back(getOutputFileName("shannoneven", variables));
}else if (Estimators[i] == "npshannon") {
- cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("npshannon"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("npshannon")); outputTypes["npshannon"].push_back(fileNameRoot+getOutputFileNameTag("npshannon"));
+ cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(getOutputFileName("npshannon", variables))));
+ outputNames.push_back(getOutputFileName("npshannon", variables)); outputTypes["npshannon"].push_back(getOutputFileName("npshannon", variables));
}else if (Estimators[i] == "heip") {
- cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("heip"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("heip")); outputTypes["heip"].push_back(fileNameRoot+getOutputFileNameTag("heip"));
+ cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(getOutputFileName("heip", variables))));
+ outputNames.push_back(getOutputFileName("heip", variables)); outputTypes["heip"].push_back(getOutputFileName("heip", variables));
}else if (Estimators[i] == "smithwilson") {
- cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("smithwilson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("smithwilson")); outputTypes["smithwilson"].push_back(fileNameRoot+getOutputFileNameTag("smithwilson"));
+ cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(getOutputFileName("smithwilson", variables))));
+ outputNames.push_back(getOutputFileName("smithwilson", variables)); outputTypes["smithwilson"].push_back(getOutputFileName("smithwilson", variables));
}else if (Estimators[i] == "simpson") {
- cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("simpson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("simpson")); outputTypes["simpson"].push_back(fileNameRoot+getOutputFileNameTag("simpson"));
+ cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("simpson", variables))));
+ outputNames.push_back(getOutputFileName("simpson", variables)); outputTypes["simpson"].push_back(getOutputFileName("simpson", variables));
}else if (Estimators[i] == "simpsoneven") {
- cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("simpsoneven"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("simpsoneven")); outputTypes["simpsoneven"].push_back(fileNameRoot+getOutputFileNameTag("simpsoneven"));
+ cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(getOutputFileName("simpsoneven", variables))));
+ outputNames.push_back(getOutputFileName("simpsoneven", variables)); outputTypes["simpsoneven"].push_back(getOutputFileName("simpsoneven", variables));
}else if (Estimators[i] == "invsimpson") {
- cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("invsimpson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("invsimpson")); outputTypes["invsimpson"].push_back(fileNameRoot+getOutputFileNameTag("invsimpson"));
+ cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("invsimpson", variables))));
+ outputNames.push_back(getOutputFileName("invsimpson", variables)); outputTypes["invsimpson"].push_back(getOutputFileName("invsimpson", variables));
}else if (Estimators[i] == "bootstrap") {
- cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("bootstrap"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("bootstrap")); outputTypes["bootstrap"].push_back(fileNameRoot+getOutputFileNameTag("bootstrap"));
+ cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(getOutputFileName("bootstrap", variables))));
+ outputNames.push_back(getOutputFileName("bootstrap", variables)); outputTypes["bootstrap"].push_back(getOutputFileName("bootstrap", variables));
}else if (Estimators[i] == "geometric") {
- cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("geometric"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("geometric")); outputTypes["geometric"].push_back(fileNameRoot+getOutputFileNameTag("geometric"));
+ cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(getOutputFileName("geometric", variables))));
+ outputNames.push_back(getOutputFileName("geometric", variables)); outputTypes["geometric"].push_back(getOutputFileName("geometric", variables));
}else if (Estimators[i] == "qstat") {
- cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("qstat"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("qstat")); outputTypes["qstat"].push_back(fileNameRoot+getOutputFileNameTag("qstat"));
+ cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(getOutputFileName("qstat", variables))));
+ outputNames.push_back(getOutputFileName("qstat", variables)); outputTypes["qstat"].push_back(getOutputFileName("qstat", variables));
}else if (Estimators[i] == "logseries") {
- cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("logseries"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("logseries")); outputTypes["logseries"].push_back(fileNameRoot+getOutputFileNameTag("logseries"));
+ cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(getOutputFileName("logseries", variables))));
+ outputNames.push_back(getOutputFileName("logseries", variables)); outputTypes["logseries"].push_back(getOutputFileName("logseries", variables));
}else if (Estimators[i] == "bergerparker") {
- cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("bergerparker"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("bergerparker")); outputTypes["bergerparker"].push_back(fileNameRoot+getOutputFileNameTag("bergerparker"));
+ cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(getOutputFileName("bergerparker", variables))));
+ outputNames.push_back(getOutputFileName("bergerparker", variables)); outputTypes["bergerparker"].push_back(getOutputFileName("bergerparker", variables));
}else if (Estimators[i] == "bstick") {
- cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("bstick"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("bstick")); outputTypes["bstick"].push_back(fileNameRoot+getOutputFileNameTag("bstick"));
+ cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(getOutputFileName("bstick", variables))));
+ outputNames.push_back(getOutputFileName("bstick", variables)); outputTypes["bstick"].push_back(getOutputFileName("bstick", variables));
}else if (Estimators[i] == "goodscoverage") {
- cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("goodscoverage"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("goodscoverage")); outputTypes["goodscoverage"].push_back(fileNameRoot+getOutputFileNameTag("goodscoverage"));
+ cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(getOutputFileName("goodscoverage", variables))));
+ outputNames.push_back(getOutputFileName("goodscoverage", variables)); outputTypes["goodscoverage"].push_back(getOutputFileName("goodscoverage", variables));
}else if (Estimators[i] == "efron") {
- cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+getOutputFileNameTag("efron"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("efron")); outputTypes["efron"].push_back(fileNameRoot+getOutputFileNameTag("efron"));
+ cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(getOutputFileName("efron", variables))));
+ outputNames.push_back(getOutputFileName("efron", variables)); outputTypes["efron"].push_back(getOutputFileName("efron", variables));
}else if (Estimators[i] == "boneh") {
- cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+getOutputFileNameTag("boneh"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("boneh")); outputTypes["boneh"].push_back(fileNameRoot+getOutputFileNameTag("boneh"));
+ cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(getOutputFileName("boneh", variables))));
+ outputNames.push_back(getOutputFileName("boneh", variables)); outputTypes["boneh"].push_back(getOutputFileName("boneh", variables));
}else if (Estimators[i] == "solow") {
- cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+getOutputFileNameTag("solow"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("solow")); outputTypes["solow"].push_back(fileNameRoot+getOutputFileNameTag("solow"));
+ cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(getOutputFileName("solow", variables))));
+ outputNames.push_back(getOutputFileName("solow", variables)); outputTypes["solow"].push_back(getOutputFileName("solow", variables));
}else if (Estimators[i] == "shen") {
- cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+getOutputFileNameTag("shen"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("shen")); outputTypes["shen"].push_back(fileNameRoot+getOutputFileNameTag("shen"));
+ cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(getOutputFileName("shen", variables))));
+ outputNames.push_back(getOutputFileName("shen", variables)); outputTypes["shen"].push_back(getOutputFileName("shen", variables));
}
}
}
string getCommandName() { return "collect.single"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.single"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getDescription() { return "generates collector's curves using calculators, that describe the richness, diversity, and other features of individual samples"; }
int execute();
//**********************************************************************************************************************
vector<string> CollectSharedCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
- CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+ CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string CollectSharedCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string CollectSharedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "sharedchao") { outputFileName = "shared.chao"; }
- else if (type == "sharedsobs") { outputFileName = "shared.sobs"; }
- else if (type == "sharedace") { outputFileName = "shared.ace"; }
- else if (type == "jabund") { outputFileName = "jabund"; }
- else if (type == "sorabund") { outputFileName = "sorabund"; }
- else if (type == "jclass") { outputFileName = "jclass"; }
- else if (type == "sorclass") { outputFileName = "sorclass"; }
- else if (type == "jest") { outputFileName = "jest"; }
- else if (type == "sorest") { outputFileName = "sorest"; }
- else if (type == "thetayc") { outputFileName = "thetayc"; }
- else if (type == "thetan") { outputFileName = "thetan"; }
- else if (type == "kstest") { outputFileName = "kstest"; }
- else if (type == "whittaker") { outputFileName = "whittaker"; }
- else if (type == "sharednseqs") { outputFileName = "shared.nseqs"; }
- else if (type == "ochiai") { outputFileName = "ochiai"; }
- else if (type == "anderberg") { outputFileName = "anderberg"; }
- else if (type == "kulczynski") { outputFileName = "kulczynski"; }
- else if (type == "kulczynskicody") { outputFileName = "kulczynskicody"; }
- else if (type == "lennon") { outputFileName = "lennon"; }
- else if (type == "morisitahorn") { outputFileName = "morisitahorn"; }
- else if (type == "braycurtis") { outputFileName = "braycurtis"; }
- else if (type == "odum") { outputFileName = "odum"; }
- else if (type == "canberra") { outputFileName = "canberra"; }
- else if (type == "structeuclidean") { outputFileName = "structeuclidean"; }
- else if (type == "structchord") { outputFileName = "structchord"; }
- else if (type == "hellinger") { outputFileName = "hellinger"; }
- else if (type == "manhattan") { outputFileName = "manhattan"; }
- else if (type == "structpearson") { outputFileName = "structpearson"; }
- else if (type == "soergel") { outputFileName = "soergel"; }
- else if (type == "spearman") { outputFileName = "spearman"; }
- else if (type == "structkulczynski") { outputFileName = "structkulczynski";}
- else if (type == "structchi2") { outputFileName = "structchi2"; }
- else if (type == "speciesprofile") { outputFileName = "speciesprofile"; }
- else if (type == "hamming") { outputFileName = "hamming"; }
- else if (type == "gower") { outputFileName = "gower"; }
- else if (type == "memchi2") { outputFileName = "memchi2"; }
- else if (type == "memchord") { outputFileName = "memchord"; }
- else if (type == "memeuclidean") { outputFileName = "memeuclidean"; }
- else if (type == "mempearson") { outputFileName = "mempearson"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "CollectSharedCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "sharedchao") { pattern = "[filename],shared.chao"; }
+ else if (type == "sharedsobs") { pattern = "[filename],shared.sobs"; }
+ else if (type == "sharedace") { pattern = "[filename],shared.ace"; }
+ else if (type == "jabund") { pattern = "[filename],jabund"; }
+ else if (type == "sorabund") { pattern = "[filename],sorabund"; }
+ else if (type == "jclass") { pattern = "[filename],jclass"; }
+ else if (type == "sorclass") { pattern = "[filename],sorclass"; }
+ else if (type == "jest") { pattern = "[filename],jest"; }
+ else if (type == "sorest") { pattern = "[filename],sorest"; }
+ else if (type == "thetayc") { pattern = "[filename],thetayc"; }
+ else if (type == "thetan") { pattern = "[filename],thetan"; }
+ else if (type == "kstest") { pattern = "[filename],kstest"; }
+ else if (type == "whittaker") { pattern = "[filename],whittaker"; }
+ else if (type == "sharednseqs") { pattern = "[filename],shared.nseqs"; }
+ else if (type == "ochiai") { pattern = "[filename],ochiai"; }
+ else if (type == "anderberg") { pattern = "[filename],anderberg"; }
+ else if (type == "kulczynski") { pattern = "[filename],kulczynski"; }
+ else if (type == "kulczynskicody") { pattern = "[filename],kulczynskicody"; }
+ else if (type == "lennon") { pattern = "[filename],lennon"; }
+ else if (type == "morisitahorn") { pattern = "[filename],morisitahorn"; }
+ else if (type == "braycurtis") { pattern = "[filename],braycurtis"; }
+ else if (type == "odum") { pattern = "[filename],odum"; }
+ else if (type == "canberra") { pattern = "[filename],canberra"; }
+ else if (type == "structeuclidean") { pattern = "[filename],structeuclidean"; }
+ else if (type == "structchord") { pattern = "[filename],structchord"; }
+ else if (type == "hellinger") { pattern = "[filename],hellinger"; }
+ else if (type == "manhattan") { pattern = "[filename],manhattan"; }
+ else if (type == "structpearson") { pattern = "[filename],structpearson"; }
+ else if (type == "soergel") { pattern = "[filename],soergel"; }
+ else if (type == "spearman") { pattern = "[filename],spearman"; }
+ else if (type == "structkulczynski") { pattern = "[filename],structkulczynski";}
+ else if (type == "structchi2") { pattern = "[filename],structchi2"; }
+ else if (type == "speciesprofile") { pattern = "[filename],speciesprofile"; }
+ else if (type == "hamming") { pattern = "[filename],hamming"; }
+ else if (type == "gower") { pattern = "[filename],gower"; }
+ else if (type == "memchi2") { pattern = "[filename],memchi2"; }
+ else if (type == "memchord") { pattern = "[filename],memchord"; }
+ else if (type == "memeuclidean") { pattern = "[filename],memeuclidean"; }
+ else if (type == "mempearson") { pattern = "[filename],mempearson"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
CollectSharedCommand::CollectSharedCommand(){
try {
if (abort == false) {
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile));
-
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
+
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("shared", Estimators[i]) == true) {
if (Estimators[i] == "sharedchao") {
- cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sharedchao"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharedchao")); outputTypes["sharedchao"].push_back(fileNameRoot+getOutputFileNameTag("sharedchao"));
+ cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(getOutputFileName("sharedchao", variables))));
+ outputNames.push_back(getOutputFileName("sharedchao", variables)); outputTypes["sharedchao"].push_back(getOutputFileName("sharedchao", variables));
}else if (Estimators[i] == "sharedsobs") {
- cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sharedsobs"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharedsobs")); outputTypes["sharedsobs"].push_back(fileNameRoot+getOutputFileNameTag("sharedsobs"));
+ cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(getOutputFileName("sharedsobs", variables))));
+ outputNames.push_back(getOutputFileName("sharedsobs", variables)); outputTypes["sharedsobs"].push_back(getOutputFileName("sharedsobs", variables));
}else if (Estimators[i] == "sharedace") {
- cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sharedace"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharedace")); outputTypes["sharedace"].push_back(fileNameRoot+getOutputFileNameTag("sharedace"));
+ cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(getOutputFileName("sharedace", variables))));
+ outputNames.push_back(getOutputFileName("sharedace", variables)); outputTypes["sharedace"].push_back(getOutputFileName("sharedace", variables));
}else if (Estimators[i] == "jabund") {
- cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("jabund"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("jabund")); outputTypes["jabund"].push_back(fileNameRoot+getOutputFileNameTag("jabund"));
+ cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(getOutputFileName("jabund", variables))));
+ outputNames.push_back(getOutputFileName("jabund", variables)); outputTypes["jabund"].push_back(getOutputFileName("jabund", variables));
}else if (Estimators[i] == "sorabund") {
- cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sorabund"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sorabund")); outputTypes["sorabund"].push_back(fileNameRoot+getOutputFileNameTag("sorabund"));
+ cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(getOutputFileName("sorabund", variables))));
+ outputNames.push_back(getOutputFileName("sorabund", variables)); outputTypes["sorabund"].push_back(getOutputFileName("sorabund", variables));
}else if (Estimators[i] == "jclass") {
- cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("jclass"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("jclass")); outputTypes["jclass"].push_back(fileNameRoot+getOutputFileNameTag("jclass"));
+ cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(getOutputFileName("jclass", variables))));
+ outputNames.push_back(getOutputFileName("jclass", variables)); outputTypes["jclass"].push_back(getOutputFileName("jclass", variables));
}else if (Estimators[i] == "sorclass") {
- cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sorclass"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sorclass")); outputTypes["sorclass"].push_back(fileNameRoot+getOutputFileNameTag("sorclass"));
+ cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(getOutputFileName("sorclass", variables))));
+ outputNames.push_back(getOutputFileName("sorclass", variables)); outputTypes["sorclass"].push_back(getOutputFileName("sorclass", variables));
}else if (Estimators[i] == "jest") {
- cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("jest"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("jest")); outputTypes["jest"].push_back(fileNameRoot+getOutputFileNameTag("jest"));
+ cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(getOutputFileName("jest", variables))));
+ outputNames.push_back(getOutputFileName("jest", variables)); outputTypes["jest"].push_back(getOutputFileName("jest", variables));
}else if (Estimators[i] == "sorest") {
- cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sorest"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sorest")); outputTypes["sorest"].push_back(fileNameRoot+getOutputFileNameTag("sorest"));
+ cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(getOutputFileName("sorest", variables))));
+ outputNames.push_back(getOutputFileName("sorest", variables)); outputTypes["sorest"].push_back(getOutputFileName("sorest", variables));
}else if (Estimators[i] == "thetayc") {
- cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("thetayc"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("thetayc")); outputTypes["thetayc"].push_back(fileNameRoot+getOutputFileNameTag("thetayc"));
+ cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(getOutputFileName("thetayc", variables))));
+ outputNames.push_back(getOutputFileName("thetayc", variables)); outputTypes["thetayc"].push_back(getOutputFileName("thetayc", variables));
}else if (Estimators[i] == "thetan") {
- cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("thetan"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("thetan")); outputTypes["thetan"].push_back(fileNameRoot+getOutputFileNameTag("thetan"));
+ cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(getOutputFileName("thetan", variables))));
+ outputNames.push_back(getOutputFileName("thetan", variables)); outputTypes["thetan"].push_back(getOutputFileName("thetan", variables));
}else if (Estimators[i] == "kstest") {
- cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("kstest"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("kstest")); outputTypes["kstest"].push_back(fileNameRoot+getOutputFileNameTag("kstest"));
+ cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(getOutputFileName("kstest", variables))));
+ outputNames.push_back(getOutputFileName("kstest", variables)); outputTypes["kstest"].push_back(getOutputFileName("kstest", variables));
}else if (Estimators[i] == "whittaker") {
- cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("whittaker"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("whittaker")); outputTypes["whittaker"].push_back(fileNameRoot+getOutputFileNameTag("whittaker"));
+ cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(getOutputFileName("whittaker", variables))));
+ outputNames.push_back(getOutputFileName("whittaker", variables)); outputTypes["whittaker"].push_back(getOutputFileName("whittaker", variables));
}else if (Estimators[i] == "sharednseqs") {
- cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("sharednseqs"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharednseqs")); outputTypes["shared.nseqs"].push_back(fileNameRoot+getOutputFileNameTag("sharednseqs"));
+ cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(getOutputFileName("sharednseqs", variables))));
+ outputNames.push_back(getOutputFileName("sharednseqs", variables)); outputTypes["shared.nseqs"].push_back(getOutputFileName("sharednseqs", variables));
}else if (Estimators[i] == "ochiai") {
- cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("ochiai"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("ochiai")); outputTypes["ochiai"].push_back(fileNameRoot+getOutputFileNameTag("ochiai"));
+ cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(getOutputFileName("ochiai", variables))));
+ outputNames.push_back(getOutputFileName("ochiai", variables)); outputTypes["ochiai"].push_back(getOutputFileName("ochiai", variables));
}else if (Estimators[i] == "anderberg") {
- cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("anderberg"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("anderberg")); outputTypes["anderberg"].push_back(fileNameRoot+getOutputFileNameTag("anderberg"));
+ cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(getOutputFileName("anderberg", variables))));
+ outputNames.push_back(getOutputFileName("anderberg", variables)); outputTypes["anderberg"].push_back(getOutputFileName("anderberg", variables));
}else if (Estimators[i] == "kulczynski") {
- cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("kulczynski"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("kulczynski")); outputTypes["kulczynski"].push_back(fileNameRoot+getOutputFileNameTag("kulczynski"));
+ cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(getOutputFileName("kulczynski", variables))));
+ outputNames.push_back(getOutputFileName("kulczynski", variables)); outputTypes["kulczynski"].push_back(getOutputFileName("kulczynski", variables));
}else if (Estimators[i] == "kulczynskicody") {
- cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("kulczynskicody"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("kulczynskicody")); outputTypes["kulczynskicody"].push_back(fileNameRoot+getOutputFileNameTag("kulczynskicody"));
+ cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(getOutputFileName("kulczynskicody", variables))));
+ outputNames.push_back(getOutputFileName("kulczynskicody", variables)); outputTypes["kulczynskicody"].push_back(getOutputFileName("kulczynskicody", variables));
}else if (Estimators[i] == "lennon") {
- cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("lennon"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("lennon")); outputTypes["lennon"].push_back(fileNameRoot+getOutputFileNameTag("lennon"));
+ cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(getOutputFileName("lennon", variables))));
+ outputNames.push_back(getOutputFileName("lennon", variables)); outputTypes["lennon"].push_back(getOutputFileName("lennon", variables));
}else if (Estimators[i] == "morisitahorn") {
- cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("morisitahorn"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("morisitahorn")); outputTypes["morisitahorn"].push_back(fileNameRoot+getOutputFileNameTag("morisitahorn"));
+ cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(getOutputFileName("morisitahorn", variables))));
+ outputNames.push_back(getOutputFileName("morisitahorn", variables)); outputTypes["morisitahorn"].push_back(getOutputFileName("morisitahorn", variables));
}else if (Estimators[i] == "braycurtis") {
- cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("braycurtis"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("braycurtis")); outputTypes["braycurtis"].push_back(fileNameRoot+getOutputFileNameTag("braycurtis"));
+ cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(getOutputFileName("braycurtis", variables))));
+ outputNames.push_back(getOutputFileName("braycurtis", variables)); outputTypes["braycurtis"].push_back(getOutputFileName("braycurtis", variables));
}else if (Estimators[i] == "odum") {
- cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("odum"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("odum")); outputTypes["odum"].push_back(fileNameRoot+getOutputFileNameTag("odum"));
+ cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(getOutputFileName("odum", variables))));
+ outputNames.push_back(getOutputFileName("odum", variables)); outputTypes["odum"].push_back(getOutputFileName("odum", variables));
}else if (Estimators[i] == "canberra") {
- cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("canberra"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("canberra")); outputTypes["canberra"].push_back(fileNameRoot+getOutputFileNameTag("canberra"));
+ cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(getOutputFileName("canberra", variables))));
+ outputNames.push_back(getOutputFileName("canberra", variables)); outputTypes["canberra"].push_back(getOutputFileName("canberra", variables));
}else if (Estimators[i] == "structeuclidean") {
- cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("structeuclidean"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("structeuclidean")); outputTypes["structeuclidean"].push_back(fileNameRoot+getOutputFileNameTag("structeuclidean"));
+ cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(getOutputFileName("structeuclidean", variables))));
+ outputNames.push_back(getOutputFileName("structeuclidean", variables)); outputTypes["structeuclidean"].push_back(getOutputFileName("structeuclidean", variables));
}else if (Estimators[i] == "structchord") {
- cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("structchord"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("structchord")); outputTypes["structchord"].push_back(fileNameRoot+getOutputFileNameTag("structchord"));
+ cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(getOutputFileName("structchord", variables))));
+ outputNames.push_back(getOutputFileName("structchord", variables)); outputTypes["structchord"].push_back(getOutputFileName("structchord", variables));
}else if (Estimators[i] == "hellinger") {
- cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("hellinger"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("hellinger")); outputTypes["hellinger"].push_back(fileNameRoot+getOutputFileNameTag("hellinger"));
+ cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(getOutputFileName("hellinger", variables))));
+ outputNames.push_back(getOutputFileName("hellinger", variables)); outputTypes["hellinger"].push_back(getOutputFileName("hellinger", variables));
}else if (Estimators[i] == "manhattan") {
- cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("manhattan"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("manhattan")); outputTypes["manhattan"].push_back(fileNameRoot+getOutputFileNameTag("manhattan"));
+ cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(getOutputFileName("manhattan", variables))));
+ outputNames.push_back(getOutputFileName("manhattan", variables)); outputTypes["manhattan"].push_back(getOutputFileName("manhattan", variables));
}else if (Estimators[i] == "structpearson") {
- cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("structpearson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("structpearson")); outputTypes["structpearson"].push_back(fileNameRoot+getOutputFileNameTag("structpearson"));
+ cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(getOutputFileName("structpearson", variables))));
+ outputNames.push_back(getOutputFileName("structpearson", variables)); outputTypes["structpearson"].push_back(getOutputFileName("structpearson", variables));
}else if (Estimators[i] == "soergel") {
- cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("soergel"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("soergel")); outputTypes["soergel"].push_back(fileNameRoot+getOutputFileNameTag("soergel"));
+ cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(getOutputFileName("soergel", variables))));
+ outputNames.push_back(getOutputFileName("soergel", variables)); outputTypes["soergel"].push_back(getOutputFileName("soergel", variables));
}else if (Estimators[i] == "spearman") {
- cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("spearman"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("spearman")); outputTypes["spearman"].push_back(fileNameRoot+getOutputFileNameTag("spearman"));
+ cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(getOutputFileName("spearman", variables))));
+ outputNames.push_back(getOutputFileName("spearman", variables)); outputTypes["spearman"].push_back(getOutputFileName("spearman", variables));
}else if (Estimators[i] == "structkulczynski") {
- cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("structkulczynski"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("structkulczynski")); outputTypes["structkulczynski"].push_back(fileNameRoot+getOutputFileNameTag("structkulczynski"));
+ cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(getOutputFileName("structkulczynski", variables))));
+ outputNames.push_back(getOutputFileName("structkulczynski", variables)); outputTypes["structkulczynski"].push_back(getOutputFileName("structkulczynski", variables));
}else if (Estimators[i] == "speciesprofile") {
- cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("speciesprofile"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("speciesprofile")); outputTypes["speciesprofile"].push_back(fileNameRoot+getOutputFileNameTag("speciesprofile"));
+ cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(getOutputFileName("speciesprofile", variables))));
+ outputNames.push_back(getOutputFileName("speciesprofile", variables)); outputTypes["speciesprofile"].push_back(getOutputFileName("speciesprofile", variables));
}else if (Estimators[i] == "hamming") {
- cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("hamming"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("hamming")); outputTypes["hamming"].push_back(fileNameRoot+getOutputFileNameTag("hamming"));
+ cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(getOutputFileName("hamming", variables))));
+ outputNames.push_back(getOutputFileName("hamming", variables)); outputTypes["hamming"].push_back(getOutputFileName("hamming", variables));
}else if (Estimators[i] == "structchi2") {
- cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("structchi2"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("structchi2")); outputTypes["structchi2"].push_back(fileNameRoot+getOutputFileNameTag("structchi2"));
+ cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(getOutputFileName("structchi2", variables))));
+ outputNames.push_back(getOutputFileName("structchi2", variables)); outputTypes["structchi2"].push_back(getOutputFileName("structchi2", variables));
}else if (Estimators[i] == "gower") {
- cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("gower"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("gower")); outputTypes["gower"].push_back(fileNameRoot+getOutputFileNameTag("gower"));
+ cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(getOutputFileName("gower", variables))));
+ outputNames.push_back(getOutputFileName("gower", variables)); outputTypes["gower"].push_back(getOutputFileName("gower", variables));
}else if (Estimators[i] == "memchi2") {
- cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("memchi2"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("memchi2")); outputTypes["memchi2"].push_back(fileNameRoot+getOutputFileNameTag("memchi2"));
+ cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(getOutputFileName("memchi2", variables))));
+ outputNames.push_back(getOutputFileName("memchi2", variables)); outputTypes["memchi2"].push_back(getOutputFileName("memchi2", variables));
}else if (Estimators[i] == "memchord") {
- cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("memchord"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("memchord")); outputTypes["memchord"].push_back(fileNameRoot+getOutputFileNameTag("memchord"));
+ cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(getOutputFileName("memchord", variables))));
+ outputNames.push_back(getOutputFileName("memchord", variables)); outputTypes["memchord"].push_back(getOutputFileName("memchord", variables));
}else if (Estimators[i] == "memeuclidean") {
- cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("memeuclidean"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("memeuclidean")); outputTypes["memeuclidean"].push_back(fileNameRoot+getOutputFileNameTag("memeuclidean"));
+ cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(getOutputFileName("memeuclidean", variables))));
+ outputNames.push_back(getOutputFileName("memeuclidean", variables)); outputTypes["memeuclidean"].push_back(getOutputFileName("memeuclidean", variables));
}else if (Estimators[i] == "mempearson") {
- cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(fileNameRoot+getOutputFileNameTag("mempearson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("mempearson")); outputTypes["mempearson"].push_back(fileNameRoot+getOutputFileNameTag("mempearson"));
+ cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(getOutputFileName("mempearson", variables))));
+ outputNames.push_back(getOutputFileName("mempearson", variables)); outputTypes["mempearson"].push_back(getOutputFileName("mempearson", variables));
}
}
vector<string> setParameters();
string getCommandName() { return "collect.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.shared"; }
string getDescription() { return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
virtual string getDescription() = 0;
virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
- virtual string getOutputFileNameTag(string, string) = 0; //we may not know the complete filename, because some commands use info from the file to create the output file name (ie label). but we do the ending tag which should be enough to find the output file name from a list. Allows for optional passing of the inputFileName for the commands that require its extension.
+ string getOutputFileName(string type, map<string, string> variableParts) { //uses the pattern to create an output filename for a given type and input file name.
+ try {
+ string filename = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+
+ string patternTemp = getOutputPattern(type);
+ vector<string> patterns;
+ m->splitAtDash(patternTemp, patterns);
+
+ //find pattern to use based on number of variables passed in
+ string pattern = "";
+ bool foundPattern = false;
+ for (int i = 0; i < patterns.size(); i++) {
+ int numVariables = 0;
+ for (int j = 0; j < patterns[i].length(); j++) { if (patterns[i][j] == '[') { numVariables++; } }
+
+ if (numVariables == variableParts.size()) { pattern = patterns[i]; foundPattern = true; break; }
+ }
+
+ if (!foundPattern) { m->mothurOut("[ERROR]: Not enough variable pieces for " + type + ".\n"); m->control_pressed = true; }
+
+ if (pattern != "") {
+ int numVariables = 0;
+ for (int i = 0; i < pattern.length(); i++) { if (pattern[i] == '[') { numVariables++; } }
+
+ vector<string> pieces;
+ m->splitAtComma(pattern, pieces);
+
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (pieces[i][0] == '[') {
+ map<string, string>::iterator it = variableParts.find(pieces[i]);
+ if (it == variableParts.end()) {
+ m->mothurOut("[ERROR]: Did not provide variable for " + pieces[i] + ".\n"); m->control_pressed = true;
+ }else {
+ if (it->second != "") {
+ if (it->first != "[filename]") { filename += it->second + "."; }
+ else { filename += it->second; }
+ }
+ }
+ }else {
+ filename += pieces[i] + ".";
+ }
+ }
+ if (filename.length() > 0) { //rip off last "."
+ filename = filename.substr(0, filename.length()-1);
+ }
+ }
+ }
+ return filename;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "command", "getOutputFileName");
+ exit(1);
+ }
+ }
+
+ virtual string getOutputPattern(string) = 0; //pass in type, returns something like: [filename],align or [filename],[distance],subsample.shared strings in [] means its a variable. This is used by the gui to predict output file names. use variable keywords: [filename], [distance], [group], [extension], [tag]
virtual vector<string> setParameters() = 0; //to fill parameters
virtual vector<CommandParameter> getParameters() { return parameters; }
class CommandParameter {
public:
- CommandParameter() { name = ""; type = ""; options = ""; optionsDefault = ""; chooseOnlyOneGroup = ""; chooseAtLeastOneGroup = ""; linkedGroup = ""; multipleSelectionAllowed = false; required = false; }
- CommandParameter(string n, string t, string o, string d, string only, string atLeast, string linked, bool m, bool r) : name(n), type(t), options(o), optionsDefault(d),
- chooseOnlyOneGroup(only), chooseAtLeastOneGroup(atLeast), linkedGroup(linked), multipleSelectionAllowed(m), required(r) {}
+ CommandParameter() { name = ""; type = ""; options = ""; optionsDefault = ""; chooseOnlyOneGroup = ""; chooseAtLeastOneGroup = ""; linkedGroup = ""; multipleSelectionAllowed = false; required = false; important = false; outputTypes = ""; }
+ CommandParameter(string n, string t, string o, string d, string only, string atLeast, string linked, string opt, bool m, bool r, bool i) : name(n), type(t), options(o), optionsDefault(d),
+ chooseOnlyOneGroup(only), chooseAtLeastOneGroup(atLeast), linkedGroup(linked), outputTypes(opt),multipleSelectionAllowed(m), required(r), important(i) {}
+ CommandParameter(string n, string t, string o, string d, string only, string atLeast, string linked, string opt, bool m, bool r) : name(n), type(t), options(o), optionsDefault(d),
+ chooseOnlyOneGroup(only), chooseAtLeastOneGroup(atLeast), linkedGroup(linked), outputTypes(opt), multipleSelectionAllowed(m), required(r) { important = false; }
~CommandParameter() {}
string name; //something like fasta, processors, method
string chooseAtLeastOneGroup; //for file inputs: if a command has several options for input files and you want to make sure one is choosen then put them in a group
//for instance in the read.dist command you must provide a phylip or column file so set chooseAtLeastOneGroup for both parameters to something like "DistanceFileGroup"
string linkedGroup; //for file inputs: if a command has a file option were if you provide one you must provide another you can put them in a group
- //for instance in the read.dist command if you provide a column file you must provide a name file so set linkedGroup for both parameters to something like "ColumnNameGroup"
+ //for instance in the cluster command if you provide a column file you must provide a name file so set linkedGroup for both parameters to something like "ColumnNameGroup"
bool multipleSelectionAllowed; //for "Multiple" type to say whether you can select multiple options, for instance for calc parameter set to true, but for method set to false
bool required; //is this parameter required
-
+
+ bool important; //is this parameter important. The gui will put "important" parameters first in the option panel.
+
+ string outputTypes; //types on files created by the command if this parameter is given. ie. get.seqs command fasta parameter makes a fasta file. can be multiple values split by dashes.
private:
};
//**********************************************************************************************************************
vector<string> ConsensusSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcutoff("cutoff", "Number", "", "100", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","fasta-name",false,false,true); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcutoff("cutoff", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ConsensusSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ConsensusSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "cons.fasta"; }
- else if (type == "name") { outputFileName = "cons.names"; }
- else if (type == "count") { outputFileName = "cons.count_table"; }
- else if (type == "summary") { outputFileName = "cons.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],cons.fasta-[filename],[tag],cons.fasta"; }
+ else if (type == "name") { pattern = "[filename],cons.names-[filename],[tag],cons.names"; }
+ else if (type == "count") { pattern = "[filename],cons.count_table-[filename],[tag],cons.count_table"; }
+ else if (type == "summary") { pattern = "[filename],cons.summary-[filename],[tag],cons.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConsensusSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
ConsensusSeqsCommand::ConsensusSeqsCommand(){
try {
if (listfile == "") {
ofstream outSummary;
- string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputSummaryFile = getOutputFileName("summary", variables);
m->openOutputFile(outputSummaryFile, outSummary);
outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
outSummary << "PositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
ofstream outFasta;
- string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
+ string outputFastaFile = getOutputFileName("fasta", variables);
m->openOutputFile(outputFastaFile, outFasta);
outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
try{
ofstream outSummary;
- string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[tag]"] = list->getLabel();
+ string outputSummaryFile = getOutputFileName("summary", variables);
m->openOutputFile(outputSummaryFile, outSummary);
outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
ofstream outName;
- string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("name");
+ string outputNameFile = getOutputFileName("name",variables);
m->openOutputFile(outputNameFile, outName);
outputNames.push_back(outputNameFile); outputTypes["name"].push_back(outputNameFile);
ofstream outFasta;
- string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("fasta");
+ string outputFastaFile = getOutputFileName("fasta",variables);
m->openOutputFile(outputFastaFile, outFasta);
outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
vector<string> setParameters();
string getCommandName() { return "consensus.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
string getDescription() { return "create a consensus sequence for each OTU or for a fasta file"; }
//**********************************************************************************************************************
vector<string> CooccurrenceCommand::setParameters() {
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pmetric("metric", "Multiple", "cscore-checker-combo-vratio", "cscore", "", "", "",false,false); parameters.push_back(pmetric);
- CommandParameter pmatrix("matrixmodel", "Multiple", "sim1-sim2-sim3-sim4-sim5-sim6-sim7-sim8-sim9", "sim2", "", "", "",false,false); parameters.push_back(pmatrix);
- CommandParameter pruns("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pruns);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);
+ CommandParameter pmetric("metric", "Multiple", "cscore-checker-combo-vratio", "cscore", "", "", "","",false,false); parameters.push_back(pmetric);
+ CommandParameter pmatrix("matrixmodel", "Multiple", "sim1-sim2-sim3-sim4-sim5-sim6-sim7-sim8-sim9", "sim2", "", "", "","",false,false); parameters.push_back(pmatrix);
+ CommandParameter pruns("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(pruns);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string CooccurrenceCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string CooccurrenceCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "summary") { outputFileName = "cooccurence.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "CooccurrenceCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],cooccurence.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CooccurrenceCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
CooccurrenceCommand::CooccurrenceCommand(){
set<string> userLabels = labels;
ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ string outputFileName = getOutputFileName("summary", variables);
m->openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
vector<string> setParameters();
string getCommandName() { return "Cooccurrence"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Ulrich W & Gotelli NJ (2010). Null model analysis of species associations using abundance data. Ecology 91:3384.\nhttp://www.mothur.org/wiki/Cooccurrence"; }
string getDescription() { return "calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance."; }
//**********************************************************************************************************************
vector<string> CorrAxesCommand::setParameters(){
try {
- CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paxes);
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata);
- CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "",false,false); parameters.push_back(pnumaxes);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none","corraxes",false,true,true); parameters.push_back(paxes);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false,true); parameters.push_back(prelabund);
+ CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false); parameters.push_back(pmetadata);
+ CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "","",false,false); parameters.push_back(pnumaxes);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false); parameters.push_back(pmethod);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string CorrAxesCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string CorrAxesCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "corraxes") { outputFileName = "corr.axes"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "CorrAxesCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "corraxes") { pattern = "[filename],[tag],corr.axes"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
CorrAxesCommand::CorrAxesCommand(){
try {
/*************************************************************************************/
// calc the r values //
/************************************************************************************/
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + "." + getOutputFileNameTag("corraxes");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[tag]"] = method;
+ string outputFileName = getOutputFileName("corraxes", variables);
outputNames.push_back(outputFileName); outputTypes["corraxes"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
vector<string> setParameters();
string getCommandName() { return "corr.axes"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Corr.axes"; }
string getDescription() { return "calculate the correlation coefficient for each column in a shared/relabund file to the axes displayed in a pcoa file"; }
//**********************************************************************************************************************
vector<string> CountGroupsCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pshared);
- CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pcount("count", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pcount);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","",false,false,true); parameters.push_back(pshared);
+ CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pcount("count", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
vector<string> setParameters();
string getCommandName() { return "count.groups"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string) { return ""; }
string getHelpString();
+ string getOutputPattern(string){ return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Count.groups"; }
string getDescription() { return "counts the number of sequences in each group"; }
//**********************************************************************************************************************
vector<string> CountSeqsCommand::setParameters(){
try {
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","count",false,true,true); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string CountSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string CountSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "counttable") { outputFileName = "count_table"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "CountSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "count") { pattern = "[filename],count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
CountSeqsCommand::CountSeqsCommand(){
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["counttable"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["counttable"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("counttable");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
+ string outputFileName = getOutputFileName("count", variables);
int total = 0;
if (!large) { total = processSmall(outputFileName); }
if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
//set rabund file as new current rabundfile
- itTypes = outputTypes.find("counttable");
+ itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { string current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
int CountSeqsCommand::processSmall(string outputFileName){
try {
ofstream out;
- m->openOutputFile(outputFileName, out); outputTypes["counttable"].push_back(outputFileName);
- outputNames.push_back(outputFileName); outputTypes["counttable"].push_back(outputFileName);
+ m->openOutputFile(outputFileName, out); outputTypes["count"].push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
out << "Representative_Sequence\ttotal\t";
GroupMap* groupMap;
for (set<string>::iterator it = namesOfGroups.begin(); it != namesOfGroups.end(); it++) { initial[(*it)] = 0; }
ofstream out;
m->openOutputFile(outputFileName, out);
- outputNames.push_back(outputFileName); outputTypes["counttable"].push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
out << "Representative_Sequence\ttotal\t";
if (groupfile == "") { out << endl; }
vector<string> setParameters();
string getCommandName() { return "count.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
string getDescription() { return "counts the number of sequences represented by each unique sequence in a namesfile"; }
//**********************************************************************************************************************
vector<string> CreateDatabaseCommand::setParameters(){
try {
- CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("repname", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
- CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcontaxonomy);
- CommandParameter plist("list", "InputTypes", "", "", "ListShared", "ListShared", "none",false,false); parameters.push_back(plist);
- CommandParameter pshared("shared", "InputTypes", "", "", "ListShared", "ListShared", "none",false,false); parameters.push_back(pshared);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none","database",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("repname", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
+ CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pcontaxonomy);
+ CommandParameter plist("list", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(pshared);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string CreateDatabaseCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string CreateDatabaseCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "database") { outputFileName = "database"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "CreateDatabaseCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "database") { pattern = "[filename],database"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
CreateDatabaseCommand::CreateDatabaseCommand(){
try {
if (m->control_pressed) { return 0; }
- string outputFileName = "";
- if (listfile != "") { outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("database"); }
- else { outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("database"); }
+ map<string, string> variables;
+ if (listfile != "") { variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); }
+ else { variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); }
+ string outputFileName = getOutputFileName("database", variables);
outputNames.push_back(outputFileName); outputTypes["database"].push_back(outputFileName);
ofstream out;
vector<string> setParameters();
string getCommandName() { return "create.database"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Create.database"; }
string getDescription() { return "creates database file that includes, abundances across groups, representative sequences, and taxonomy for each OTU"; }
//**********************************************************************************************************************
vector<string> DeconvoluteCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string DeconvoluteCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string DeconvoluteCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "unique" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "names"; }
- else if (type == "count") { outputFileName = "count_table"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "DeconvoluteCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],unique,[extension]"; }
+ else if (type == "name") { pattern = "[filename],names-[filename],[tag],names"; }
+ else if (type == "count") { pattern = "[filename],count_table-[filename],[tag],count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
DeconvoluteCommand::DeconvoluteCommand(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//prepare filenames and open files
- string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + getOutputFileNameTag("name");
- string outCountFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + getOutputFileNameTag("count");
- string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + getOutputFileNameTag("fasta", inFastaName);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inFastaName));
+ string outNameFile = getOutputFileName("name", variables);
+ string outCountFile = getOutputFileName("count", variables);
+ variables["[extension]"] = m->getExtension(inFastaName);
+ string outFastaFile = getOutputFileName("fasta", variables);
map<string, string> nameMap;
map<string, string>::iterator itNames;
if (oldNameMapFName != "") {
m->readNames(oldNameMapFName, nameMap);
- if (oldNameMapFName == outNameFile){ outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique." + getOutputFileNameTag("name"); }
+ if (oldNameMapFName == outNameFile){
+ variables["[tag]"] = "unique";
+ outNameFile = getOutputFileName("name", variables); }
}
CountTable ct;
if (countfile != "") {
ct.readTable(countfile);
- if (countfile == outCountFile){ outCountFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique." + getOutputFileNameTag("count"); }
+ if (countfile == outCountFile){
+ variables["[tag]"] = "unique";
+ outCountFile = getOutputFileName("count", variables); }
}
if (m->control_pressed) { return 0; }
vector<string> setParameters();
string getCommandName() { return "unique.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
string getDescription() { return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
//**********************************************************************************************************************
vector<string> DegapSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string DegapSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string DegapSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "ng.fasta"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "DegapSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],ng.fasta"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DegapSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
DegapSeqsCommand::DegapSeqsCommand(){
ofstream outFASTA;
string tempOutputDir = outputDir;
if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); }
- string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ string degapFile = getOutputFileName("fasta", variables);
m->openOutputFile(degapFile, outFASTA);
while(!inFASTA.eof()){
vector<string> setParameters();
string getCommandName() { return "degap.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Degap.seqs"; }
string getDescription() { return "removes gap characters from sequences"; }
//**********************************************************************************************************************
vector<string> DeUniqueSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string DeUniqueSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string DeUniqueSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "redundant.fasta"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "DeUniqueSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],redundant.fasta"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeUniqueSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
DeUniqueSeqsCommand::DeUniqueSeqsCommand(){
ofstream out;
string outFastaFile = m->getRootName(m->getSimpleName(fastaFile));
int pos = outFastaFile.find("unique");
- if (pos != string::npos) {
- outFastaFile = outputDir + outFastaFile.substr(0, pos) + getOutputFileNameTag("fasta");
- }else{
- outFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + getOutputFileNameTag("fasta");
- }
+ if (pos != string::npos) { outFastaFile = outputDir + outFastaFile.substr(0, pos); }
+ else { outFastaFile = outputDir + outFastaFile; }
+ map<string, string> variables;
+ variables["[filename]"] = outFastaFile;
+ outFastaFile = getOutputFileName("fasta", variables);
m->openOutputFile(outFastaFile, out);
readNamesFile();
vector<string> setParameters();
string getCommandName() { return "deunique.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Deunique.seqs"; }
string getDescription() { return "reverse of the unique.seqs command, and creates a fasta file from a fasta and name file"; }
//**********************************************************************************************************************
vector<string> DeuniqueTreeCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","tree",false,true,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string DeuniqueTreeCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string DeuniqueTreeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "tree") { outputFileName = "deunique.tre"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "DeuniqueTreeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "tree") { pattern = "[filename],deunique.tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
DeuniqueTreeCommand::DeuniqueTreeCommand(){
delete reader;
//print new Tree
- string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ string outputFile = getOutputFileName("tree", variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
ofstream out;
m->openOutputFile(outputFile, out);
vector<string> setParameters();
string getCommandName() { return "deunique.tree"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Deunique.tree"; }
string getDescription() { return "add the redundant sequence names back into a tree of unique sequences"; }
//**********************************************************************************************************************
vector<string> DistanceCommand::setParameters(){
try {
- CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(pcolumn);
- CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(poldfasta);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
- CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
- CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn","column",false,false); parameters.push_back(pcolumn);
+ CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn","",false,false); parameters.push_back(poldfasta);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","phylip-column",false,true, true); parameters.push_back(pfasta);
+ CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "","phylip-column",false,false, true); parameters.push_back(poutput);
+ CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "","",false,false); parameters.push_back(pcalc);
+ CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcountends);
+ CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcompress);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false, true); parameters.push_back(pprocessors);
+ CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false, true); parameters.push_back(pcutoff);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string DistanceCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string DistanceCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "phylip") { outputFileName = "dist"; }
- else if (type == "column") { outputFileName = "dist"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "phylip") { pattern = "[filename],[outputtag],dist"; }
+ else if (type == "column") { pattern = "[filename],dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
DistanceCommand::DistanceCommand(){
if (!alignDB.sameLength()) { m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
string outputFile;
-
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
if (output == "lt") { //does the user want lower triangle phylip formatted file
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip." + getOutputFileNameTag("phylip");
+ variables["[outputtag]"] = "phylip";
+ outputFile = getOutputFileName("phylip", variables);
m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
//output numSeqs to phylip formatted dist file
}else if (output == "column") { //user wants column format
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("column");
+ outputFile = getOutputFileName("column", variables);
outputTypes["column"].push_back(outputFile);
//so we don't accidentally overwrite
m->mothurRemove(outputFile);
}else { //assume square
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square." + getOutputFileNameTag("phylip");
+ variables["[outputtag]"] = "square";
+ outputFile = getOutputFileName("phylip", variables);
m->mothurRemove(outputFile);
outputTypes["phylip"].push_back(outputFile);
}
vector<string> setParameters();
string getCommandName() { return "dist.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
string getDescription() { return "calculate the pairwaise distances between aligned sequences"; }
//**********************************************************************************************************************
vector<string> FilterSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
- CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
- CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
- CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta);
+ CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard);
+ CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump);
+ CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft);
+ CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false, true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string FilterSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string FilterSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "filter.fasta"; }
- else if (type == "filter") { outputFileName = "filter"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],filter.fasta"; }
+ else if (type == "filter") { pattern = "[filename],filter"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
FilterSeqsCommand::FilterSeqsCommand(){
ofstream outFilter;
//prevent giantic file name
- string filterFile;
- if (fastafileNames.size() > 3) { filterFile = outputDir + "merge." + getOutputFileNameTag("filter"); }
- else { filterFile = outputDir + filterFileName + "." + getOutputFileNameTag("filter"); }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + filterFileName + ".";
+ if (fastafileNames.size() > 3) { variables["[filename]"] = outputDir + "merge."; }
+ string filterFile = getOutputFileName("filter", variables);
m->openOutputFile(filterFile, outFilter);
outFilter << filter << endl;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s]));
+ string filteredFasta = getOutputFileName("fasta", variables);
#ifdef USE_MPI
int pid, numSeqsPerProcessor, num;
int tag = 2001;
vector<string> setParameters();\r
string getCommandName() { return "filter.seqs"; }\r
string getCommandCategory() { return "Sequence Processing"; }\r
- string getOutputFileNameTag(string, string);\r
+ \r
string getHelpString(); \r
+ string getOutputPattern(string); \r
string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }\r
string getDescription() { return "removes columns from alignments based on a criteria defined by the user"; }\r
\r
//**********************************************************************************************************************
vector<string> GetCommandInfoCommand::setParameters(){
try {
- CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
map<string, vector<string> > thisOutputTypes = thisCommand->getOutputFiles();
map<string, vector<string> >::iterator itTypes;
- if (thisOutputTypes.size() == 0) { out << "outputTypes=none" << endl; }
+ if (thisOutputTypes.size() == 0) { out << "outputTypesNames=0" << endl; }
else {
- string types = "";
- for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) { types += itTypes->first + "-"; }
+ //string types = "";
+ //for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) { types += itTypes->first + "-"; }
//rip off last -
- types = types.substr(0, types.length()-1);
- out << "outputTypes=" << types << endl;
+ //types = types.substr(0, types.length()-1);
+ out << "outputTypesNames=" << thisOutputTypes.size() << endl;
+
+ for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) {
+ out << itTypes->first << "=" << thisCommand->getOutputPattern(itTypes->first) << endl;
+ }
}
vector<string> booleans; vector<string> numbers; vector<string> multiples; vector<string> Strings;
for (int i = 0; i < para.size(); i++) {
if ((para[i].name == "inputdir") || (para[i].name == "outputdir")) {} //ignore
else {
+ string important = "|F";
+ if (para[i].important || para[i].required) { important = "|T"; }
+
+ string outputType = "|none";
+ if (para[i].outputTypes != "") { outputType = "|" + para[i].outputTypes; }
+
if (para[i].type == "Boolean") {
- string temp = para[i].name + "=" + para[i].optionsDefault;
+ string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
booleans.push_back(temp);
}else if (para[i].type == "Multiple") {
string multAllowed = "F";
if (para[i].multipleSelectionAllowed) { multAllowed = "T"; }
- string temp = para[i].name + "=" + para[i].options + "|" + para[i].optionsDefault + "|" + multAllowed;
+ string temp = para[i].name + "=" + para[i].options + "|" + para[i].optionsDefault + "|" + multAllowed + important + outputType;
multiples.push_back(temp);
}else if (para[i].type == "Number") {
- string temp = para[i].name + "=" + para[i].optionsDefault;
+ string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
numbers.push_back(temp);
}else if (para[i].type == "String") {
- string temp = para[i].name + "=" + para[i].optionsDefault;
+ string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
strings.push_back(temp);
}else if (para[i].type == "InputTypes") {
string required = "F";
if (para[i].required) { required = "T"; }
- string temp = required + "|" + para[i].chooseOnlyOneGroup + "|" + para[i].chooseAtLeastOneGroup + "|" + para[i].linkedGroup;
+ string temp = required + important + "|" + para[i].chooseOnlyOneGroup + "|" + para[i].chooseAtLeastOneGroup + "|" + para[i].linkedGroup + outputType;
inputTypes[para[i].name] = temp;
//add choose only one groups
- groups[para[i].chooseOnlyOneGroup].insert(para[i].name);
-
+ vector<string> tempGroups;
+ m->splitAtDash(para[i].chooseOnlyOneGroup, tempGroups);
+ for (int l = 0; l < tempGroups.size(); l++) {
+ groups[tempGroups[l]].insert(para[i].name);
+ }
+ tempGroups.clear();
+
//add at least one group names
- groups[para[i].chooseAtLeastOneGroup].insert(para[i].name);
+ m->splitAtDash(para[i].chooseAtLeastOneGroup, tempGroups);
+ for (int l = 0; l < tempGroups.size(); l++) {
+ groups[tempGroups[l]].insert(para[i].name);
+ }
+ tempGroups.clear();
+
//add at linked group names
- groups[para[i].linkedGroup].insert(para[i].name);
+ m->splitAtDash(para[i].linkedGroup, tempGroups);
+ for (int l = 0; l < tempGroups.size(); l++) {
+ groups[tempGroups[l]].insert(para[i].name);
+ }
+ tempGroups.clear();
}else { m->mothurOut("[ERROR]: " + para[i].type + " is an unknown parameter type, please correct."); m->mothurOutEndLine(); }
}
vector<string> setParameters();
string getCommandName() { return "get.commandinfo"; }
string getCommandCategory() { return "Hidden"; }
- string getOutputFileNameTag(string, string) { return ""; }
string getHelpString();
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "no citation"; }
string getDescription() { return "get.commandinfo"; }
//**********************************************************************************************************************
vector<string> GetCoreMicroBiomeCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter poutput("output", "Multiple", "fraction-count", "fraction", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pabund("abundance", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter psamples("samples", "Number", "", "-1", "", "", "",false,false); parameters.push_back(psamples);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter poutput("output", "Multiple", "fraction-count", "fraction", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pabund("abundance", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter psamples("samples", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(psamples);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetCoreMicroBiomeCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetCoreMicroBiomeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "coremicrobiome") { outputFileName = "core.microbiome"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetCoreMicroBiomeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "coremicrobiome") { pattern = "[filename],[tag],core.microbiome"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCoreMicroBiomeCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(){
try {
int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
try {
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("coremicrobiome");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[tag]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("coremicrobiome", variables);
outputNames.push_back(outputFileName); outputTypes["coremicrobiome"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
string getCommandName() { return "get.coremicrobiome"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
//commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.coremicrobiome"; }
string getDescription() { return "determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances"; }
//**********************************************************************************************************************
vector<string> GetCurrentCommand::setParameters(){
try {
- CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
vector<string> setParameters();
string getCommandName() { return "get.current"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string) { return ""; }
string getHelpString();
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Get.current"; }
string getDescription() { return "get current files saved by mothur"; }
//**********************************************************************************************************************
vector<string> GetgroupCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none","",false,true, true); parameters.push_back(pshared);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
vector<string> setParameters();
string getCommandName() { return "get.group"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string) { return ""; }
string getHelpString();
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Get.group"; }
string getDescription() { return "outputs group names"; }
//**********************************************************************************************************************
vector<string> GetGroupsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(pfasta);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pdesign);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT","fasta",false,false, true); parameters.push_back(pfasta);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false, true); parameters.push_back(pshared);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false, true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false, true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT","group",false,false, true); parameters.push_back(pgroup);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT","design",false,false, true); parameters.push_back(pdesign);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT","list",false,false, true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT","taxonomy",false,false, true); parameters.push_back(ptaxonomy);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetGroupsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetGroupsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "pick.count_table"; }
- else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "shared") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "design") { outputFileName = "pick" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "name") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "shared") { pattern = "[filename],[tag],pick,[extension]"; }
+ else if (type == "design") { pattern = "[filename],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
GetGroupsCommand::GetGroupsCommand(){
try {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
InputData input(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
bool wroteSomething = false;
while(lookup[0] != NULL) {
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("shared", sharedfile);
+ variables["[tag]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("shared", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputFileName = getOutputFileName("count", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(designfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + getOutputFileNameTag("design", designfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(designfile));
+ variables["[extension]"] = m->getExtension(designfile);
+ string outputFileName = getOutputFileName("design", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
vector<string> setParameters();
string getCommandName() { return "get.groups"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
string getDescription() { return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
//**********************************************************************************************************************
vector<string> GetlabelCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(psabund);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
vector<string> setParameters();
string getCommandName() { return "get.label"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string) { return ""; }
string getHelpString();
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Get.label"; }
string getDescription() { return "outputs labels"; }
//**********************************************************************************************************************
vector<string> GetLineageCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
- CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon);
- CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false, true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false, true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false, true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false, true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false, true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,true, true); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
+ CommandParameter ptaxon("taxon", "String", "", "", "", "", "","",false,true, true); parameters.push_back(ptaxon);
+ CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetLineageCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetLineageCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "pick.count_table"; }
- else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "alignreport") { outputFileName = "pick.align.report"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetLineageCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "name") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "alignreport") { pattern = "[filename],pick.align.report"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetLineageCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
GetLineageCommand::GetLineageCommand(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputFileName = getOutputFileName("count", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(alignfile));
+ variables["[extension]"] = m->getExtension(alignfile);
+ string outputFileName = getOutputFileName("alignreport", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
vector<string> setParameters();
string getCommandName() { return "get.lineage"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
string getDescription() { return "gets sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
//**********************************************************************************************************************
vector<string> GetListCountCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "",false,false); parameters.push_back(parasort);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otu",false,true, true); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "","",false,false); parameters.push_back(parasort);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetListCountCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetListCountCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "otu") { outputFileName = "otu"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetListCountCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "otu") { pattern = "[filename],[tag],otu"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetListCountCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
GetListCountCommand::GetListCountCommand(){
try {
string binnames;
if (outputDir == "") { outputDir += m->hasPath(listfile); }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + "." +getOutputFileNameTag("otu");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[tag]"] = list->getLabel();
+ string outputFileName = getOutputFileName("otu", variables);
+
m->openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);
string getCitation() { return "http://www.mothur.org/wiki/Get.otulist"; }
string getDescription() { return "lists each OTU number and the sequence contained in that OTU"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
int execute();
void help() { m->mothurOut(getHelpString()); }
//**********************************************************************************************************************
vector<string> GetOtuLabelsCommand::setParameters(){
try {
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
- CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pconstaxonomy);
- CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(potucorr);
- CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pcorraxes);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true, true); parameters.push_back(paccnos);
+ CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none","constaxonomy",false,false, true); parameters.push_back(pconstaxonomy);
+ CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none","otucorr",false,false, true); parameters.push_back(potucorr);
+ CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none","corraxes",false,false, true); parameters.push_back(pcorraxes);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetOtuLabelsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetOtuLabelsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "constaxonomy") { outputFileName = "pick.taxonomy"; }
- else if (type == "otucorr") { outputFileName = "pick.corr"; }
- else if (type == "corraxes") { outputFileName = "pick.axes"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtuLabelsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "constaxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "otucorr") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "corraxes") { pattern = "[filename],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOtuLabelsCommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
GetOtuLabelsCommand::GetOtuLabelsCommand(){
try {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomyfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + getOutputFileNameTag("constaxonomy");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
+ variables["[extension]"] = m->getExtension(constaxonomyfile);
+ string outputFileName = getOutputFileName("constaxonomy", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(otucorrfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + getOutputFileNameTag("otucorr");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
+ variables["[extension]"] = m->getExtension(otucorrfile);
+ string outputFileName = getOutputFileName("otucorr", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(corraxesfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + getOutputFileNameTag("corraxes");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
+ variables["[extension]"] = m->getExtension(corraxesfile);
+ string outputFileName = getOutputFileName("corraxes", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
vector<string> setParameters();
string getCommandName() { return "get.otulabels"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.otulabels"; }
string getDescription() { return "Can be used with output from classify.otu, otu.association, or corr.axes to select specific otus."; }
//**********************************************************************************************************************
vector<string> GetOTURepCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "ColumnName",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter pweighted("weighted", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pweighted);
- CommandParameter psorted("sorted", "Multiple", "none-name-bin-size-group", "none", "", "", "",false,false); parameters.push_back(psorted);
- CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","name",false,true, true); parameters.push_back(plist);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,false, true); parameters.push_back(pfasta);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false, true); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","",false,false, true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "ColumnName","count",false,false, true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false, true); parameters.push_back(pgroup);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","",false,false, true); parameters.push_back(pcolumn);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+ CommandParameter pweighted("weighted", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pweighted);
+ CommandParameter psorted("sorted", "Multiple", "none-name-bin-size-group", "none", "", "", "","",false,false); parameters.push_back(psorted);
+ CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetOTURepCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetOTURepCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "rep.fasta"; }
- else if (type == "name") { outputFileName = "rep.names"; }
- else if (type == "count") { outputFileName = "rep.count_table"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetOTURepCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],[tag],rep.fasta-[filename],[tag],[group],rep.fasta"; }
+ else if (type == "name") { pattern = "[filename],[tag],rep.names-[filename],[tag],[group],rep.names"; }
+ else if (type == "count") { pattern = "[filename],[tag],rep.count_table-[filename],[tag],[group],rep.count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
GetOTURepCommand::GetOTURepCommand(){
string outputNamesFile;
map<string, ofstream*> filehandles;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+
if (Groups.size() == 0) { //you don't want to use groups
- outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".";
+ variables["[tag]"] = processList->getLabel();
if (countfile == "") {
- outputNamesFile += getOutputFileNameTag("name");
+ outputNamesFile = getOutputFileName("name", variables);
outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile);
}else {
- outputNamesFile += getOutputFileNameTag("count");
+ outputNamesFile = getOutputFileName("count", variables);
outputNames.push_back(outputNamesFile); outputTypes["count"].push_back(outputNamesFile);
}
outputNameFiles[outputNamesFile] = processList->getLabel();
ofstream* temp;
for (int i=0; i<Groups.size(); i++) {
temp = new ofstream;
+ variables["[tag]"] = processList->getLabel();
+ variables["[group]"] = Groups[i];
filehandles[Groups[i]] = temp;
outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".";
if (countfile == "") {
- outputNamesFile += getOutputFileNameTag("name");
+ outputNamesFile = getOutputFileName("name", variables);
outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile);
}else {
- outputNamesFile += getOutputFileNameTag("count");
+ outputNamesFile = getOutputFileName("count", variables);
outputNames.push_back(outputNamesFile); outputTypes["count"].push_back(outputNamesFile);
}
//create output file
if (outputDir == "") { outputDir += m->hasPath(listfile); }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[tag]"] = label;
+ string outputFileName = getOutputFileName("fasta",variables);
m->openOutputFile(outputFileName, out);
vector<repStruct> reps;
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
vector<string> setParameters();
string getCommandName() { return "get.oturep"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.oturep"; }
string getDescription() { return "gets a representative sequence for each OTU"; }
//**********************************************************************************************************************
vector<string> GetOtusCommand::setParameters(){
try {
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true, true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true, true); parameters.push_back(plist);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetOtusCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetOtusCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "group") { pattern = "[filename],[tag],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],[tag],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOtusCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
GetOtusCommand::GetOtusCommand(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("list", listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[tag]"] = label;
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
string GroupOutputDir = outputDir;
if (outputDir == "") { GroupOutputDir += m->hasPath(groupfile); }
- string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + label + "." + getOutputFileNameTag("group", groupfile);
+ variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputGroupFileName = getOutputFileName("group", variables);
ofstream outGroup;
m->openOutputFile(outputGroupFileName, outGroup);
vector<string> setParameters();
string getCommandName() { return "get.otus"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
string getDescription() { return "outputs a new list file containing the otus containing sequences from the groups specified"; }
//**********************************************************************************************************************
vector<string> GetRAbundCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
- CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(psorted);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(plist);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(psabund);
+ CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(psorted);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetRAbundCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetRAbundCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "rabund") { outputFileName = "rabund"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetRAbundCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "rabund") { pattern = "[filename],rabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
GetRAbundCommand::GetRAbundCommand(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("rabund");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ filename = getOutputFileName("rabund", variables);
m->openOutputFile(filename, out);
input = new InputData(inputfile, format);
vector<string> setParameters();
string getCommandName() { return "get.rabund"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
string getDescription() { return "creates a rabund file"; }
//**********************************************************************************************************************
vector<string> GetRelAbundCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "",false,false); parameters.push_back(pscale);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","relabund",false,true, true); parameters.push_back(pshared);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "","",false,false); parameters.push_back(pscale);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetRelAbundCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetRelAbundCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "relabund") { outputFileName = "relabund" ; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "relabund") { pattern = "[filename],relabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
GetRelAbundCommand::GetRelAbundCommand(){
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("relabund");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ string outputFileName = getOutputFileName("relabund", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
vector<string> setParameters();
string getCommandName() { return "get.relabund"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.relabund"; }
string getDescription() { return "calculates the relative abundance of each OTU in a sample"; }
//**********************************************************************************************************************
vector<string> GetSAbundCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","sabund",false,false, true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","sabund",false,false, true); parameters.push_back(prabund);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetSAbundCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetSAbundCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "sabund") { outputFileName = "sabund"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetSAbundCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "sabund") { pattern = "[filename],sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
GetSAbundCommand::GetSAbundCommand(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("sabund");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ filename = getOutputFileName("sabund", variables);
m->openOutputFile(filename, out);
input = new InputData(inputfile, format);
vector<string> setParameters();
string getCommandName() { return "get.sabund"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.sabund"; }
string getDescription() { return "creates a sabund file"; }
//**********************************************************************************************************************
vector<string> GetSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
- CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
- CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
+ CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos2);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "pick.count_table"; }
- else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "qfile") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "accnosreport"){ outputFileName = "accnos.report"; }
- else if (type == "alignreport") { outputFileName = "pick.align.report"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "name") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "qfile") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "accnosreport") { pattern = "[filename],pick.accnos.report"; }
+ else if (type == "alignreport") { pattern = "[filename],pick.align.report"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
GetSeqsCommand::GetSeqsCommand(string option) {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(qualfile));
+ variables["[extension]"] = m->getExtension(qualfile);
+ string outputFileName = getOutputFileName("qfile", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputFileName = getOutputFileName("count", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(alignfile));
+ string outputFileName = getOutputFileName("alignreport", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(accnosfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + getOutputFileNameTag("accnosreport");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile));
+ string outputFileName = getOutputFileName("accnosreport", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
vector<string> setParameters();
string getCommandName() { return "get.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
string getDescription() { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
//**********************************************************************************************************************
vector<string> GetSharedOTUCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist);
- CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique);
- CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(plist);
+ CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter punique("unique", "String", "", "", "", "", "","",false,false,true); parameters.push_back(punique);
+ CommandParameter pshared("shared", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pshared);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string GetSharedOTUCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetSharedOTUCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],[distance],[group],shared.fasta"; }
+ else if (type == "accnos") { pattern = "[filename],[distance],[group],accnos"; }
+ else if (type == "sharedseqs") { pattern = "[filename],[distance],[group],shared.seqs"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "shared.fasta"; }
- else if (type == "accnos") { outputFileName = "accnos"; }
- else if (type == "sharedseqs") { outputFileName = "shared.seqs"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "GetSharedOTUCommand", "getOutputFileNameTag");
- exit(1);
- }
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
GetSharedOTUCommand::GetSharedOTUCommand(){
try {
string outputFileNames;
if (outputDir == "") { outputDir += m->hasPath(listfile); }
- if (output != "accnos") {
- outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("sharedseqs");
- }else {
- outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("accnos");
- }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = shared->getLabel();
+ variables["[group]"] = userGroups;
+ if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }
+ else { outputFileNames = getOutputFileName("accnos", variables); }
+
m->openOutputFile(outputFileNames, outNames);
bool wroteSomething = false;
//if fasta file provided output new fasta file
if ((fastafile != "") && wroteSomething) {
if (outputDir == "") { outputDir += m->hasPath(fastafile); }
- string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("fasta");
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileFasta = getOutputFileName("fasta", variables);
ofstream outFasta;
m->openOutputFile(outputFileFasta, outFasta);
outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
string getCommandName() { return "get.sharedseqs"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getRequiredCommand() { return "none"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
string getDescription() { return "identifies sequences that are either unique or shared by specific groups"; }
//**********************************************************************************************************************
vector<string> HClusterCommand::setParameters(){
try {
- CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
- CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
- CommandParameter psorted("sorted", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psorted);
- CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund);
- CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","list-rabund-sabund",false,false,true); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list-rabund-sabund",false,false,true); parameters.push_back(pcolumn);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false); parameters.push_back(pmethod);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
+ CommandParameter psorted("sorted", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psorted);
+ CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund);
+ CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string HClusterCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string HClusterCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "list") { outputFileName = "list"; }
- else if (type == "rabund") { outputFileName = "rabund"; }
- else if (type == "sabund") { outputFileName = "sabund"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "HClusterCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "list") { pattern = "[filename],[clustertag],list"; }
+ else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; }
+ else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HClusterCommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
HClusterCommand::HClusterCommand(){
try {
else if (method == "nearest") { tag = "nn"; }
else if (method == "weighted") { tag = "wn"; }
else { tag = "an"; }
+
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[clustertag]"] = tag;
- string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
- string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
- string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+ string sabundFileName = getOutputFileName("sabund",variables);
+ string rabundFileName = getOutputFileName("rabund",variables);
+ string listFileName = getOutputFileName("list", variables);
m->openOutputFile(sabundFileName, sabundFile);
m->openOutputFile(rabundFileName, rabundFile);
vector<string> setParameters();
string getCommandName() { return "hcluster"; }
string getCommandCategory() { return "Clustering"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Sun Y, Cai Y, Liu L, Yu F, Farrell ML, Mckendree W, Farmerie W (2009). ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37: e76. \nhttp://www.mothur.org/wiki/Hcluster"; }
string getDescription() { return "cluster your sequences into OTUs using a distance matrix"; }
//**********************************************************************************************************************
vector<string> HeatMapCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "",false,false); parameters.push_back(pscale);
- CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "",false,false); parameters.push_back(psorted);
- CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "",false,false); parameters.push_back(pnumotu);
- CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(psabund);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "","",false,false); parameters.push_back(pscale);
+ CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "","",false,false); parameters.push_back(psorted);
+ CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnumotu);
+ CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
//**********************************************************************************************************************
-
-string HeatMapCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string HeatMapCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "svg") { outputFileName = "svg"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "svg") { pattern = "[filename],svg"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
vector<string> setParameters();
string getCommandName() { return "heatmap.bin"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Heatmap.bin"; }
string getDescription() { return "generate a heatmap where the color represents the relative abundanceof an OTU"; }
//**********************************************************************************************************************
vector<string> HeatMapSimCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","svg",false,false,true); parameters.push_back(pshared);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","svg",false,false); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pcount);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName","svg",false,false); parameters.push_back(pcolumn);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "","",true,false); parameters.push_back(pcalc);
+ CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-
-string HeatMapSimCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string HeatMapSimCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "svg") { outputFileName = "svg"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "svg") { pattern = "[filename],svg"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
HeatMapSimCommand::HeatMapSimCommand(){
try {
vector<string> setParameters();
string getCommandName() { return "heatmap.sim"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Heatmap.sim"; }
string getDescription() { return "generate a heatmap indicating the pairwise distance between multiple samples using a variety of calculators"; }
string getCommandName() { return "help"; }
string getCommandCategory() { return "Hidden"; }
string getHelpString() { return "For more information about a specific command type 'commandName(help)' i.e. 'cluster(help)'"; }
- string getOutputFileNameTag(string, string) { return ""; }
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "no citation"; }
string getDescription() { return "help"; }
//**********************************************************************************************************************
vector<string> HomovaCommand::setParameters(){
try {
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(palpha);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","homova",false,true,true); parameters.push_back(pdesign);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","homova",false,true,true); parameters.push_back(pphylip);
+ CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string HomovaCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string HomovaCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "homova") { outputFileName = "homova"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "HomovaCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "homova") { pattern = "[filename],homova"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HomovaCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
HomovaCommand::HomovaCommand(){
//create a new filename
ofstream HOMOVAFile;
- string HOMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("homova");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
+ string HOMOVAFileName = getOutputFileName("homova", variables);
m->openOutputFile(HOMOVAFileName, HOMOVAFile);
outputNames.push_back(HOMOVAFileName); outputTypes["homova"].push_back(HOMOVAFileName);
vector<string> setParameters();
string getCommandName() { return "homova"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71. \nhttp://www.mothur.org/wiki/Homova"; }
string getDescription() { return "homova"; }
//**********************************************************************************************************************
vector<string> IndicatorCommand::setParameters(){
try {
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pdesign("design", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none",false,false); parameters.push_back(pdesign);
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter ptree("tree", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none",false,false); parameters.push_back(ptree);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pdesign("design", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none","summary",false,false,true); parameters.push_back(pdesign);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","summary",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","summary",false,false); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter ptree("tree", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none","tree-summary",false,false,true); parameters.push_back(ptree);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pprocessors);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string IndicatorCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string IndicatorCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "tree") { outputFileName = "indicator.tre"; }
- else if (type == "summary") { outputFileName = "indicator.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "IndicatorCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "tree") { pattern = "[filename],indicator.tre"; }
+ else if (type == "summary") { pattern = "[filename],indicator.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
IndicatorCommand::IndicatorCommand(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName));
+ string outputFileName = getOutputFileName("summary", variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName));
+ string outputFileName = getOutputFileName("summary",variables);
outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
ofstream out;
string treeOutputDir = outputDir;
if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
- string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
+ variables["[filename]"] = treeOutputDir + m->getRootName(m->getSimpleName(treefile));
+ string outputTreeFileName = getOutputFileName("tree", variables);
//create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
vector<string> setParameters();
string getCommandName() { return "indicator"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Dufrene M, Legendre P (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecol Monogr 67: 345-66.\n McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Indicator"; }
string getDescription() { return "calculate the indicator value for each OTU"; }
//**********************************************************************************************************************
vector<string> LibShuffCommand::setParameters(){
try {
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter piters("iters", "Number", "", "10000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pstep("step", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pstep);
- CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pform("form", "Multiple", "discrete-integral", "integral", "", "", "",false,false); parameters.push_back(pform);
- CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","coverage-libshuffsummary",false,true,true); parameters.push_back(pphylip);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "10000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pstep("step", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pstep);
+ CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pform("form", "Multiple", "discrete-integral", "integral", "", "", "","",false,false); parameters.push_back(pform);
+ CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string LibShuffCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string LibShuffCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "coverage") { outputFileName = "libshuff.coverage"; }
- else if (type == "libshuffsummary") { outputFileName = "libshuff.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "LibShuffCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "coverage") { pattern = "[filename],libshuff.coverage"; }
+ else if (type == "libshuffsummary") { pattern = "[filename],libshuff.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
LibShuffCommand::LibShuffCommand(){
try {
ofstream outCov;
- summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("coverage");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+ summaryFile = getOutputFileName("coverage", variables);
m->openOutputFile(summaryFile, outCov);
outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
try {
ofstream outSum;
- summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("libshuffsummary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+ summaryFile = getOutputFileName("libshuffsummary",variables);
m->openOutputFile(summaryFile, outSum);
outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);
vector<string> setParameters();
string getCommandName() { return "libshuff"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001). Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-6. \nSchloss PD, Larget BR, Handelsman J (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70: 5485-92. \nhttp://www.mothur.org/wiki/Libshuff"; }
string getDescription() { return "a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic"; }
//**********************************************************************************************************************
vector<string> ListOtuLabelsCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","otulabels",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","otulabels",false,false); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
//every command must have inputdir and outputdir. This allows mothur users to redirect input and output files.
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ListOtuLabelsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ListOtuLabelsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "otulabels") { outputFileName = "otulabels"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ListOtuLabelsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "otulabels") { pattern = "[filename],[distance],otulabels"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListOtuLabelsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
ListOtuLabelsCommand::ListOtuLabelsCommand(){
try {
int ListOtuLabelsCommand::createList(vector<SharedRAbundVector*>& lookup){
try {
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("otulabels");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[distance]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("otulabels",variables);
outputNames.push_back(outputFileName); outputTypes["otulabels"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
int ListOtuLabelsCommand::createList(vector<SharedRAbundFloatVector*>& lookup){
try {
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("otulabels");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[distance]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("otulabels",variables);
outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
string getCommandName() { return "list.otulabels"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
//commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/List.otulabels"; }
string getDescription() { return "lists otu labels from shared or relabund file. Can be used by get.otulabels with output from classify.otu, otu.association, or corr.axes to select specific otus."; }
//**********************************************************************************************************************
vector<string> ListSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
- CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(palignreport);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false); parameters.push_back(palignreport);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ListSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ListSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "accnos") { outputFileName = "accnos"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ListSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "accnos") { pattern = "[filename],accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ListSeqsCommand::ListSeqsCommand(){
if (outputDir == "") { outputDir += m->hasPath(inputFileName); }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("accnos");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ string outputFileName = getOutputFileName("accnos", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
vector<string> setParameters();
string getCommandName() { return "list.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/List.seqs"; }
string getDescription() { return "lists sequences from a list, fasta, name, group, alignreport or taxonomy file"; }
//**********************************************************************************************************************
vector<string> LoadLogfileCommand::setParameters(){
try {
- CommandParameter plogfile("logfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plogfile);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plogfile("logfile", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plogfile);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
//look for "mothur >"
int pos = line.find("mothur > "); //command line
int pos2 = line.find("Output File "); //indicates command completed and we can update the current file
- int pos3 = line.find("*****************");
+ int pos3 = line.find("/*****************");
//skipping over parts where a command runs another command
if (pos3 != string::npos) {
while (!in.eof()) {
if (m->control_pressed) { break; }
line = m->getline(in); m->gobble(in);
- int posTemp = line.find("*****************");
+ int posTemp = line.find("/*****************");
if (posTemp != string::npos) { break; }
}
}
Command* command = cFactory->getCommand(commandName);
map<string, vector<string> > thisOutputTypes = command->getOutputFiles();
+
for (map<string, vector<string> >::iterator it = thisOutputTypes.begin(); it != thisOutputTypes.end(); it++) {
if (currentTypes.count((it->first)) != 0) { //do we save this type
//if yes whats its tag
string thisTypesCurrentFile = "";
if (itCurrentFiles != currentFiles.end()) { thisTypesCurrentFile = itCurrentFiles->second; }
- string tag = command->getOutputFileNameTag(it->first, thisTypesCurrentFile); //pass it "fasta" and the current fasta file name. some commands use the current name to get the extension, the others wont care.
- //search for the tag in the list of output files
- for (int h = 0; h < theseOutputNames.size(); h++) {
- string ending = theseOutputNames[h].substr(theseOutputNames[h].length()-tag.length(), tag.length());
- if (ending == tag) { //if it's there and this is a type we save a current version of, save it
- if ((it->first == "column") || (it->first == "phylip")) { //check for format
- string RippedName = "";
- bool foundDot = false;
- for (int i = theseOutputNames[h].length()-1; i >= 0; i--) {
- if (foundDot && (theseOutputNames[h][i] != '.')) { RippedName = theseOutputNames[h][i] + RippedName; }
- else if (foundDot && (theseOutputNames[h][i] == '.')) { break; }
- else if (!foundDot && (theseOutputNames[h][i] == '.')) { foundDot = true; }
- }
- if ((RippedName == "phylip") || (RippedName == "lt") || (RippedName == "square")) { currentFiles["phylip"] = theseOutputNames[h]; }
- else { currentFiles["column"] = theseOutputNames[h]; }
- }else { currentFiles[it->first] = theseOutputNames[h]; }
- break;
- }
- }
+ //outputfilename pattern for this input type
+ string pattern = command->getOutputPattern(it->first);
+ updateCurrent(pattern, it->first, thisTypesCurrentFile, theseOutputNames, currentFiles);
+
+ //cout << "current=\n\n";
+ //for (map<string, string>::iterator itcc = currentFiles.begin(); itcc != currentFiles.end(); itcc++) {
+ // cout << itcc->first << '\t' << itcc->second << endl;
+ // }
}
}
}
}
//**********************************************************************************************************************
+int LoadLogfileCommand::updateCurrent(string pattern, string type, string thisTypesCurrentFile, vector<string> filenames, map<string, string>& currentFiles){
+ try {
+
+ vector<string> patterns; m->splitAtChar(pattern, patterns, '-');
+
+ for (int i = 0; i < patterns.size(); i++) {
+
+ vector<string> peices; m->splitAtChar(patterns[i], peices, ',');
+ //cout << "patterns i = " << patterns[i] << endl;
+ if (peices.size() != 0) {
+ string tag = peices[peices.size()-1];
+ //cout << "tag = " << tag << endl;
+ if (peices[peices.size()-1] == "[extension]") { tag = m->getExtension(thisTypesCurrentFile); }
+
+ //search for the tag in the list of output files
+ for (int h = 0; h < filenames.size(); h++) {
+
+ if (m->control_pressed) { return 0; }
+ //cout << "filename h = " << filenames[h]<< endl;
+ string ending = filenames[h].substr(filenames[h].length()-tag.length(), tag.length());
+ if (ending == tag) { //if it's there and this is a type we save a current version of, save it
+ if ((type == "column") || (type == "phylip")) { //check for format
+ string RippedName = "";
+ bool foundDot = false;
+ for (int i = filenames[h].length()-1; i >= 0; i--) {
+ if (foundDot && (filenames[h][i] != '.')) { RippedName = filenames[h][i] + RippedName; }
+ else if (foundDot && (filenames[h][i] == '.')) { break; }
+ else if (!foundDot && (filenames[h][i] == '.')) { foundDot = true; }
+ }
+ if ((RippedName == "phylip") || (RippedName == "lt") || (RippedName == "square")) { currentFiles["phylip"] = filenames[h]; }
+ else { currentFiles["column"] = filenames[h]; }
+ }else { currentFiles[type] = filenames[h]; }
+ break;
+ }
+ }
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LoadLogfileCommand", "updateCurrent");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
vector<string> setParameters();
string getCommandName() { return "load.logfile"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string) { return ""; }
string getHelpString();
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Load.logfile"; }
string getDescription() { return "extracts current files from a logfile"; }
bool abort;
string outputDir, logfile;
vector<string> outputNames;
+
+ int updateCurrent(string pattern, string type, string, vector<string> outputNames, map<string, string>& currentFiles);
};
/**************************************************************************************************/
//**********************************************************************************************************************
vector<string> MakeBiomCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcontaxonomy);
- CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pmetadata);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter pmatrixtype("matrixtype", "Multiple", "sparse-dense", "sparse", "", "", "",false,false); parameters.push_back(pmatrixtype);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","biom",false,true,true); parameters.push_back(pshared);
+ CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcontaxonomy);
+ CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pmetadata);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter pmatrixtype("matrixtype", "Multiple", "sparse-dense", "sparse", "", "", "","",false,false); parameters.push_back(pmatrixtype);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string MakeBiomCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MakeBiomCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "biom") { outputFileName = "biom"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MakeBiomCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "biom") { pattern = "[filename],[distance],biom"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeBiomCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
//**********************************************************************************************************************
int MakeBiomCommand::getBiom(vector<SharedRAbundVector*>& lookup){
try {
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("biom");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("biom",variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName);
vector<string> setParameters();
string getCommandName() { return "make.biom"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://biom-format.org/documentation/biom_format.html, http://www.mothur.org/wiki/Make.biom"; }
string getDescription() { return "creates a biom file"; }
//**********************************************************************************************************************
vector<string> MakeContigsCommand::setParameters(){
try {
- CommandParameter pfasta("ffastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter prfasta("rfastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(prfasta);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
- CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
+ CommandParameter pfasta("ffastq", "InputTypes", "", "", "none", "none", "none","fasta-qfile",false,true,true); parameters.push_back(pfasta);
+ CommandParameter prfasta("rfastq", "InputTypes", "", "", "none", "none", "none","fasta-qfile",false,true,true); parameters.push_back(prfasta);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
// CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
// CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
- CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
- CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "",false,false); parameters.push_back(palign);
- CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pallfiles);
- CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
- CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
- CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
- CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
- CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "",false,false); parameters.push_back(pthreshold);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "","",false,false); parameters.push_back(palign);
+ CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles);
+ CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
+ CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+ CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
+ CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
+ CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string MakeContigsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MakeContigsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "contigs.fasta"; }
- else if (type == "qfile") { outputFileName = "contigs.qual"; }
- else if (type == "group") { outputFileName = "groups"; }
- else if (type == "mismatch") { outputFileName = "contigs.mismatch"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MakeContigsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],[tag],contigs.fasta"; }
+ else if (type == "qfile") { pattern = "[filename],[tag],contigs.qual"; }
+ else if (type == "group") { pattern = "[filename],[tag],groups"; }
+ else if (type == "mismatch") { pattern = "[filename],[tag],contigs.mismatch"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
MakeContigsCommand::MakeContigsCommand(){
temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
m->mothurConvert(temp, pdiffs);
- // temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
+ // temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
// m->mothurConvert(temp, ldiffs);
+ ldiffs = 0;
// temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
-// m->mothurConvert(temp, sdiffs);
+ // m->mothurConvert(temp, sdiffs);
+ sdiffs = 0;
- temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs; temp = toString(tempTotal); }
m->mothurConvert(temp, tdiffs);
if(tdiffs == 0){ tdiffs = bdiffs + pdiffs; } //+ ldiffs + sdiffs;
vector<vector<string> > qualFileNames;
createGroup = false;
string outputGroupFileName;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(ffastqfile));
+ variables["[tag]"] = "";
if(oligosfile != ""){
createGroup = getOligos(fastaFileNames, qualFileNames);
if (createGroup) {
- outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("group");
+ outputGroupFileName = getOutputFileName("group",variables);
outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
}
}
- string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "trim." + getOutputFileNameTag("fasta");
- string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "trim." + getOutputFileNameTag("qfile");
- string outScrapFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "scrap." + getOutputFileNameTag("fasta");
- string outScrapQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "scrap." + getOutputFileNameTag("qfile");
+ variables["[tag]"] = "trim";
+ string outFastaFile = getOutputFileName("fasta",variables);
+ string outQualFile = getOutputFileName("qfile",variables);
+ variables["[tag]"] = "scrap";
+ string outScrapFastaFile = getOutputFileName("fasta",variables);
+ string outScrapQualFile = getOutputFileName("qfile",variables);
- string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("mismatch");
+ variables["[tag]"] = "";
+ string outMisMatchFile = getOutputFileName("mismatch",variables);
outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
ofstream out;
string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first));
- thisGroupName += getOutputFileNameTag("group"); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
+ thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
m->openOutputFile(thisGroupName, out);
while (!in.eof()){
string getCommandName() { return "make.contigs"; }
string getCommandCategory() { return "Sequence Processing"; }
//commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Make.contigs"; }
string getDescription() { return "description"; }
//**********************************************************************************************************************
vector<string> MakeFastQCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqfile);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pqfile);
+ CommandParameter pformat("format", "Multiple", "sanger-illumina", "sanger", "", "", "","",false,false); parameters.push_back(pformat);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
string MakeFastQCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The make.fastq command read a fasta and quality file and creates a fastq file.\n";
- helpString += "The make.fastq command parameters are fasta and qfile, both are required.\n";
- helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
+ helpString += "The make.fastq command reads a fasta and quality file and creates a fastq file.\n";
+ helpString += "The make.fastq command parameters are fasta, qfile and format. fasta and qfile are required.\n";
+ helpString += "The format parameter is used to indicate whether your sequences are sanger or illumina, default=sanger.\n";
helpString += "The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n";
helpString += "Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
}
}
//**********************************************************************************************************************
-string MakeFastQCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MakeFastQCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fastq") { outputFileName = "fastq"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MakeFastQCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fastq") { pattern = "[filename],fastq"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeFastQCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
MakeFastQCommand::MakeFastQCommand(){
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(fastafile); }
+
+ format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "sanger"; }
+
+ if ((format != "sanger") && (format != "illumina") && (format != "solexa")) {
+ m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa and illumina, aborting." ); m->mothurOutEndLine();
+ abort=true;
+ }
+
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fastq");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFile = getOutputFileName("fastq",variables);
outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
ofstream out;
ifstream fFile;
m->openInputFile(fastafile, fFile);
-
+
while (!fFile.eof() && !qFile.eof()) {
if (m->control_pressed) { break; }
try {
string qualScores;
- int controlChar = int('@');
-
- for (int i = 0; i < qual.size(); i++) {
+ for (int i = 0; i < qual.size(); i++) {
+ int controlChar = int('!');
+ if (format == "illumina") { controlChar = int('@'); }
+
int temp = qual[i] + controlChar;
char qualChar = (char) temp;
vector<string> setParameters();
string getCommandName() { return "make.fastq"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
string getDescription() { return "creates a fastq file from a fasta and quality file"; }
private:
- string fastafile, qualfile, outputDir;
+ string fastafile, qualfile, outputDir, format;
bool abort;
vector<string> outputNames;
//**********************************************************************************************************************
vector<string> MakeGroupCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups);
+ CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string MakeGroupCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MakeGroupCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "group") { outputFileName = "groups"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MakeGroupCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "group") { pattern = "[filename],groups"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(){
}
//prevent giantic file name
- if (fastaFileNames.size() > 3) { filename = outputDir + "merge." + getOutputFileNameTag("group"); }
- else { filename += getOutputFileNameTag("group"); }
+ map<string, string> variables;
+ variables["[filename]"] = filename;
+ if (fastaFileNames.size() > 3) { variables["[filename]"] = outputDir + "merge"; }
+ filename = getOutputFileName("group",variables);
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
vector<string> setParameters();
string getCommandName() { return "make.group"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Make.group"; }
string getDescription() { return "creates a group file"; }
//**********************************************************************************************************************
vector<string> MantelCommand::setParameters(){
try {
- CommandParameter pphylip1("phylip1", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip1);
- CommandParameter pphylip2("phylip2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip2);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pphylip1("phylip1", "InputTypes", "", "", "none", "none", "none","mantel",false,true,true); parameters.push_back(pphylip1);
+ CommandParameter pphylip2("phylip2", "InputTypes", "", "", "none", "none", "none","mantel",false,true,true); parameters.push_back(pphylip2);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false); parameters.push_back(pmethod);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string MantelCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MantelCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "mantel") { outputFileName = "mantel"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MantelCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "mantel") { pattern = "[filename],mantel"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MantelCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
MantelCommand::MantelCommand(){
if (m->control_pressed) { return 0; }
- string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + getOutputFileNameTag("mantel");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile1));
+ string outputFile = getOutputFileName("mantel",variables);
outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile);
ofstream out;
vector<string> setParameters();
string getCommandName() { return "mantel"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Mantel"; }
string getDescription() { return "Mantel’s test for correlation between matrices"; }
//**********************************************************************************************************************
vector<string> MatrixOutputCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "",false,false); parameters.push_back(pmode);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","phylip",false,true,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "","",false,false); parameters.push_back(pmode);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string MatrixOutputCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MatrixOutputCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "phylip") { outputFileName = "dist"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MatrixOutputCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "phylip") { pattern = "[filename],[calc],[distance],[outputtag],dist-[filename],[calc],[distance],[outputtag],[tag2],dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
MatrixOutputCommand::MatrixOutputCommand(){
try {
vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size());
-
+
for (int thisIter = 0; thisIter < iters+1; thisIter++) {
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[tag2]"] = "";
vector<SharedRAbundVector*> thisItersLookup = thisLookup;
matrix[column][row] = dist;
}
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + "." + getOutputFileNameTag("phylip");
+ variables["[outputtag]"] = output;
+ variables["[calc]"] = matrixCalculators[i]->getName();
+ string distFileName = getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outDist;
stdmatrix[row][column] = stdDist;
stdmatrix[column][row] = stdDist;
}
-
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".ave." + getOutputFileNameTag("phylip");
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[outputtag]"] = output;
+ variables["[tag2]"] = "ave";
+ variables["[calc]"] = matrixCalculators[i]->getName();
+ string distFileName = getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outAve;
m->openOutputFile(distFileName, outAve);
outAve.close();
- distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".std." + getOutputFileNameTag("phylip");
+ variables["[tag2]"] = "std";
+ distFileName = outputDir + getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outSTD;
m->openOutputFile(distFileName, outSTD);
vector<string> setParameters();
string getCommandName() { return "dist.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
string getDescription() { return "generate a distance matrix that describes the dissimilarity among multiple groups"; }
//**********************************************************************************************************************
vector<string> MergeFileCommand::setParameters(){
try {
- CommandParameter pinput("input", "String", "", "", "", "", "",false,true); parameters.push_back(pinput);
- CommandParameter poutput("output", "String", "", "", "", "", "",false,true); parameters.push_back(poutput);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pinput("input", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pinput);
+ CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,true); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
vector<string> setParameters();
string getCommandName() { return "merge.files"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string) { return ""; }
string getHelpString();
+ string getOutputPattern(string){ return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Merge.files"; }
string getDescription() { return "appends files creating one file"; }
//**********************************************************************************************************************
vector<string> MergeGroupsCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
exit(1);
}
}
+
//**********************************************************************************************************************
-string MergeGroupsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MergeGroupsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "shared") { outputFileName = "merge" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "merge" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MergeGroupsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "shared") { pattern = "[filename],merge,[extension]"; }
+ else if (type == "group") { pattern = "[filename],merge,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeGroupsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
MergeGroupsCommand::MergeGroupsCommand(){
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("shared", sharedfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
+ string outputFileName = getOutputFileName("shared", variables);
outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
vector<string> setParameters();
string getCommandName() { return "merge.groups"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Merge.groups"; }
string getDescription() { return "reads shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file"; }
//**********************************************************************************************************************
vector<string> MetaStatsCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(pthreshold);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","metastats",false,true,true); parameters.push_back(pshared);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string MetaStatsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MetaStatsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "metastats") { outputFileName = "metastats"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MetaStatsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "metastats") { pattern = "[filename],[distance],[groups],metastats"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
MetaStatsCommand::MetaStatsCommand(){
try {
string setB = namesOfGroupCombos[c][1];
//get filename
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + "." + getOutputFileNameTag("metastats");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = thisLookUp[0]->getLabel();
+ variables["[group]"] = setA + "-" + setB;
+ string outputFileName = getOutputFileName("metastats",variables);
outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
//int nameLength = outputFileName.length();
//char * output = new char[nameLength];
vector<string> setParameters();
string getCommandName() { return "metastats"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "White JR, Nagarajan N, Pop M (2009). Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352. \nhttp://www.mothur.org/wiki/Metastats"; }
string getDescription() { return "detects differentially abundant features in clinical metagenomic samples"; }
//**********************************************************************************************************************
vector<string> MGClusterCommand::setParameters(){
try {
- CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
- CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
- CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "average", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
- CommandParameter pmin("min", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmin);
- CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmerge);
- CommandParameter phcluster("hcluster", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phcluster);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(pblast);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter plength("length", "Number", "", "5", "", "", "","",false,false); parameters.push_back(plength);
+ CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "","",false,false); parameters.push_back(ppenalty);
+ CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "average", "", "", "","",false,false); parameters.push_back(pmethod);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
+ CommandParameter pmin("min", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmin);
+ CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmerge);
+ CommandParameter phcluster("hcluster", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(phcluster);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string MGClusterCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MGClusterCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "list") { outputFileName = "list"; }
- else if (type == "rabund") { outputFileName = "rabund"; }
- else if (type == "sabund") { outputFileName = "sabund"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "MGClusterCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; }
+ else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; }
+ else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MGClusterCommand", "getOutputPattern");
+ exit(1);
+ }
}
-//**********************************************************************************************************************
+//*******************************************************************************************************************
MGClusterCommand::MGClusterCommand(){
try {
abort = true; calledHelp = true;
else if (method == "nearest") { tag = "nn"; }
else { tag = "an"; }
- string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
- string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
- string listFileName = fileroot+ tag + ".";
- if (countfile != "") { listFileName += "unique_"; }
- listFileName += getOutputFileNameTag("list");
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ if (countfile != "") { variables["[tag2]"] = "unique_list"; }
+ variables["[clustertag]"] = tag;
+ string sabundFileName = getOutputFileName("sabund", variables);
+ string rabundFileName = getOutputFileName("rabund", variables);
+ string listFileName = getOutputFileName("list", variables);
if (countfile == "") {
m->openOutputFile(sabundFileName, sabundFile);
vector<string> setParameters();
string getCommandName() { return "mgcluster"; }
string getCommandCategory() { return "Clustering"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
string getDescription() { return "cluster your sequences into OTUs using a blast file"; }
vector<string> NewCommand::setParameters(){
try {
//eaxamples of each type of parameter. more info on the types of parameters can be found in commandparameter.h
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pprocessors);
//files that have dependancies
- CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","outputType",false,false); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName","outputType",false,false); parameters.push_back(pname);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","outputType",false,false); parameters.push_back(pcolumn);
//files that do not have dependancies - fasta is set to not be required whereas shared is set to be required
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","outputType",false,false); parameters.push_back(pfasta);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","outputType",false,true); parameters.push_back(pshared);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
//choose more than one multiple options
- CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "","",true,false); parameters.push_back(pcalc);
//choose only one multiple options
- CommandParameter pdistance("distance", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(pdistance);
+ CommandParameter pdistance("distance", "Multiple", "column-lt-square", "column", "", "", "","",false,false); parameters.push_back(pdistance);
- CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming);
+ CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
//every command must have inputdir and outputdir. This allows mothur users to redirect input and output files.
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string NewCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string tag = "";
- map<string, vector<string> >::iterator it;
+string NewCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fileType1") { tag = "tag1"; }
- else if (type == "fileType2") { tag = "tag2"; }
- else if (type == "fileType3") { tag = "tag3"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return tag;
- }
- catch(exception& e) {
- m->errorOut(e, "NewCommand", "getOutputFileName");
- exit(1);
- }
+ if (type == "fileType1") { pattern = "[filename],tag1"; }
+ else if (type == "fileType2") { pattern = "[filename],tag2"; }
+ else if (type == "fileType3") { pattern = "[filename],tag3"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NewCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
NewCommand::NewCommand(){
vector<string> setParameters();
string getCommandName() { return "newCommandNameToBeSeenByUser"; }
string getCommandCategory() { return "commandCategory"; }
- string getOutputFileNameTag(string, string);
+
+ string getOutputPattern(string);
//commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
- string getHelpString();
+ string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/newCommandNameToBeSeenByUser"; }
string getDescription() { return "brief description"; }
//**********************************************************************************************************************
vector<string> NMDSCommand::setParameters(){
try {
- CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paxes);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter pmaxdim("maxdim", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmaxdim);
- CommandParameter pmindim("mindim", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmindim);
- CommandParameter piters("iters", "Number", "", "10", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pmaxiters("maxiters", "Number", "", "500", "", "", "",false,false); parameters.push_back(pmaxiters);
- CommandParameter pepsilon("epsilon", "Number", "", "0.000000000001", "", "", "",false,false); parameters.push_back(pepsilon);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(paxes);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","nmds-stress",false,true,true); parameters.push_back(pphylip);
+ CommandParameter pmaxdim("maxdim", "Number", "", "2", "", "", "","",false,false); parameters.push_back(pmaxdim);
+ CommandParameter pmindim("mindim", "Number", "", "2", "", "", "","",false,false); parameters.push_back(pmindim);
+ CommandParameter piters("iters", "Number", "", "10", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pmaxiters("maxiters", "Number", "", "500", "", "", "","",false,false); parameters.push_back(pmaxiters);
+ CommandParameter pepsilon("epsilon", "Number", "", "0.000000000001", "", "", "","",false,false); parameters.push_back(pepsilon);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string NMDSCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string NMDSCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "nmds") { outputFileName = "nmds.axes"; }
- else if (type == "stress") { outputFileName = "nmds.stress"; }
- else if (type == "iters") { outputFileName = "nmds.iters"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "NMDSCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "nmds") { pattern = "[filename],nmds.axes"; }
+ else if (type == "stress") { pattern = "[filename],nmds.stress"; }
+ else if (type == "iters") { pattern = "[filename],nmds.iters"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
NMDSCommand::NMDSCommand(){
try {
vector< vector<double> > axes;
if (axesfile != "") { axes = readAxes(names); }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("iters");
- string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("stress");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+ string outputFileName = getOutputFileName("iters",variables);
+ string stressFileName = getOutputFileName("stress",variables);
outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
out.close(); out2.close();
//output best config
- string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("nmds");
+ string BestFileName = getOutputFileName("nmds",variables);
outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");
vector<string> setParameters();
string getCommandName() { return "nmds"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Borg, Groenen (1997). Non-metric multidimensional scaling function using the majorization algorithm, in Modern Multidimensional Scaling. Ed. T.F. Cox and M.A.A. Cox. Chapman and Hall. \nhttp://www.mothur.org/wiki/Nmds"; }
string getDescription() { return "nmds"; }
string getCommandName() { return "NoCommand"; }
string getCommandCategory() { return "Hidden"; }
string getHelpString() { return "No Command"; }
- string getOutputFileNameTag(string, string) { return ""; }
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "no citation"; }
string getDescription() { return "no description"; }
//**********************************************************************************************************************
vector<string> NormalizeSharedCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pmethod("method", "Multiple", "totalgroup-zscore", "totalgroup", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter pnorm("norm", "Number", "", "0", "", "", "",false,false); parameters.push_back(pnorm);
- CommandParameter pmakerelabund("makerelabund", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pmakerelabund);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","shared",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","shared",false,false,true); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pmethod("method", "Multiple", "totalgroup-zscore", "totalgroup", "", "", "","",false,false,true); parameters.push_back(pmethod);
+ CommandParameter pnorm("norm", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnorm);
+ CommandParameter pmakerelabund("makerelabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pmakerelabund);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
exit(1);
}
}
-
//**********************************************************************************************************************
-string NormalizeSharedCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string NormalizeSharedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "shared") { outputFileName = "norm.shared"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "NormalizeSharedCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "shared") { pattern = "[filename],[distance],norm.shared"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NormalizeSharedCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
NormalizeSharedCommand::NormalizeSharedCommand(){
if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + "." + getOutputFileNameTag("shared");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ variables["[distance]"] = thisLookUp[0]->getLabel();
+ string outputFileName = getOutputFileName("shared",variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
//save mothurOut's binLabels to restore for next label
vector<string> saveBinLabels = m->currentBinLabels;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + "." + getOutputFileNameTag("shared");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ variables["[distance]"] = thisLookUp[0]->getLabel();
+ string outputFileName = getOutputFileName("shared",variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
vector<string> setParameters();
string getCommandName() { return "normalize.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
string getDescription() { return "normalize samples in a shared or relabund file"; }
//**********************************************************************************************************************
vector<string> OTUAssociationCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata);
- CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false); parameters.push_back(prelabund);
+ CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pmetadata);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false,true); parameters.push_back(pmethod);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string OTUAssociationCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string OTUAssociationCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "otucorr") { outputFileName = "otu.corr"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "OTUAssociationCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "otucorr") { pattern = "[filename],[distance],[tag],otu.corr"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OTUAssociationCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
OTUAssociationCommand::OTUAssociationCommand(){
//**********************************************************************************************************************
int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
try {
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + "." + getOutputFileNameTag("otucorr");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[distance]"] = lookup[0]->getLabel();
+ variables["[tag]"] = method;
+ string outputFileName = getOutputFileName("otucorr",variables);
outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
ofstream out;
int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
try {
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + "." + getOutputFileNameTag("otucorr");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[distance]"] = lookup[0]->getLabel();
+ variables["[tag]"] = method;
+ string outputFileName = getOutputFileName("otucorr",variables);
outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
ofstream out;
vector<string> setParameters();
string getCommandName() { return "otu.association"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Otu.association"; }
string getDescription() { return "calculate the correlation coefficient for the otus in a shared/relabund file"; }
//**********************************************************************************************************************
vector<string> OtuHierarchyCommand::setParameters(){
try {
- CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otuheirarchy",false,true,true); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string OtuHierarchyCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string OtuHierarchyCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "otuheirarchy") { outputFileName = "otu.hierarchy"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "OtuHierarchyCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "otuheirarchy") { pattern = "[filename],[distance1],[tag],[distance2],otu.hierarchy"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
OtuHierarchyCommand::OtuHierarchyCommand(){
}
ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + "." + getOutputFileNameTag("otuheirarchy");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+ variables["[distance1]"] = lists[0].getLabel();
+ variables["[tag]"] = "-";
+ variables["[distance2]"] = lists[1].getLabel();
+ string outputFileName = getOutputFileName("otuheirarchy",variables);
m->openOutputFile(outputFileName, out);
//go through each bin in "big" otu and output the bins in "little" otu which created it
vector<string> setParameters();
string getCommandName() { return "otu.hierarchy"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; }
string getDescription() { return "relates OTUs at different distances"; }
//**********************************************************************************************************************
vector<string> PairwiseSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
- CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
- CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
- CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
- CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
- CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
- CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
- CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","phylip-column",false,true,true); parameters.push_back(pfasta);
+ CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false); parameters.push_back(palign);
+ CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
+ CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+ CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
+ CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "","phylip-column",false,false,true); parameters.push_back(poutput);
+ CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "","",false,false); parameters.push_back(pcalc);
+ CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcountends);
+ CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcompress);
+ CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string PairwiseSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PairwiseSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "phylip") { outputFileName = "dist"; }
- else if (type == "column") { outputFileName = "dist"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "phylip") { pattern = "[filename],[outputtag],dist"; }
+ else if (type == "column") { pattern = "[filename],dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PairwiseSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
PairwiseSeqsCommand::PairwiseSeqsCommand(){
int numSeqs = alignDB.getNumSeqs();
int startTime = time(NULL);
string outputFile = "";
-
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
if (output == "lt") { //does the user want lower triangle phylip formatted file
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip." + getOutputFileNameTag("phylip");
+ variables["[outputtag]"] = "phylip";
+ outputFile = getOutputFileName("phylip", variables);
m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
}else if (output == "column") { //user wants column format
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("column");
+ outputFile = getOutputFileName("column", variables);
outputTypes["column"].push_back(outputFile);
m->mothurRemove(outputFile);
}else { //assume square
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square." + getOutputFileNameTag("phylip");
+ variables["[outputtag]"] = "square";
+ outputFile = getOutputFileName("phylip", variables);
m->mothurRemove(outputFile);
outputTypes["phylip"].push_back(outputFile);
}
vector<string> setParameters();
string getCommandName() { return "pairwise.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
string getDescription() { return "calculates pairwise distances from an unaligned fasta file"; }
//**********************************************************************************************************************
vector<string> ParseFastaQCommand::setParameters(){
try {
- CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfastq);
- CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
- CommandParameter pqual("qfile", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqual);
- CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa", "sanger", "", "", "",false,false); parameters.push_back(pformat);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pfastq);
+ CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pqual("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqual);
+ CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa", "sanger", "", "", "","",false,false,true); parameters.push_back(pformat);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ParseFastaQCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ParseFastaQCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "fasta"; }
- else if (type == "qfile") { outputFileName = "qual"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ParseFastaQCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],fasta"; }
+ else if (type == "qfile") { pattern = "[filename],qual"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseFastaQCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//open Output Files
- string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("fasta");
- string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("qfile");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+ string fastaFile = getOutputFileName("fasta",variables);
+ string qualFile = getOutputFileName("qfile",variables);
ofstream outFasta, outQual;
if (fasta) { m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile); }
temp -= 64; //char '@'
}else if (format == "solexa") {
temp = int(convertTable[temp]); //convert to sanger
- temp -= 33; //char '!'
+ temp -= int('!'); //char '!'
}else {
- temp -= 33; //char '!'
+ temp -= int('!'); //char '!'
}
qualScores.push_back(temp);
}
vector<string> setParameters();
string getCommandName() { return "parse.fastq"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
string getDescription() { return "reads a fastq file and creates a fasta and quality file"; }
//**********************************************************************************************************************
vector<string> ParseListCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(plist);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pgroup);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ParseListCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ParseListCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "list") { outputFileName = "list"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ParseListCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "list") { pattern = "[filename],[group],list"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParseListCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
ParseListCommand::ParseListCommand(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//set fileroot
- string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
//fill filehandles with neccessary ofstreams
int i;
temp = new ofstream;
filehandles[gGroups[i]] = temp;
- string filename = fileroot + gGroups[i] + "." + getOutputFileNameTag("list");
+ variables["[group]"] = gGroups[i];
+ string filename = getOutputFileName("list",variables);
outputNames.push_back(filename); outputTypes["list"].push_back(filename);
m->openOutputFile(filename, *temp);
}
vector<string> setParameters();
string getCommandName() { return "parse.list"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
string getDescription() { return "parses a list file by group"; }
//**********************************************************************************************************************
vector<string> ParsimonyCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter prandom("random", "String", "", "", "", "", "",false,false); parameters.push_back(prandom);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","parsimony-psummary",false,true,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter prandom("random", "String", "", "", "", "", "","",false,false); parameters.push_back(prandom);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ParsimonyCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ParsimonyCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "parsimony") { outputFileName = "parsimony"; }
- else if (type == "psummary") { outputFileName = "psummary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ParsimonyCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "parsimony") { pattern = "[filename],parsimony"; }
+ else if (type == "psummary") { pattern = "[filename],psummary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ParsimonyCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
ParsimonyCommand::ParsimonyCommand(){
try {
delete reader;
if(outputDir == "") { outputDir += m->hasPath(treefile); }
- output = new ColumnFile(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony"), itersString);
- outputNames.push_back(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony"));
- outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("parsimony"));
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getSimpleName(treefile) + ".";
+
+ output = new ColumnFile(getOutputFileName("parsimony",variables), itersString);
+ outputNames.push_back(getOutputFileName("parsimony",variables));
+ outputTypes["parsimony"].push_back(getOutputFileName("parsimony",variables));
- sumFile = outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("psummary");
+ sumFile = getOutputFileName("psummary",variables);
m->openOutputFile(sumFile, outSum);
outputNames.push_back(sumFile);
outputTypes["psummary"].push_back(sumFile);
//set tmaps namesOfSeqs
for (int j = 0; j < num; j++) {
- groupMap[toString(count)] = i;
+ groupMap[toString(count)] = toString(i);
nameMap.insert(toString(count));
count++;
}
getline(cin, s);
m->Treenames = ct->getNamesOfSeqs();
+ m->runParse = false;
}
catch(exception& e) {
m->errorOut(e, "ParsimonyCommand", "getUserInput");
vector<string> setParameters();
string getCommandName() { return "parsimony"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Slatkin M, Maddison WP (1989). A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-13. \nSlatkin M, Maddison WP (1990). Detecting isolation by distance using phylogenies of genes. Genetics 126: 249-60. \nMartin AP (2002). Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-82. \nSchloss PD, Handelsman J (2006). Introducing TreeClimber, a test to compare microbial community structure. Appl Environ Microbiol 72: 2379-84.\nhttp://www.mothur.org/wiki/Parsimony"; }
string getDescription() { return "generic test that describes whether two or more communities have the same structure"; }
//**********************************************************************************************************************
vector<string> PCACommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string PCACommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PCACommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "pca") { outputFileName = "pca.axes"; }
- else if (type == "loadings") { outputFileName = "pca.loadings"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "PCACommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "pca") { pattern = "[filename],[distance],pca.axes"; }
+ else if (type == "loadings") { pattern = "[filename],[distance],pca.loadings"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
if (m->control_pressed) { return 0; }
string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
- string outputFileName = fbase + lookupFloat[0]->getLabel();
- output(outputFileName, m->getGroups(), X, d);
+ //string outputFileName = fbase + lookupFloat[0]->getLabel();
+ output(fbase, lookupFloat[0]->getLabel(), m->getGroups(), X, d);
if (metric) {
}
/*********************************************************************************************************************************/
-void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
+void PCACommand::output(string fbase, string label, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
try {
int numEigenValues = d.size();
}
ofstream pcaData;
- m->openOutputFile((fnameRoot+"."+getOutputFileNameTag("pca")), pcaData);
+ map<string, string> variables;
+ variables["[filename]"] = fbase;
+ variables["[distance]"] = label;
+ string pcaFileName = getOutputFileName("pca",variables);
+ m->openOutputFile(pcaFileName, pcaData);
pcaData.setf(ios::fixed, ios::floatfield);
pcaData.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"."+getOutputFileNameTag("pca"));
- outputTypes["pca"].push_back(fnameRoot+"."+getOutputFileNameTag("pca"));
+ outputNames.push_back(pcaFileName);
+ outputTypes["pca"].push_back(pcaFileName);
ofstream pcaLoadings;
- m->openOutputFile((fnameRoot+"."+getOutputFileNameTag("loadings")), pcaLoadings);
+ string loadingsFilename = getOutputFileName("loadings",variables);
+ m->openOutputFile(loadingsFilename, pcaLoadings);
pcaLoadings.setf(ios::fixed, ios::floatfield);
pcaLoadings.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"."+getOutputFileNameTag("loadings"));
- outputTypes["loadings"].push_back(fnameRoot+"."+getOutputFileNameTag("loadings"));
+ outputNames.push_back(loadingsFilename);
+ outputTypes["loadings"].push_back(loadingsFilename);
pcaLoadings << "axis\tloading\n";
for(int i=0;i<numEigenValues;i++){
vector<string> setParameters();
string getCommandName() { return "pca"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Pca"; }
string getDescription() { return "pca"; }
//vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);
int process(vector<SharedRAbundFloatVector*>&);
- void output(string, vector<string>, vector<vector<double> >&, vector<double>);
+ void output(string, string, vector<string>, vector<vector<double> >&, vector<double>);
};
//**********************************************************************************************************************
vector<string> PCOACommand::setParameters(){
try {
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
- CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","pcoa-loadings",false,true,true); parameters.push_back(pphylip);
+ CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
exit(1);
}
}
-
//**********************************************************************************************************************
-string PCOACommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PCOACommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "pcoa") { outputFileName = "pcoa.axes"; }
- else if (type == "loadings") { outputFileName = "pcoa.loadings"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "pcoa") { pattern = "[filename],pcoa.axes"; }
+ else if (type == "loadings") { pattern = "[filename],pcoa.loadings"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCOACommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
PCOACommand::PCOACommand(){
try {
}
ofstream pcaData;
- string pcoaDataFile = fnameRoot+getOutputFileNameTag("pcoa");
+ map<string, string> variables;
+ variables["[filename]"] = fnameRoot;
+ string pcoaDataFile = getOutputFileName("pcoa",variables);
m->openOutputFile(pcoaDataFile, pcaData);
pcaData.setf(ios::fixed, ios::floatfield);
pcaData.setf(ios::showpoint);
outputTypes["pcoa"].push_back(pcoaDataFile);
ofstream pcaLoadings;
- string loadingsFile = fnameRoot+getOutputFileNameTag("loadings");
+ string loadingsFile = getOutputFileName("loadings",variables);
m->openOutputFile(loadingsFile, pcaLoadings);
pcaLoadings.setf(ios::fixed, ios::floatfield);
pcaLoadings.setf(ios::showpoint);
vector<string> setParameters();
string getCommandName() { return "pcoa"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Pcoa"; }
string getDescription() { return "pcoa"; }
vector<string> setParameters();
string getCommandName() { return "pcr.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Pcr.seqs"; }
string getDescription() { return "pcr.seqs"; }
vector<string> PhyloDiversityCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter prarefy("rarefy", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prarefy);
- CommandParameter psummary("summary", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(psummary);
- CommandParameter pcollect("collect", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcollect);
- CommandParameter pscale("scale", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pscale);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","phylodiv",false,true,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter prarefy("rarefy", "Boolean", "", "F", "", "", "","rarefy",false,false); parameters.push_back(prarefy);
+ CommandParameter psummary("summary", "Boolean", "", "T", "", "", "","summary",false,false); parameters.push_back(psummary);
+ CommandParameter pcollect("collect", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcollect);
+ CommandParameter pscale("scale", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pscale);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string PhyloDiversityCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PhyloDiversityCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "phylodiv") { outputFileName = "phylodiv"; }
- else if (type == "rarefy") { outputFileName = "phylodiv.rarefaction"; }
- else if (type == "summary") { outputFileName = "phylodiv.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "PhyloDiversityCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "phylodiv") { pattern = "[filename],[tag],phylodiv"; }
+ else if (type == "rarefy") { pattern = "[filename],[tag],phylodiv.rarefaction"; }
+ else if (type == "summary") { pattern = "[filename],[tag],phylodiv.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloDiversityCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
if (m->control_pressed) { delete ct; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
ofstream outSum, outRare, outCollect;
- string outSumFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + "." + getOutputFileNameTag("summary");
- string outRareFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + "." + getOutputFileNameTag("rarefy");
- string outCollectFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + "." + getOutputFileNameTag("phylodiv");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ variables["[tag]"] = toString(i+1);
+ string outSumFile = getOutputFileName("summary",variables);
+ string outRareFile = getOutputFileName("rarefy",variables);
+ string outCollectFile = getOutputFileName("phylodiv",variables);
if (summary) { m->openOutputFile(outSumFile, outSum); outputNames.push_back(outSumFile); outputTypes["summary"].push_back(outSumFile); }
if (rarefy) { m->openOutputFile(outRareFile, outRare); outputNames.push_back(outRareFile); outputTypes["rarefy"].push_back(outRareFile); }
randomLeaf.push_back(j);
}
}
+
+ /* float sum = 0;
+ vector<float> sums; sums.resize(m->getGroups().size(), 0);
+ vector<float> sumsAboveRoot; sumsAboveRoot.resize(m->getGroups().size(), 0);
+ for (int j = 0; j < trees[i]->getNumNodes(); j++) {
+ if (trees[i]->tree[j].getBranchLength() < 0) { cout << j << '\t' << trees[i]->tree[j].getName() << '\t' << trees[i]->tree[j].getBranchLength() << endl; }
+
+ sum += abs(trees[i]->tree[j].getBranchLength());
+ for (int k = 0; k < m->getGroups().size(); k++) {
+ map<string, int>::iterator itGroup = trees[i]->tree[j].pcount.find(m->getGroups()[k]);
+ if (itGroup != trees[i]->tree[j].pcount.end()) { //this branch belongs to a group we care about
+ if (j < rootForGroup[m->getGroups()[k]]) {
+ sums[k] += abs(trees[i]->tree[j].getBranchLength());
+ }else {
+ sumsAboveRoot[k] += abs(trees[i]->tree[j].getBranchLength());
+ }
+ }
+ }
+ }
+ cout << sum << endl; //exit(1);
+
+ for (int k = 0; k < m->getGroups().size(); k++) {
+ cout << m->getGroups()[k] << "root node = " << rootForGroup[m->getGroups()[k]] << "sum below root = " << sums[k] << "sum above root = " << sumsAboveRoot[k] << endl;
+ }
+ exit(1); */
numLeafNodes = randomLeaf.size(); //reset the number of leaf nodes you are using
else { score = div[mGroups[j]][numSampled] / (float)numIters; }
out << setprecision(4) << score << endl;
+ cout << mGroups[j] << '\t' << numSampled << '\t'<< setprecision(4) << score << endl;
}
out.close();
//you are a leaf
if(t->tree[index].getBranchLength() != -1){
for (int k = 0; k < groups.size(); k++) {
- sums[k] += abs(t->tree[index].getBranchLength());
+ sums[k] += abs(t->tree[index].getBranchLength());
}
}
for (int j = 0; j < groups.size(); j++) {
- if (done[groups[j]] == false) { //we haven't found the root for this group yet
-
- done[groups[j]] = true;
- roots[groups[j]] = i; //set root to self to start
+ if (done[groups[j]] == false) { //we haven't found the root for this group yet, initialize it
+ done[groups[j]] = true;
+ roots[groups[j]] = i; //set root to self to start
+ }
//while you aren't at root
while(t->tree[index].getParent() != -1){
if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
if ((LpcountSize != 0) && (RpcountSize != 0)) { //possible root
- roots[groups[j]] = index;
+ if (index > roots[groups[j]]) { roots[groups[j]] = index; }
}else { ;}
index = t->tree[index].getParent();
}
- }
+ //}
}
}
+
+
return roots;
}
vector<string> setParameters();
string getCommandName() { return "phylo.diversity"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Faith DP (1994). Phylogenetic pattern and the quantification of organismal biodiversity. Philos Trans R Soc Lond B Biol Sci 345: 45-58. \nhttp://www.mothur.org/wiki/Phylo.diversity"; }
string getDescription() { return "phylo.diversity"; }
//**********************************************************************************************************************
vector<string> PhylotypeCommand::setParameters(){
try {
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","list-rabund-sabund",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string PhylotypeCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PhylotypeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "list") { outputFileName = "list"; }
- else if (type == "rabund") { outputFileName = "rabund"; }
- else if (type == "sabund") { outputFileName = "sabund"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "PhylotypeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "list") { pattern = "[filename],[tag],list"; }
+ else if (type == "rabund") { pattern = "[filename],[tag],rabund"; }
+ else if (type == "sabund") { pattern = "[filename],[tag],sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
PhylotypeCommand::PhylotypeCommand(){
if (m->control_pressed) { delete tree; return 0; }
string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
-
- ofstream outList;
- string outputListFile = fileroot + "tx." + getOutputFileNameTag("list");
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = "tx";
+ ofstream outList;
+ string outputListFile = getOutputFileName("list",variables);
m->openOutputFile(outputListFile, outList);
ofstream outSabund;
- string outputSabundFile = fileroot + "tx." + getOutputFileNameTag("sabund");
+ string outputSabundFile = getOutputFileName("sabund",variables);
m->openOutputFile(outputSabundFile, outSabund);
ofstream outRabund;
- string outputRabundFile = fileroot + "tx." + getOutputFileNameTag("rabund");
+ string outputRabundFile = getOutputFileName("rabund",variables);
m->openOutputFile(outputRabundFile, outRabund);
outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
vector<string> setParameters();
string getCommandName() { return "phylotype"; }
string getCommandCategory() { return "Clustering"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
string getDescription() { return "cluster your sequences into OTUs based on their classifications"; }
//**********************************************************************************************************************
vector<string> PipelineCommand::setParameters(){
try {
- CommandParameter psff("sff", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(psff);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(poligos);
- CommandParameter palign("align", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(palign);
- CommandParameter pchimera("chimera", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(pchimera);
- CommandParameter pclassify("classify", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(pclassify);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(ptaxonomy);
- CommandParameter ppipeline("pipeline", "InputTypes", "", "", "none", "oneRequired", "none",false,false); parameters.push_back(ppipeline);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter psff("sff", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(psff);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(poligos);
+ CommandParameter palign("align", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(palign);
+ CommandParameter pchimera("chimera", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(pchimera);
+ CommandParameter pclassify("classify", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(pclassify);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(ptaxonomy);
+ CommandParameter ppipeline("pipeline", "InputTypes", "", "", "none", "oneRequired", "none","",false,false,true); parameters.push_back(ppipeline);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
vector<string> setParameters();
string getCommandName() { return "pipeline.pds"; }
string getCommandCategory() { return "Hidden"; }
- string getOutputFileNameTag(string, string) { return ""; }
string getHelpString();
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nhttp://www.mothur.org/wiki/Pipeline.pds"; }
string getDescription() { return "pat's pipeline"; }
//**********************************************************************************************************************
vector<string> PcrSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter poligos("oligos", "InputTypes", "", "", "ecolioligos", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptax);
- CommandParameter pecoli("ecoli", "InputTypes", "", "", "ecolioligos", "none", "none",false,false); parameters.push_back(pecoli);
- CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
- CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
- CommandParameter pnomatch("nomatch", "Multiple", "reject-keep", "reject", "", "", "",false,false); parameters.push_back(pnomatch);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepprimer);
- CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pkeepdots);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "ecolioligos", "none", "none","",false,false,true); parameters.push_back(poligos);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false,true); parameters.push_back(ptax);
+ CommandParameter pecoli("ecoli", "InputTypes", "", "", "ecolioligos", "none", "none","",false,false); parameters.push_back(pecoli);
+ CommandParameter pstart("start", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pstart);
+ CommandParameter pend("end", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pend);
+ CommandParameter pnomatch("nomatch", "Multiple", "reject-keep", "reject", "", "", "","",false,false); parameters.push_back(pnomatch);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkeepprimer);
+ CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pkeepdots);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
exit(1);
}
}
-
//**********************************************************************************************************************
-string PcrSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PcrSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "pcr.fasta"; }
- else if (type == "taxonomy") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "accnos") { outputFileName = "bad.accnos"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "PcrSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],pcr,[extension]-[filename],[tag],pcr,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "name") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "accnos") { pattern = "[filename],bad.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PcrSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string trimSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string trimSeqFile = getOutputFileName("fasta",variables);
outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
-
- string badSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "scrap." + getOutputFileNameTag("fasta");
+ variables["[tag]"] = "scrap";
+ string badSeqFile = getOutputFileName("fasta",variables);
length = 0;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileName = getOutputFileName("accnos",variables);
outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
m->openInputFile(countfile, in);
set<string>::iterator it;
- string goodCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string goodCountFile = getOutputFileName("count", variables);
+
outputNames.push_back(goodCountFile); outputTypes["count"].push_back(goodCountFile);
ofstream goodCountOut; m->openOutputFile(goodCountFile, goodCountOut);
//**********************************************************************************************************************
vector<string> PreClusterCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pdiffs);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string PreClusterCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PreClusterCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "precluster" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "precluster.names"; }
- else if (type == "count") { outputFileName = "precluster.count_table"; }
- else if (type == "map") { outputFileName = "precluster.map"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "PreClusterCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],precluster,[extension]"; }
+ else if (type == "name") { pattern = "[filename],precluster.names"; }
+ else if (type == "count") { pattern = "[filename],precluster.count_table"; }
+ else if (type == "map") { pattern = "[filename],precluster.map"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
PreClusterCommand::PreClusterCommand(){
int start = time(NULL);
string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
- string newFastaFile = fileroot + getOutputFileNameTag("fasta", fastafile);
- string newNamesFile = fileroot + getOutputFileNameTag("name");
- string newCountFile = fileroot + getOutputFileNameTag("count");
- string newMapFile = fileroot + getOutputFileNameTag("map"); //add group name if by group
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ string newNamesFile = getOutputFileName("name",variables);
+ string newCountFile = getOutputFileName("count",variables);
+ string newMapFile = getOutputFileName("map",variables); //add group name if by group
+ variables["[extension]"] = m->getExtension(fastafile);
+ string newFastaFile = getOutputFileName("fasta", variables);
outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
if (countfile == "") { outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile); }
else { outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile); }
vector<string> setParameters();
string getCommandName() { return "pre.cluster"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nhttp://www.mothur.org/wiki/Pre.cluster"; }
string getDescription() { return "implements a pseudo-single linkage algorithm with the goal of removing sequences that are likely due to pyrosequencing errors"; }
string getCommandName() { return "quit"; }
string getCommandCategory() { return "Hidden"; }
string getHelpString() { return "The quit command will terminate mothur and should be in the following format: quit() or quit. \n"; }
- string getOutputFileNameTag(string, string) { return ""; }
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "no citation"; }
string getDescription() { return "quit"; }
//**********************************************************************************************************************
vector<string> RareFactCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap", "sobs", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(psabund);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap", "sobs", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string RareFactCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string RareFactCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+ if (type == "rarefaction") { pattern = "[filename],rarefaction"; }
+ else if (type == "r_chao") { pattern = "[filename],r_chao"; }
+ else if (type == "r_ace") { pattern = "[filename],r_ace"; }
+ else if (type == "r_jack") { pattern = "[filename],r_jack"; }
+ else if (type == "r_shannon") { pattern = "[filename],r_shannon"; }
+ else if (type == "r_shannoneven") { pattern = "[filename],r_shannoneven"; }
+ else if (type == "r_smithwilson") { pattern = "[filename],r_smithwilson"; }
+ else if (type == "r_npshannon") { pattern = "[filename],r_npshannon"; }
+ else if (type == "r_simpson") { pattern = "[filename],r_simpson"; }
+ else if (type == "r_simpsoneven") { pattern = "[filename],r_simpsoneven"; }
+ else if (type == "r_invsimpson") { pattern = "[filename],r_invsimpson"; }
+ else if (type == "r_bootstrap") { pattern = "[filename],r_bootstrap"; }
+ else if (type == "r_coverage") { pattern = "[filename],r_coverage"; }
+ else if (type == "r_nseqs") { pattern = "[filename],r_nseqs"; }
+ else if (type == "r_heip") { pattern = "[filename],r_heip"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "rarefaction") { outputFileName = "rarefaction"; }
- else if (type == "r_chao") { outputFileName = "r_chao"; }
- else if (type == "r_ace") { outputFileName = "r_ace"; }
- else if (type == "r_jack") { outputFileName = "r_jack"; }
- else if (type == "r_shannon") { outputFileName = "r_shannon"; }
- else if (type == "r_shannoneven") { outputFileName = "r_shannoneven"; }
- else if (type == "r_smithwilson") { outputFileName = "r_smithwilson"; }
- else if (type == "r_npshannon") { outputFileName = "r_npshannon"; }
- else if (type == "r_simpson") { outputFileName = "r_simpson"; }
- else if (type == "r_simpsoneven") { outputFileName = "r_simpsoneven"; }
- else if (type == "r_invsimpson") { outputFileName = "r_invsimpson"; }
- else if (type == "r_bootstrap") { outputFileName = "r_bootstrap"; }
- else if (type == "r_coverage") { outputFileName = "r_coverage"; }
- else if (type == "r_nseqs") { outputFileName = "r_nseqs"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "RareFactCommand", "getOutputFileNameTag");
- exit(1);
- }
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
RareFactCommand::RareFactCommand(){
try {
int i;
ValidCalculators validCalculator;
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
for (i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
- rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("rarefaction"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("rarefaction")); outputTypes["rarefaction"].push_back(fileNameRoot+getOutputFileNameTag("rarefaction"));
+ rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(getOutputFileName("rarefaction",variables))));
+ outputNames.push_back(getOutputFileName("rarefaction",variables)); outputTypes["rarefaction"].push_back(getOutputFileName("rarefaction",variables));
}else if (Estimators[i] == "chao") {
- rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_chao"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_chao")); outputTypes["r_chao"].push_back(fileNameRoot+getOutputFileNameTag("r_chao"));
+ rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("r_chao",variables))));
+ outputNames.push_back(getOutputFileName("r_chao",variables)); outputTypes["r_chao"].push_back(getOutputFileName("r_chao",variables));
}else if (Estimators[i] == "ace") {
if(abund < 5)
abund = 10;
- rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_ace"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_ace")); outputTypes["r_ace"].push_back(fileNameRoot+getOutputFileNameTag("r_ace"));
+ rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("r_ace",variables))));
+ outputNames.push_back(getOutputFileName("r_ace",variables)); outputTypes["r_ace"].push_back(getOutputFileName("r_ace",variables));
}else if (Estimators[i] == "jack") {
- rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_jack"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_jack")); outputTypes["r_jack"].push_back(fileNameRoot+getOutputFileNameTag("r_jack"));
+ rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("r_jack",variables))));
+ outputNames.push_back(getOutputFileName("r_jack",variables)); outputTypes["r_jack"].push_back(getOutputFileName("r_jack",variables));
}else if (Estimators[i] == "shannon") {
- rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_shannon"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_shannon")); outputTypes["r_shannon"].push_back(fileNameRoot+getOutputFileNameTag("r_shannon"));
+ rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("r_shannon",variables))));
+ outputNames.push_back(getOutputFileName("r_shannon",variables)); outputTypes["r_shannon"].push_back(getOutputFileName("r_shannon",variables));
}else if (Estimators[i] == "shannoneven") {
- rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_shannoneven"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_shannoneven")); outputTypes["r_shannoneven"].push_back(fileNameRoot+getOutputFileNameTag("r_shannoneven"));
+ rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(getOutputFileName("r_shannoneven",variables))));
+ outputNames.push_back(getOutputFileName("r_shannoneven",variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannoneven",variables));
}else if (Estimators[i] == "heip") {
- rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_heip"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_heip")); outputTypes["r_heip"].push_back(fileNameRoot+getOutputFileNameTag("r_heip"));
+ rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(getOutputFileName("r_heip",variables))));
+ outputNames.push_back(getOutputFileName("r_heip",variables)); outputTypes["r_heip"].push_back(getOutputFileName("r_heip",variables));
}else if (Estimators[i] == "smithwilson") {
- rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_smithwilson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_smithwilson")); outputTypes["r_smithwilson"].push_back(fileNameRoot+getOutputFileNameTag("r_smithwilson"));
+ rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(getOutputFileName("r_smithwilson",variables))));
+ outputNames.push_back(getOutputFileName("r_smithwilson",variables)); outputTypes["r_smithwilson"].push_back(getOutputFileName("r_smithwilson",variables));
}else if (Estimators[i] == "npshannon") {
- rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_npshannon"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_npshannon")); outputTypes["r_npshannon"].push_back(fileNameRoot+getOutputFileNameTag("r_npshannon"));
+ rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(getOutputFileName("r_npshannon",variables))));
+ outputNames.push_back(getOutputFileName("r_npshannon",variables)); outputTypes["r_npshannon"].push_back(getOutputFileName("r_npshannon",variables));
}else if (Estimators[i] == "simpson") {
- rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_simpson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_simpson")); outputTypes["r_simpson"].push_back(fileNameRoot+getOutputFileNameTag("r_simpson"));
+ rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("r_simpson",variables))));
+ outputNames.push_back(getOutputFileName("r_simpson",variables)); outputTypes["r_simpson"].push_back(getOutputFileName("r_simpson",variables));
}else if (Estimators[i] == "simpsoneven") {
- rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_simpsoneven"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_simpsoneven")); outputTypes["r_simpsoneven"].push_back(fileNameRoot+getOutputFileNameTag("r_simpsoneven"));
+ rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(getOutputFileName("r_simpsoneven",variables))));
+ outputNames.push_back(getOutputFileName("r_simpsoneven",variables)); outputTypes["r_simpsoneven"].push_back(getOutputFileName("r_simpsoneven",variables));
}else if (Estimators[i] == "invsimpson") {
- rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_invsimpson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_invsimpson")); outputTypes["r_invsimpson"].push_back(fileNameRoot+getOutputFileNameTag("r_invsimpson"));
+ rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("r_invsimpson",variables))));
+ outputNames.push_back(getOutputFileName("r_invsimpson",variables)); outputTypes["r_invsimpson"].push_back(getOutputFileName("r_invsimpson",variables));
}else if (Estimators[i] == "bootstrap") {
- rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_bootstrap"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_bootstrap")); outputTypes["r_bootstrap"].push_back(fileNameRoot+getOutputFileNameTag("r_bootstrap"));
+ rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(getOutputFileName("r_bootstrap",variables))));
+ outputNames.push_back(getOutputFileName("r_bootstrap",variables)); outputTypes["r_bootstrap"].push_back(getOutputFileName("r_bootstrap",variables));
}else if (Estimators[i] == "coverage") {
- rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_coverage"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_coverage")); outputTypes["r_coverage"].push_back(fileNameRoot+getOutputFileNameTag("r_coverage"));
+ rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(getOutputFileName("r_coverage",variables))));
+ outputNames.push_back(getOutputFileName("r_coverage",variables)); outputTypes["r_coverage"].push_back(getOutputFileName("r_coverage",variables));
}else if (Estimators[i] == "nseqs") {
- rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("r_nseqs"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("r_nseqs")); outputTypes["r_nseqs"].push_back(fileNameRoot+getOutputFileNameTag("r_nseqs"));
+ rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(getOutputFileName("r_nseqs",variables))));
+ outputNames.push_back(getOutputFileName("r_nseqs",variables)); outputTypes["r_nseqs"].push_back(getOutputFileName("r_nseqs",variables));
}
if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; }
}
vector<string> setParameters();
string getCommandName() { return "rarefaction.single"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.single"; }
string getDescription() { return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
//**********************************************************************************************************************
vector<string> RareFactSharedCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pcalc("calc", "Multiple", "sharednseqs-sharedobserved", "sharedobserved", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter psubsampleiters("subsampleiters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(psubsampleiters);
- CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
- CommandParameter pjumble("jumble", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pjumble);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
- CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pshared);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pcalc("calc", "Multiple", "sharednseqs-sharedobserved", "sharedobserved", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter psubsampleiters("subsampleiters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(psubsampleiters);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter pjumble("jumble", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pjumble);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+ CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string RareFactSharedCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string RareFactSharedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "sharedrarefaction") { outputFileName = "shared.rarefaction"; }
- else if (type == "sharedr_nseqs") { outputFileName = "shared.r_nseqs"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "RareFactSharedCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "sharedrarefaction") { pattern = "[filename],shared.rarefaction"; }
+ else if (type == "sharedr_nseqs") { pattern = "[filename],shared.r_nseqs"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
RareFactSharedCommand::RareFactSharedCommand(){
if (subset.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
}
/******************************************************/
-
+
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sharedobserved") {
- rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+getOutputFileNameTag("sharedrarefaction"), "")));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharedrarefaction")); outputTypes["sharedrarefaction"].push_back(fileNameRoot+getOutputFileNameTag("sharedrarefaction"));
+ rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(getOutputFileName("sharedrarefaction",variables), "")));
+ outputNames.push_back(getOutputFileName("sharedrarefaction",variables)); outputTypes["sharedrarefaction"].push_back(getOutputFileName("sharedrarefaction",variables));
}else if (Estimators[i] == "sharednseqs") {
- rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+getOutputFileNameTag("sharedr_nseqs"), "")));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sharedr_nseqs")); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+getOutputFileNameTag("sharedr_nseqs"));
+ rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(getOutputFileName("sharedr_nseqs",variables), "")));
+ outputNames.push_back(getOutputFileName("sharedr_nseqs",variables)); outputTypes["sharedr_nseqs"].push_back(getOutputFileName("sharedr_nseqs",variables));
}
}
file2Group[outputNames.size()-1] = thisSet;
string thisfileNameRoot = fileNameRoot + toString(thisIter);
+ map<string, string> variables;
+ variables["[filename]"] = thisfileNameRoot;
+
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sharedobserved") {
- rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(thisfileNameRoot+getOutputFileNameTag("sharedrarefaction"), "")));
- filenames["sharedrarefaction"].push_back(thisfileNameRoot+getOutputFileNameTag("sharedrarefaction"));
+ rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(getOutputFileName("sharedrarefaction",variables), "")));
+ filenames["sharedrarefaction"].push_back(getOutputFileName("sharedrarefaction",variables));
}else if (Estimators[i] == "sharednseqs") {
- rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(thisfileNameRoot+getOutputFileNameTag("sharedr_nseqs"), "")));
- filenames["sharedr_nseqs"].push_back(thisfileNameRoot+getOutputFileNameTag("sharedr_nseqs"));
+ rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(getOutputFileName("sharedr_nseqs",variables), "")));
+ filenames["sharedr_nseqs"].push_back(getOutputFileName("sharedr_nseqs",variables));
}
}
}
if (!m->control_pressed) {
//process results
- string outputFile = fileNameRoot + "ave-std." + thisLookup[0]->getLabel() + "." + getOutputFileNameTag(it->first);
+ map<string, string> variables; variables["[filename]"] = fileNameRoot + "ave-std." + thisLookup[0]->getLabel() + ".";
+
+ string outputFile = getOutputFileName(it->first,variables);
ofstream out;
m->openOutputFile(outputFile, out);
outputNames.push_back(outputFile); outputTypes[it->first].push_back(outputFile);
vector<string> setParameters();
string getCommandName() { return "rarefaction.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.shared"; }
string getDescription() { return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
//set group info
vector<string> group = ct->getGroups(name);
-
+ //cout << name << endl;
//find index in tree of name
int n1 = T->getIndex(name);
//**********************************************************************************************************************
vector<string> RemoveGroupsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(pfasta);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup); CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pdesign);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT","fasta",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT","design",false,false); parameters.push_back(pdesign);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT","list",false,false,true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string RemoveGroupsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string RemoveGroupsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "pick.count_table"; }
- else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "shared") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "design") { outputFileName = "pick" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveGroupsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "name") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "shared") { pattern = "[filename],[tag],pick,[extension]"; }
+ else if (type == "design") { pattern = "[filename],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
RemoveGroupsCommand::RemoveGroupsCommand(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
//that way we can take advantage of the reads in inputdata and sharedRabundVector
InputData* tempInput = new InputData(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
+
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
//save m->Groups
vector<string> allGroupsNames = m->getAllGroups();
while(lookup[0] != NULL) {
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("shared", sharedfile);
+ variables["[tag]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("shared", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputFileName = getOutputFileName("count", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(designfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + getOutputFileNameTag("design", designfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(designfile));
+ variables["[extension]"] = m->getExtension(designfile);
+ string outputFileName = getOutputFileName("design", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
vector<string> setParameters();
string getCommandName() { return "remove.groups"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
string getDescription() { return "removes sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
//**********************************************************************************************************************
vector<string> RemoveLineageCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
- CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon);
- CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
+ CommandParameter ptaxon("taxon", "String", "", "", "", "", "","",false,true,true); parameters.push_back(ptaxon);
+ CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string RemoveLineageCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string RemoveLineageCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "pick.count_table"; }
- else if (type == "alignreport") { outputFileName = "pick.align.report"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveLineageCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "name") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "alignreport") { pattern = "[filename],pick.align.report"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveLineageCommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
RemoveLineageCommand::RemoveLineageCommand(){
try {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputFileName = getOutputFileName("count", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(alignfile));
+ variables["[extension]"] = m->getExtension(alignfile);
+ string outputFileName = getOutputFileName("alignreport", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
vector<string> setParameters();
string getCommandName() { return "remove.lineage"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
//**********************************************************************************************************************
vector<string> RemoveOtuLabelsCommand::setParameters(){
try {
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
- CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pconstaxonomy);
- CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(potucorr);
- CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pcorraxes);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
+ CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none","constaxonomy",false,false); parameters.push_back(pconstaxonomy);
+ CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none","otucorr",false,false); parameters.push_back(potucorr);
+ CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none","corraxes",false,false); parameters.push_back(pcorraxes);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string RemoveOtuLabelsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string RemoveOtuLabelsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "constaxonomy") { outputFileName = "pick.taxonomy"; }
- else if (type == "otucorr") { outputFileName = "pick.corr"; }
- else if (type == "corraxes") { outputFileName = "pick.axes"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtuLabelsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "constaxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "otucorr") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "corraxes") { pattern = "[filename],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtuLabelsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["contaxonomy"] = tempOutNames;
+ outputTypes["constaxonomy"] = tempOutNames;
outputTypes["otucorr"] = tempOutNames;
outputTypes["corraxes"] = tempOutNames;
}
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomyfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + getOutputFileNameTag("constaxonomy");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
+ variables["[extension]"] = m->getExtension(constaxonomyfile);
+ string outputFileName = getOutputFileName("constaxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(otucorrfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + getOutputFileNameTag("otucorr");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
+ variables["[extension]"] = m->getExtension(otucorrfile);
+ string outputFileName = getOutputFileName("otucorr", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(corraxesfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + getOutputFileNameTag("corraxes");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
+ variables["[extension]"] = m->getExtension(corraxesfile);
+ string outputFileName = getOutputFileName("corraxes", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
vector<string> setParameters();
string getCommandName() { return "remove.otulabels"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.otulabels"; }
string getDescription() { return "Can be used with output from classify.otu, otu.association, or corr.axes to remove specific otus."; }
//**********************************************************************************************************************
vector<string> RemoveOtusCommand::setParameters(){
try {
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(plist);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string RemoveOtusCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string RemoveOtusCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtusCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "group") { pattern = "[filename],[tag],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],[tag],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveOtusCommand", "getOutputPattern");
+ exit(1);
+ }
}
///**********************************************************************************************************************
RemoveOtusCommand::RemoveOtusCommand(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("list", listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[tag]"] = label;
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
string GroupOutputDir = outputDir;
if (outputDir == "") { GroupOutputDir += m->hasPath(groupfile); }
- string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + label + "." + getOutputFileNameTag("group", groupfile);
+ variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputGroupFileName = getOutputFileName("group", variables);
ofstream outGroup;
m->openOutputFile(outputGroupFileName, outGroup);
vector<string> setParameters();
string getCommandName() { return "remove.otus"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.otus"; }
string getDescription() { return "outputs a new list file containing the otus NOT containing sequences from the groups specified"; }
//**********************************************************************************************************************
vector<string> RemoveRareCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
- CommandParameter pcount("count", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pnseqs("nseqs", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnseqs);
- CommandParameter pbygroup("bygroup", "Boolean", "", "f", "", "", "",false,true); parameters.push_back(pbygroup);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "atleast", "none","list",false,false,true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "none", "atleast", "none","rabund",false,false,true); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "none", "atleast", "none","sabund",false,false,true); parameters.push_back(psabund);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "atleast", "none","shared",false,false,true); parameters.push_back(pshared);
+ CommandParameter pcount("count", "InputTypes", "", "", "CountGroup", "none", "none","count",false,false); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pnseqs("nseqs", "Number", "", "0", "", "", "","",false,true,true); parameters.push_back(pnseqs);
+ CommandParameter pbygroup("bygroup", "Boolean", "", "f", "", "", "","",false,false); parameters.push_back(pbygroup);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string RemoveRareCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string RemoveRareCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "rabund") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "sabund") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "shared") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveRareCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "rabund") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "sabund") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "shared") { pattern = "[filename],[tag],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveRareCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
RemoveRareCommand::RemoveRareCommand(){
try {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
- string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
- string outputCountFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputGroupFileName = getOutputFileName("group", variables);
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputCountFileName = getOutputFileName("count", variables);
ofstream out, outGroup;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + getOutputFileNameTag("sabund", sabundfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile));
+ variables["[extension]"] = m->getExtension(sabundfile);
+ string outputFileName = getOutputFileName("sabund", variables);
outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + getOutputFileNameTag("rabund", rabundfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile));
+ variables["[extension]"] = m->getExtension(rabundfile);
+ string outputFileName = getOutputFileName("rabund", variables);
outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("shared", sharedfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
+ string outputFileName = getOutputFileName("shared", variables);
outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
vector<string> setParameters();
string getCommandName() { return "remove.rare"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
string getDescription() { return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
//**********************************************************************************************************************
vector<string> RemoveSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
- CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
- CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
+ CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string RemoveSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string RemoveSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "qfile") { outputFileName = "pick" + m->getExtension(inputName); }
- else if (type == "alignreport") { outputFileName = "pick.align.report"; }
- else if (type == "count") { outputFileName = "pick.count_table"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "name") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "qfile") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "alignreport") { pattern = "[filename],pick.align.report"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
RemoveSeqsCommand::RemoveSeqsCommand(){
try {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(qualfile));
+ variables["[extension]"] = m->getExtension(qualfile);
+ string outputFileName = getOutputFileName("qfile", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputFileName = getOutputFileName("count", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(alignfile));
+ string outputFileName = getOutputFileName("alignreport", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
vector<string> setParameters();
string getCommandName() { return "remove.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
//**********************************************************************************************************************
vector<string> ReverseSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pqfile);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none","fasta",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none","qfile",false,false,true); parameters.push_back(pqfile);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ReverseSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ReverseSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "rc" + m->getExtension(inputName); }
- else if (type == "qfile") { outputFileName = "rc" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ReverseSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],rc,[extension]"; }
+ else if (type == "qfile") { pattern = "[filename],rc,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ReverseSeqsCommand::ReverseSeqsCommand(){
ofstream outFASTA;
string tempOutputDir = outputDir;
if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it
- fastaReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName)) + getOutputFileNameTag("fasta", fastaFileName);
+ map<string, string> variables;
+ variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName));
+ variables["[extension]"] = m->getExtension(fastaFileName);
+ fastaReverseFileName = getOutputFileName("fasta", variables);
m->openOutputFile(fastaReverseFileName, outFASTA);
while(!inFASTA.eof()){
ofstream outQual;
string tempOutputDir = outputDir;
if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it
- string qualReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName)) + getOutputFileNameTag("qfile", qualFileName);
+ map<string, string> variables;
+ variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName));
+ variables["[extension]"] = m->getExtension(qualFileName);
+ string qualReverseFileName = getOutputFileName("qfile", variables);
m->openOutputFile(qualReverseFileName, outQual);
while(!inQual.eof()){
vector<string> setParameters();
string getCommandName() { return "reverse.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Reverse.seqs"; }
string getDescription() { return "outputs a fasta file containing the reverse-complements"; }
//**********************************************************************************************************************
vector<string> ScreenSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
- CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(palignreport);
- CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptax);
- CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
- CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
- CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
- CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxhomop);
- CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pminlength);
- CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxlength);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "",false,false); parameters.push_back(pcriteria);
- CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "",true,false); parameters.push_back(poptimize);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","qfile",false,false); parameters.push_back(pqfile);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none","alignreport",false,false); parameters.push_back(palignreport);
+ CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false); parameters.push_back(ptax);
+ CommandParameter pstart("start", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pstart);
+ CommandParameter pend("end", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pend);
+ CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxambig);
+ CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxhomop);
+ CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminlength);
+ CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxlength);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pcriteria);
+ CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "","",true,false); parameters.push_back(poptimize);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ScreenSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ScreenSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "good" + m->getExtension(inputName); }
- else if (type == "taxonomy") { outputFileName = "good" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "good" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "good" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "good" + m->getExtension(inputName); }
- else if (type == "accnos") { outputFileName = "bad.accnos"; }
- else if (type == "qfile") { outputFileName = "good" + m->getExtension(inputName); }
- else if (type == "alignreport") { outputFileName = "good.align.report"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ScreenSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],good,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],good,[extension]"; }
+ else if (type == "name") { pattern = "[filename],good,[extension]"; }
+ else if (type == "group") { pattern = "[filename],good,[extension]"; }
+ else if (type == "count") { pattern = "[filename],good,[extension]"; }
+ else if (type == "accnos") { pattern = "[filename],bad.accnos"; }
+ else if (type == "qfile") { pattern = "[filename],good,[extension]"; }
+ else if (type == "alignreport") { pattern = "[filename],good.align.report"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
ScreenSeqsCommand::ScreenSeqsCommand(){
try {
}
#endif
}
-
- string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
- string badAccnosFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string badAccnosFile = getOutputFileName("accnos",variables);
+ variables["[extension]"] = m->getExtension(fastafile);
+ string goodSeqFile = getOutputFileName("fasta", variables);
+
int numFastaSeqs = 0;
set<string> badSeqNames;
set<string> badSeqGroups;
string seqName, seqList, group;
set<string>::iterator it;
-
- string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string goodNameFile = getOutputFileName("name", variables);
outputNames.push_back(goodNameFile); outputTypes["name"].push_back(goodNameFile);
ofstream goodNameOut; m->openOutputFile(goodNameFile, goodNameOut);
ifstream inputGroups;
m->openInputFile(groupfile, inputGroups);
-
- string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string goodGroupFile = getOutputFileName("group", variables);
+
outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
m->openInputFile(groupfile, inputGroups);
string seqName, group;
set<string>::iterator it;
-
- string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string goodGroupFile = getOutputFileName("group", variables);
outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
ifstream in;
m->openInputFile(countfile, in);
set<string>::iterator it;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string goodCountFile = getOutputFileName("count", variables);
- string goodCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
outputNames.push_back(goodCountFile); outputTypes["count"].push_back(goodCountFile);
ofstream goodCountOut; m->openOutputFile(goodCountFile, goodCountOut);
string seqName, group;
set<string>::iterator it;
- string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + getOutputFileNameTag("alignreport");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(alignreport));
+ string goodAlignReportFile = getOutputFileName("alignreport", variables);
+
outputNames.push_back(goodAlignReportFile); outputTypes["alignreport"].push_back(goodAlignReportFile);
ofstream goodAlignReportOut; m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
m->openInputFile(taxonomy, input);
string seqName, tax;
set<string>::iterator it;
-
- string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + getOutputFileNameTag("taxonomy", taxonomy);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(taxonomy));
+ variables["[extension]"] = m->getExtension(taxonomy);
+ string goodTaxFile = getOutputFileName("taxonomy", variables);
+
outputNames.push_back(goodTaxFile); outputTypes["taxonomy"].push_back(goodTaxFile);
ofstream goodTaxOut; m->openOutputFile(goodTaxFile, goodTaxOut);
ifstream in;
m->openInputFile(qualfile, in);
set<string>::iterator it;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qualfile));
+ variables["[extension]"] = m->getExtension(qualfile);
+ string goodQualFile = getOutputFileName("qfile", variables);
- string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
outputNames.push_back(goodQualFile); outputTypes["qfile"].push_back(goodQualFile);
ofstream goodQual; m->openOutputFile(goodQualFile, goodQual);
vector<string> setParameters();
string getCommandName() { return "screen.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
string getDescription() { return "enables you to keep sequences that fulfill certain user defined criteria"; }
//**********************************************************************************************************************
vector<string> AlignCheckCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pmap);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","aligncheck",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pmap);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pcount);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string AlignCheckCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string AlignCheckCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "aligncheck") { outputFileName = "align.check"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCheckCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "aligncheck") { pattern = "[filename],align.check"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
AlignCheckCommand::AlignCheckCommand(){
m->openInputFile(fastafile, in);
ofstream out;
- string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("aligncheck");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outfile = getOutputFileName("aligncheck",variables);
m->openOutputFile(outfile, out);
vector<string> setParameters();
string getCommandName() { return "align.check"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
string getDescription() { return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
//**********************************************************************************************************************
vector<string> SensSpecCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pcolumn);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","sensspec",false,true,true); parameters.push_back(plist);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pphylip);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pcolumn);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SensSpecCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SensSpecCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "sensspec") { outputFileName = "sensspec"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SensSpecCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "sensspec") { pattern = "[filename],sensspec"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
SensSpecCommand::SensSpecCommand(){
else { allLines = 1; }
}
- sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + getOutputFileNameTag("sensspec");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+ sensSpecFileName = getOutputFileName("sensspec",variables);
}
}
catch(exception& e) {
vector<string> setParameters();
string getCommandName() { return "sens.spec"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nhttp://www.mothur.org/wiki/Sens.spec"; }
string getDescription() { return "sens.spec"; }
//**********************************************************************************************************************
vector<string> SeqErrorCommand::setParameters(){
try {
- CommandParameter pquery("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pquery);
- CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(preference);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(pqfile);
- CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(preport);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
- CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pquery("fasta", "InputTypes", "", "", "none", "none", "none","errorType",false,true,true); parameters.push_back(pquery);
+ CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(preference);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(pqfile);
+ CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(preport);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
+ CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pignorechimeras);
+ CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SeqErrorCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SeqErrorCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "errorsummary") { outputFileName = "error.summary"; }
- else if (type == "errorseq") { outputFileName = "error.seq"; }
- else if (type == "errorquality") { outputFileName = "error.quality"; }
- else if (type == "errorqualforward") { outputFileName = "error.qual.forward"; }
- else if (type == "errorqualreverse") { outputFileName = "error.qual.reverse"; }
- else if (type == "errorforward") { outputFileName = "error.seq.forward"; }
- else if (type == "errorreverse") { outputFileName = "error.seq.reverse"; }
- else if (type == "errorcount") { outputFileName = "error.count"; }
- else if (type == "errormatrix") { outputFileName = "error.matrix"; }
- else if (type == "errorchimera") { outputFileName = "error.chimera"; }
- else if (type == "errorref-query") { outputFileName = "error.ref-query"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqErrorCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "errorsummary") { pattern = "[filename],error.summary"; }
+ else if (type == "errorseq") { pattern = "[filename],error.seq"; }
+ else if (type == "errorquality") { pattern = "[filename],error.quality"; }
+ else if (type == "errorqualforward") { pattern = "[filename],error.qual.forward"; }
+ else if (type == "errorqualreverse") { pattern = "[filename],error.qual.reverse"; }
+ else if (type == "errorforward") { pattern = "[filename],error.seq.forward"; }
+ else if (type == "errorreverse") { pattern = "[filename],error.seq.reverse"; }
+ else if (type == "errorcount") { pattern = "[filename],error.count"; }
+ else if (type == "errormatrix") { pattern = "[filename],error.matrix"; }
+ else if (type == "errorchimera") { pattern = "[filename],error.chimera"; }
+ else if (type == "errorref-query") { pattern = "[filename],error.ref-query"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqErrorCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
SeqErrorCommand::SeqErrorCommand(){
totalMatches = 0;
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
- string errorSummaryFileName = fileNameRoot + getOutputFileNameTag("errorsummary");
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
+ string errorSummaryFileName = getOutputFileName("errorsummary",variables);
outputNames.push_back(errorSummaryFileName); outputTypes["errorsummary"].push_back(errorSummaryFileName);
- string errorSeqFileName = fileNameRoot + getOutputFileNameTag("errorseq");
+ string errorSeqFileName = getOutputFileName("errorseq",variables);
outputNames.push_back(errorSeqFileName); outputTypes["errorseq"].push_back(errorSeqFileName);
- string errorChimeraFileName = fileNameRoot + getOutputFileNameTag("errorchimera");
+ string errorChimeraFileName = getOutputFileName("errorchimera",variables);
outputNames.push_back(errorChimeraFileName); outputTypes["errorchimera"].push_back(errorChimeraFileName);
getReferences(); //read in reference sequences - make sure there's no ambiguous bases
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
- string errorCountFileName = fileNameRoot + getOutputFileNameTag("errorcount");
+ string errorCountFileName = getOutputFileName("errorcount",variables);
ofstream errorCountFile;
m->openOutputFile(errorCountFileName, errorCountFile);
outputNames.push_back(errorCountFileName); outputTypes["errorcount"].push_back(errorCountFileName);
printSubMatrix();
- string megAlignmentFileName = fileNameRoot + getOutputFileNameTag("errorref-query");
+ string megAlignmentFileName = getOutputFileName("errorref-query",variables);
ofstream megAlignmentFile;
m->openOutputFile(megAlignmentFileName, megAlignmentFile);
outputNames.push_back(megAlignmentFileName); outputTypes["errorref-query"].push_back(megAlignmentFileName);
void SeqErrorCommand::printSubMatrix(){
try {
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
- string subMatrixFileName = fileNameRoot + getOutputFileNameTag("errormatrix");
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
+ string subMatrixFileName = getOutputFileName("errormatrix",variables);
ofstream subMatrixFile;
m->openOutputFile(subMatrixFileName, subMatrixFile);
outputNames.push_back(subMatrixFileName); outputTypes["errormatrix"].push_back(subMatrixFileName);
void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map<char, vector<int> > errorReverse){
try{
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
- string errorForwardFileName = fileNameRoot + getOutputFileNameTag("errorforward");
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
+ string errorForwardFileName = getOutputFileName("errorforward",variables);
ofstream errorForwardFile;
m->openOutputFile(errorForwardFileName, errorForwardFile);
outputNames.push_back(errorForwardFileName); outputTypes["errorforward"].push_back(errorForwardFileName);
}
errorForwardFile.close();
- string errorReverseFileName = fileNameRoot + getOutputFileNameTag("errorreverse");
+ string errorReverseFileName = getOutputFileName("errorreverse",variables);
ofstream errorReverseFile;
m->openOutputFile(errorReverseFileName, errorReverseFile);
outputNames.push_back(errorReverseFileName); outputTypes["errorreverse"].push_back(errorReverseFileName);
void SeqErrorCommand::printErrorQuality(map<char, vector<int> > qScoreErrorMap){
try{
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
- string errorQualityFileName = fileNameRoot + getOutputFileNameTag("errorquality");
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
+ string errorQualityFileName = getOutputFileName("errorquality",variables);
ofstream errorQualityFile;
m->openOutputFile(errorQualityFileName, errorQualityFile);
outputNames.push_back(errorQualityFileName); outputTypes["errorquality"].push_back(errorQualityFileName);
}
}
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
- string qualityForwardFileName = fileNameRoot + getOutputFileNameTag("errorqualforward");
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
+ string qualityForwardFileName = getOutputFileName("errorqualforward",variables);
ofstream qualityForwardFile;
m->openOutputFile(qualityForwardFileName, qualityForwardFile);
outputNames.push_back(qualityForwardFileName); outputTypes["errorqualforward"].push_back(qualityForwardFileName);
qualityForwardFile.close();
- string qualityReverseFileName = fileNameRoot + getOutputFileNameTag("errorqualreverse");
+ string qualityReverseFileName = getOutputFileName("errorqualreverse",variables);
ofstream qualityReverseFile;
m->openOutputFile(qualityReverseFileName, qualityReverseFile);
outputNames.push_back(qualityReverseFileName); outputTypes["errorqualreverse"].push_back(qualityReverseFileName);
vector<string> setParameters();
string getCommandName() { return "seq.error"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nhttp://www.mothur.org/wiki/Seq.error"; }
string getDescription() { return "seq.error"; }
//**********************************************************************************************************************
vector<string> SeqSummaryCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SeqSummaryCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SeqSummaryCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "summary") { outputFileName = "summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqSummaryCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
//set current fasta to fastafile
m->setFastaFile(fastafile);
- string summaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string summaryFile = getOutputFileName("summary",variables);
int numSeqs = 0;
vector<string> setParameters();
string getCommandName() { return "summary.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
string getDescription() { return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
vector<string> SetCurrentCommand::setParameters(){
try {
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pflow);
- CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pbiom);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcolumn);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptaxonomy);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
- CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(porder);
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptree);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
- CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
- CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prelabund);
- CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pflow);
+ CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pbiom);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pphylip);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcolumn);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pqfile);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psabund);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign);
+ CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(porder);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptree);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pshared);
+ CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pordergroup);
+ CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcount);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prelabund);
+ CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psff);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
+ CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
vector<string> setParameters();
string getCommandName() { return "set.current"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string) { return ""; }
+
string getHelpString();
+ string getOutputPattern(string){ return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
string getDescription() { return "set current files for mothur"; }
//**********************************************************************************************************************
vector<string> SetDirectoryCommand::setParameters(){
try {
- CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault);
- CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdebug);
- CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput);
- CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "","",false,false); parameters.push_back(ptempdefault);
+ CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdebug);
+ CommandParameter pinput("input", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pinput);
+ CommandParameter poutput("output", "String", "", "", "", "", "","",false,false,true); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
vector<string> setParameters();
string getCommandName() { return "set.dir"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string) { return ""; }
+
string getHelpString();
+ string getOutputPattern(string){ return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Set.dir"; }
string getDescription() { return "set input, output and default directories"; }
//**********************************************************************************************************************
vector<string> SetLogFileCommand::setParameters(){
try {
- CommandParameter pappend("append", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pappend);
- CommandParameter pname("name", "String", "", "", "", "", "",false,true); parameters.push_back(pname);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pappend("append", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pappend);
+ CommandParameter pname("name", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pname);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
vector<string> setParameters();
string getCommandName() { return "set.logfile"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string) { return ""; }
+
string getHelpString();
+ string getOutputPattern(string){ return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Set.logfile"; }
string getDescription() { return "set logfile name"; }
//**********************************************************************************************************************
vector<string> SffInfoCommand::setParameters(){
try {
- CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "",false,false); parameters.push_back(psfftxt);
- CommandParameter pflow("flow", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pflow);
- CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
- CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
- CommandParameter pqfile("name", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqfile);
- CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
- CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
- CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
- CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
- CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(psff);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "","",false,false); parameters.push_back(psfftxt);
+ CommandParameter pflow("flow", "Boolean", "", "T", "", "", "","flow",false,false); parameters.push_back(pflow);
+ CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptrim);
+ CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pqfile("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqfile);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pbdiffs);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
exit(1);
}
}
+
//**********************************************************************************************************************
-string SffInfoCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SffInfoCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "fasta"; }
- else if (type == "flow") { outputFileName = "flow"; }
- else if (type == "sfftxt") { outputFileName = "sff.txt"; }
- else if (type == "sff") { outputFileName = "sff"; }
- else if (type == "qfile") { outputFileName = "qual"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],fasta-[filename],[tag],fasta"; }
+ else if (type == "flow") { pattern = "[filename],flow"; }
+ else if (type == "sfftxt") { pattern = "[filename],sff.txt"; }
+ else if (type == "sff") { pattern = "[filename],[group],sff"; }
+ else if (type == "qfile") { pattern = "[filename],qual-[filename],[tag],qual"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
-
//**********************************************************************************************************************
SffInfoCommand::SffInfoCommand(){
try {
string rootName = outputDir + m->getRootName(m->getSimpleName(input));
if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
- string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("sfftxt");
- string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("flow");
- if (trim) {
- outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("fasta");
- outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("qfile");
- }else{
- outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw." + getOutputFileNameTag("fasta");
- outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw." + getOutputFileNameTag("qfile");
- }
-
+ map<string, string> variables;
+ variables["[filename]"] = rootName;
+ string sfftxtFileName = getOutputFileName("sfftxt",variables);
+ string outFlowFileName = getOutputFileName("flow",variables);
+ if (!trim) { variables["[tag]"] = "raw"; }
+ outFastaFileName = getOutputFileName("fasta",variables);
+ outQualFileName = getOutputFileName("qfile",variables);
+
if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint); outputNames.push_back(sfftxtFileName); outputTypes["sfftxt"].push_back(sfftxtFileName); }
if (fasta) { m->openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
if (qual) { m->openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
fileRoot = m->getRootName(fileRoot);
}
- string outFlowFileName = outputDir + fileRoot + getOutputFileNameTag("flow");
- if (trim) {
- outFastaFileName = outputDir + fileRoot + getOutputFileNameTag("fasta");
- outQualFileName = outputDir + fileRoot + getOutputFileNameTag("qfile");
- }else{
- outFastaFileName = outputDir + fileRoot + "raw." + getOutputFileNameTag("fasta");
- outQualFileName = outputDir + fileRoot + "raw." + getOutputFileNameTag("qfile");
- }
+ map<string, string> variables;
+ variables["[filename]"] = fileRoot;
+ string sfftxtFileName = getOutputFileName("sfftxt",variables);
+ string outFlowFileName = getOutputFileName("flow",variables);
+ if (!trim) { variables["[tag]"] = "raw"; }
+ outFastaFileName = getOutputFileName("fasta",variables);
+ outQualFileName = getOutputFileName("qfile",variables);
if (fasta) { m->openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
if (qual) { m->openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
}
ofstream temp;
- string thisFilename = outputDir + m->getRootName(m->getSimpleName(currentFileName)) + comboGroupName + "." + getOutputFileNameTag("sff");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
+ variables["[group]"] = comboGroupName;
+ string thisFilename = getOutputFileName("sff",variables);
if (uniqueNames.count(thisFilename) == 0) {
outputNames.push_back(thisFilename);
outputTypes["sff"].push_back(thisFilename);
numFPrimers = primers.size();
numLinkers = linker.size();
numSpacers = spacer.size();
- noMatchFile = outputDir + m->getRootName(m->getSimpleName(currentFileName)) + "scrap." + getOutputFileNameTag("sff");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
+ variables["[group]"] = "scrap";
+ noMatchFile = getOutputFileName("sff",variables);
m->mothurRemove(noMatchFile);
bool allBlank = true;
vector<string> setParameters();
string getCommandName() { return "sffinfo"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
string getDescription() { return "extract sequences reads from a .sff file"; }
//**********************************************************************************************************************
vector<string> SffMultipleCommand::setParameters(){
try {
- CommandParameter pfile("file", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfile);
+ CommandParameter pfile("file", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfile);
//sffinfo
- CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
+ CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptrim);
//trim.flows
- CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
- CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
- CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
- CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
- CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
- CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
- CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
- CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
- CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
- CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
- CommandParameter porder("order", "String", "", "TACG", "", "", "",false,false); parameters.push_back(porder);
+ CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "","",false,false); parameters.push_back(pmaxhomop);
+ CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pmaxflows);
+ CommandParameter pminflows("minflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pminflows);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
+ CommandParameter psignal("signal", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(psignal);
+ CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "","",false,false); parameters.push_back(pnoise);
+ CommandParameter porder("order", "String", "", "TACG", "", "", "","",false,false); parameters.push_back(porder);
//shhh.flows
- CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plookup);
- CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter);
- CommandParameter plarge("large", "Number", "", "-1", "", "", "",false,false); parameters.push_back(plarge);
- CommandParameter psigma("sigma", "Number", "", "60", "", "", "",false,false); parameters.push_back(psigma);
- CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "",false,false); parameters.push_back(pmindelta);
+ CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(plookup);
+ CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(pmaxiter);
+ CommandParameter plarge("large", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(plarge);
+ CommandParameter psigma("sigma", "Number", "", "60", "", "", "","",false,false); parameters.push_back(psigma);
+ CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "","",false,false); parameters.push_back(pmindelta);
//trim.seqs parameters
- CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
- CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
- CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
- CommandParameter pminlength("minlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pminlength);
- CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
- CommandParameter pkeepforward("keepforward", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepforward);
- CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "",false,false); parameters.push_back(pkeepfirst);
- CommandParameter premovelast("removelast", "Number", "", "0", "", "", "",false,false); parameters.push_back(premovelast);
+ CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(pallfiles);
+ CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(pflip);
+ CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxambig);
+ CommandParameter pminlength("minlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pminlength);
+ CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxlength);
+ CommandParameter pkeepforward("keepforward", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkeepforward);
+ CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pkeepfirst);
+ CommandParameter premovelast("removelast", "Number", "", "0", "", "", "","",false,false); parameters.push_back(premovelast);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SffMultipleCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SffMultipleCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "fasta"; }
- else if (type == "name") { outputFileName = "names"; }
- else if (type == "group") { outputFileName = "groups"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SffMultipleCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],fasta"; }
+ else if (type == "name") { pattern = "[filename],names"; }
+ else if (type == "group") { pattern = "[filename],groups"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffMultipleCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
-
//**********************************************************************************************************************
SffMultipleCommand::SffMultipleCommand(){
try {
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
- outputTypes["flow"] = tempOutNames;
- outputTypes["qfile"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "SffMultipleCommand", "SffMultipleCommand");
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- outputTypes["flow"] = tempOutNames;
- outputTypes["qfile"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputDir = m->hasPath(filename);
string fileroot = outputDir + m->getRootName(m->getSimpleName(filename));
- string fasta = fileroot + getOutputFileNameTag("fasta");
- string name = fileroot + getOutputFileNameTag("name");
- string group = fileroot + getOutputFileNameTag("group");
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ string fasta = fileroot + getOutputFileName("fasta",variables);
+ string name = fileroot + getOutputFileName("name",variables);
+ string group = fileroot + getOutputFileName("group",variables);
if (m->control_pressed) { return 0; }
vector<string> setParameters();
string getCommandName() { return "sff.multiple"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sff.multiple"; }
string getDescription() { return "run multiple sff files through, sffinfo, trim.flow, shhh.flows and trim.seqs combining the results"; }
//**********************************************************************************************************************
vector<string> SharedCommand::setParameters(){
try {
- CommandParameter pbiom("biom", "InputTypes", "", "", "BiomListGroup", "BiomListGroup", "none",false,false); parameters.push_back(pbiom);
- CommandParameter plist("list", "InputTypes", "", "", "BiomListGroup", "BiomListGroup", "ListGroup",false,false); parameters.push_back(plist);
- CommandParameter pcount("count", "InputTypes", "", "", "", "GroupCount", "",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "GroupCount", "ListGroup",false,false); parameters.push_back(pgroup);
+ CommandParameter pbiom("biom", "InputTypes", "", "", "BiomListGroup", "BiomListGroup", "none","shared",false,false); parameters.push_back(pbiom);
+ CommandParameter plist("list", "InputTypes", "", "", "BiomListGroup", "BiomListGroup", "ListGroup","shared",false,false,true); parameters.push_back(plist);
+ CommandParameter pcount("count", "InputTypes", "", "", "none", "GroupCount", "none","",false,false); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "GroupCount", "ListGroup","",false,false,true); parameters.push_back(pgroup);
//CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","group",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SharedCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SharedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "shared") { outputFileName = "shared"; }
- else if (type == "rabund") { outputFileName = "rabund"; }
- else if (type == "group") { outputFileName = "groups"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SharedCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "shared") { pattern = "[filename],shared"; }
+ else if (type == "rabund") { pattern = "[filename],[group],rabund"; }
+ else if (type == "group") { pattern = "[filename],[group],groups"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
SharedCommand::SharedCommand(){
try {
if (outputDir == "") { outputDir += m->hasPath(filename); }
- filename = outputDir + m->getRootName(m->getSimpleName(filename));
- filename = filename + getOutputFileNameTag("shared");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(filename));
+ filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
if (listfile != "") { createSharedFromListGroup(filename); }
//set fileroot
fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
-
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
//clears file before we start to write to it below
for (int i=0; i<Groups.size(); i++) {
- m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));
- outputNames.push_back((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));
- outputTypes["rabund"].push_back((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund")));
+ variables["[group]"] = Groups[i];
+ string rabundFIleName = getOutputFileName("rabund",variables);
+ m->mothurRemove(rabundFIleName);
+ outputNames.push_back(rabundFIleName);
+ outputTypes["rabund"].push_back(rabundFIleName);
}
string errorOff = "no error";
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
- for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); }
+ for (int i=0; i<Groups.size(); i++) { variables["[group]"] = Groups[i];
+ string rabundFIleName = getOutputFileName("rabund",variables);
+ m->mothurRemove(rabundFIleName); }
return 0;
}
groups += (m->getGroups())[i] + ".";
}
}else { groups = "merge"; }
-
- string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + getOutputFileNameTag("group");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[group]"] = groups;
+ string newGroupFile = getOutputFileName("group",variables);
outputTypes["group"].push_back(newGroupFile);
outputNames.push_back(newGroupFile);
ofstream outGroups;
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
- for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); }
+ for (int i=0; i<Groups.size(); i++) { variables["[group]"] = Groups[i];
+ string rabundFIleName = getOutputFileName("rabund",variables);
+ m->mothurRemove(rabundFIleName); }
return 0;
}
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
- for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); }
+ for (int i=0; i<Groups.size(); i++) { variables["[group]"] = Groups[i];
+ string rabundFIleName = getOutputFileName("rabund",variables);
+ m->mothurRemove(rabundFIleName); }
return 0;
}
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
- for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); }
+ for (int i=0; i<Groups.size(); i++) { variables["[group]"] = Groups[i];
+ string rabundFIleName = getOutputFileName("rabund",variables);
+ m->mothurRemove(rabundFIleName); }
return 0;
}
if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
- for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); }
+ for (int i=0; i<Groups.size(); i++) { variables["[group]"] = Groups[i];
+ string rabundFIleName = getOutputFileName("rabund",variables);
+ m->mothurRemove(rabundFIleName); }
return 0;
}
if (m->control_pressed) {
m->mothurRemove(filename);
- for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + "." + getOutputFileNameTag("rabund"))); }
+ for (int i=0; i<Groups.size(); i++) { variables["[group]"] = Groups[i];
+ string rabundFIleName = getOutputFileName("rabund",variables);
+ m->mothurRemove(rabundFIleName); }
return 0;
}
Groups.push_back(thislookup[i]->getGroup());
RAbundVector rav = thislookup[i]->getRAbundVector();
- m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + "." + getOutputFileNameTag("rabund"), *(filehandles[thislookup[i]->getGroup()]));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[group]"] = thislookup[i]->getGroup();
+ m->openOutputFileAppend(getOutputFileName("rabund",variables), *(filehandles[thislookup[i]->getGroup()]));
rav.print(*(filehandles[thislookup[i]->getGroup()]));
(*(filehandles[thislookup[i]->getGroup()])).close();
}
Groups.push_back((myIt->second)->getGroup());
RAbundVector rav = (myIt->second)->getRAbundVector();
- m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + "." + getOutputFileNameTag("rabund"), *(filehandles[(myIt->second)->getGroup()]));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[group]"] = (myIt->second)->getGroup();
+ m->openOutputFileAppend(getOutputFileName("rabund",variables), *(filehandles[(myIt->second)->getGroup()]));
rav.print(*(filehandles[(myIt->second)->getGroup()]));
(*(filehandles[(myIt->second)->getGroup()])).close();
}else{
vector<string> setParameters();
string getCommandName() { return "make.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
string getDescription() { return "make a shared file from a list and group file"; }
//**********************************************************************************************************************
vector<string> ShhherCommand::setParameters(){
try {
- CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pflow);
- CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pfile);
- CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plookup);
- CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter);
- CommandParameter plarge("large", "Number", "", "-1", "", "", "",false,false); parameters.push_back(plarge);
- CommandParameter psigma("sigma", "Number", "", "60", "", "", "",false,false); parameters.push_back(psigma);
- CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "",false,false); parameters.push_back(pmindelta);
- CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none","fasta-name-group-counts-qfile",false,false,true); parameters.push_back(pflow);
+ CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none","fasta-name-group-counts-qfile",false,false,true); parameters.push_back(pfile);
+ CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(plookup);
+ CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(pmaxiter);
+ CommandParameter plarge("large", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(plarge);
+ CommandParameter psigma("sigma", "Number", "", "60", "", "", "","",false,false); parameters.push_back(psigma);
+ CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "","",false,false); parameters.push_back(pmindelta);
+ CommandParameter porder("order", "String", "", "", "", "", "","",false,false); parameters.push_back(porder);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ShhherCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
-
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "shhh.fasta"; }
- else if (type == "name") { outputFileName = "shhh.names"; }
- else if (type == "group") { outputFileName = "shhh.groups"; }
- else if (type == "counts") { outputFileName = "shhh.counts"; }
- else if (type == "qfile") { outputFileName = "shhh.qual"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ShhherCommand", "getOutputFileNameTag");
- exit(1);
- }
+string ShhherCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],shhh.fasta"; }
+ else if (type == "name") { pattern = "[filename],shhh.names"; }
+ else if (type == "group") { pattern = "[filename],shhh.groups"; }
+ else if (type == "counts") { pattern = "[filename],shhh.counts"; }
+ else if (type == "qfile") { pattern = "[filename],shhh.qual"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
for(int i=0;i<numSeqs;i++){
duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
}
-
- string nameFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string nameFileName = getOutputFileName("name",variables);
ofstream nameFile;
m->openOutputFile(nameFileName, nameFile);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
- string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("qfile");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string qualityFileName = getOutputFileName("qfile",variables);
ofstream qualityFile;
m->openOutputFile(qualityFileName, qualityFile);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
- string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string fastaFileName = getOutputFileName("fasta",variables);
ofstream fastaFile;
m->openOutputFile(fastaFileName, fastaFile);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
- string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string nameFileName = getOutputFileName("name",variables);
ofstream nameFile;
m->openOutputFile(nameFileName, nameFile);
int pos = fileRoot.find_first_of('.');
string fileGroup = fileRoot;
if (pos != string::npos) { fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1))); }
- string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + fileRoot;
+ string groupFileName = getOutputFileName("group",variables);
ofstream groupFile;
m->openOutputFile(groupFileName, groupFile);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
- string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) +getOutputFileNameTag("counts");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string otuCountsFileName = getOutputFileName("counts",variables);
ofstream otuCountsFile;
m->openOutputFile(otuCountsFileName, otuCountsFile);
if ((large) && (g == 0)) { flowFileName = filenames[i]; theseFlowFileNames[0] = filenames[i]; }
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir = m->hasPath(flowFileName); }
- string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("qfile");
- string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
- string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
- string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("counts");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string qualityFileName = getOutputFileName("qfile",variables);
+ string fastaFileName = getOutputFileName("fasta",variables);
+ string nameFileName = getOutputFileName("name",variables);
+ string otuCountsFileName = getOutputFileName("counts",variables);
string fileRoot = m->getRootName(m->getSimpleName(flowFileName));
int pos = fileRoot.find_first_of('.');
string fileGroup = fileRoot;
if (pos != string::npos) { fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1))); }
- string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group");
+ string groupFileName = getOutputFileName("group",variables);
writeQualities(numOTUs, numFlowCells, qualityFileName, otuCounts, nSeqsPerOTU, seqNumber, singleTau, flowDataIntI, uniqueFlowgrams, cumNumSeqs, mapUniqueToSeq, seqNameVector, centroids, aaI); if (m->control_pressed) { break; }
if (large) {
if (g > 0) {
- m->appendFiles(qualityFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("qfile")));
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0]));
+ m->appendFiles(qualityFileName, getOutputFileName("qfile",variables));
m->mothurRemove(qualityFileName);
- m->appendFiles(fastaFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("fasta")));
+ m->appendFiles(fastaFileName, getOutputFileName("fasta",variables));
m->mothurRemove(fastaFileName);
- m->appendFiles(nameFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("name")));
+ m->appendFiles(nameFileName, getOutputFileName("name",variables));
m->mothurRemove(nameFileName);
- m->appendFiles(otuCountsFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("counts")));
+ m->appendFiles(otuCountsFileName, getOutputFileName("counts",variables));
m->mothurRemove(otuCountsFileName);
- m->appendFiles(groupFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("group")));
+ m->appendFiles(groupFileName, getOutputFileName("group",variables));
m->mothurRemove(groupFileName);
}
m->mothurRemove(theseFlowFileNames[g]);
vector<string> setParameters();
string getCommandName() { return "shhh.flows"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38.\nQuince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009). Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6:639.\nhttp://www.mothur.org/wiki/Shhh.flows"; }
string getDescription() { return "shhh.flows"; }
//**********************************************************************************************************************
vector<string> ShhhSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter psigma("sigma", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(psigma);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-map",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","name",false,true,true); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter psigma("sigma", "Number", "", "0.01", "", "", "","",false,false); parameters.push_back(psigma);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ShhhSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ShhhSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "shhh_seqs.fasta"; }
- else if (type == "name") { outputFileName = "shhh_seqs.names"; }
- else if (type == "map") { outputFileName = "shhh_seqs.map"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "ShhhSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],shhh_seqs.fasta"; }
+ else if (type == "name") { pattern = "[filename],shhh_seqs.names"; }
+ else if (type == "map") { pattern = "[filename],shhh_seqs.map"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhhSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- if (outputDir == "") { outputDir = m->hasPath(fastafile); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
- string nameFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("name");
- string mapFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("map");
+ if (outputDir == "") { outputDir = m->hasPath(fastafile); }//if user entered a file with a path then preserve it
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileName = getOutputFileName("fasta",variables);
+ string nameFileName = getOutputFileName("name",variables);
+ string mapFileName = getOutputFileName("map",variables);
if (groupfile != "") {
//Parse sequences by group
vector<string> setParameters();
string getCommandName() { return "shhh.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38.\nhttp://www.mothur.org/wiki/Shhh.seqs"; }
string getDescription() { return "shhh.seqs"; }
//**********************************************************************************************************************
vector<string> SortSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pflow("flow", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pflow);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
- CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "FNGLT", "none","flow",false,false); parameters.push_back(pflow);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false); parameters.push_back(pgroup);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
+ CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
exit(1);
}
}
-
//**********************************************************************************************************************
-string SortSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SortSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "taxonomy") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "flow") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "qfile") { outputFileName = "sorted" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SortSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "name") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "group") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "count") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "flow") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "qfile") { pattern = "[filename],sorted,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
SortSeqsCommand::SortSeqsCommand(){
try {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowfile)) + getOutputFileNameTag("flow", flowfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowfile));
+ variables["[extension]"] = m->getExtension(flowfile);
+ string outputFileName = getOutputFileName("flow", variables);
outputTypes["flow"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(qualfile));
+ variables["[extension]"] = m->getExtension(qualfile);
+ string outputFileName = getOutputFileName("qfile", variables);
outputTypes["qfile"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputFileName = getOutputFileName("count", variables);
outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
+
outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
vector<string> setParameters();
string getCommandName() { return "sort.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sort.seqs"; }
string getDescription() { return "puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order"; }
//**********************************************************************************************************************
vector<string> SplitAbundCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter paccnos("accnos", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(paccnos);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "","",false,true); parameters.push_back(pcutoff);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter paccnos("accnos", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(paccnos);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
exit(1);
}
}
+
//**********************************************************************************************************************
-string SplitAbundCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SplitAbundCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "fasta"; }
- else if (type == "list") { outputFileName = "list"; }
- else if (type == "name") { outputFileName = "names"; }
- else if (type == "count") { outputFileName = "count_table"; }
- else if (type == "group") { outputFileName = "groups"; }
- else if (type == "accnos") { outputFileName = "accnos"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SplitAbundCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],[tag],[tag2],fasta-[filename],[tag],[group],[tag2],fasta"; }
+ else if (type == "list") { pattern = "[filename],[tag],[tag2],list-[filename],[group],[tag],[tag2],list"; }
+ else if (type == "name") { pattern = "[filename],[tag],names-[filename],[group],[tag],names"; }
+ else if (type == "count") { pattern = "[filename],[tag],[tag2],count_table-[filename],[tag],count_table"; }
+ else if (type == "group") { pattern = "[filename],[tag],[tag2],groups-[filename],[tag],[group],[tag2],groups"; }
+ else if (type == "accnos") { pattern = "[filename],[tag],[tag2],accnos-[filename],[tag],[group],[tag2],accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
SplitAbundCommand::SplitAbundCommand(){
}//end for
- string tag = thisList->getLabel() + ".";
+ string tag = thisList->getLabel();
writeList(thisList, tag, numRareBins);
ofstream aout;
ofstream rout;
- string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare." + getOutputFileNameTag("list");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ string rare = getOutputFileName("list",variables);
m->openOutputFile(rare, rout);
outputNames.push_back(rare); outputTypes["list"].push_back(rare);
- string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund." + getOutputFileNameTag("list");
+ variables["[tag2]"] = "abund";
+ string abund = getOutputFileName("list",variables);
m->openOutputFile(abund, aout);
outputNames.push_back(abund); outputTypes["list"].push_back(abund);
temp2 = new ofstream;
filehandles[Groups[i]+".abund"] = temp2;
- string rareGroupFileName = fileroot + Groups[i] +"."+ tag + "rare." + getOutputFileNameTag("list");
- string abundGroupFileName = fileroot + Groups[i] +"."+ tag + "abund." + getOutputFileNameTag("list");
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ variables["[group]"] = Groups[i];
+ string rareGroupFileName = getOutputFileName("list",variables);
+ variables["[tag2]"] = "abund";
+ string abundGroupFileName = getOutputFileName("list",variables);
m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"]));
m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"]));
outputNames.push_back(rareGroupFileName); outputTypes["list"].push_back(rareGroupFileName);
map<string, ofstream*> filehandles;
if (Groups.size() == 0) {
- string rare = outputDir + m->getRootName(m->getSimpleName(countfile)) + tag + "rare." + getOutputFileNameTag("count");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ string rare = getOutputFileName("count",variables);
outputNames.push_back(rare); outputTypes["count"].push_back(rare);
-
- string abund = outputDir + m->getRootName(m->getSimpleName(countfile)) + tag + "abund." + getOutputFileNameTag("count");
+ variables["[tag2]"] = "abund";
+ string abund = getOutputFileName("count",variables);
outputNames.push_back(abund); outputTypes["count"].push_back(abund);
CountTable rareTable;
for (it3 = countTableMap.begin(); it3 != countTableMap.end(); it3++) {
string fileroot = outputDir + m->getRootName(m->getSimpleName(countfile));
- string filename = fileroot + it3->first + "." + getOutputFileNameTag("count");
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = it3->first;
+ string filename = getOutputFileName("count",variables);
outputNames.push_back(filename); outputTypes["count"].push_back(filename);
(it3->second)->printTable(filename);
delete it3->second;
ofstream aout;
ofstream rout;
- string rare = outputDir + m->getRootName(m->getSimpleName(namefile)) + "rare." + getOutputFileNameTag("name");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[tag]"] = "rare";
+ string rare = getOutputFileName("name", variables);
m->openOutputFile(rare, rout);
outputNames.push_back(rare); outputTypes["name"].push_back(rare);
- string abund = outputDir + m->getRootName(m->getSimpleName(namefile)) + "abund." + getOutputFileNameTag("name");
+ variables["[tag]"] = "abund";
+ string abund = getOutputFileName("name", variables);
m->openOutputFile(abund, aout);
outputNames.push_back(abund); outputTypes["name"].push_back(abund);
temp2 = new ofstream;
filehandles[Groups[i]+".abund"] = temp2;
- string rareGroupFileName = fileroot + Groups[i] + ".rare." + getOutputFileNameTag("name");
- string abundGroupFileName = fileroot + Groups[i] + ".abund." + getOutputFileNameTag("name");
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = "rare";
+ variables["[group]"] = Groups[i];
+ string rareGroupFileName = getOutputFileName("name",variables);
+ variables["[tag]"] = "abund";
+ string abundGroupFileName = getOutputFileName("name",variables);
m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"]));
m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"]));
}
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
(*(filehandles[it3->first])).close();
- outputNames.push_back(fileroot + it3->first + "." + getOutputFileNameTag("name")); outputTypes["name"].push_back(fileroot + it3->first + "." + getOutputFileNameTag("name"));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = it3->first;
+ outputNames.push_back(getOutputFileName("name",variables)); outputTypes["name"].push_back(getOutputFileName("name",variables));
delete it3->second;
}
}
ofstream aout;
ofstream rout;
-
- string rare = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag + "rare." + getOutputFileNameTag("accnos");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFile));
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ string rare = getOutputFileName("accnos",variables);
m->openOutputFile(rare, rout);
outputNames.push_back(rare); outputTypes["accnos"].push_back(rare);
}
rout.close();
- string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag + "abund." + getOutputFileNameTag("accnos");
+ variables["[tag2]"] = "abund";
+ string abund = getOutputFileName("accnos",variables);
m->openOutputFile(abund, aout);
outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
temp2 = new ofstream;
filehandles[Groups[i]+".abund"] = temp2;
- m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".rare"]));
- m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".abund"]));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ variables["[group]"] = Groups[i];
+ m->openOutputFile(getOutputFileName("accnos",variables), *(filehandles[Groups[i]+".rare"]));
+ variables["[tag2]"] = "abund";
+ m->openOutputFile(getOutputFileName("accnos",variables), *(filehandles[Groups[i]+".abund"]));
}
//write rare
//close files
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
(*(filehandles[it3->first])).close();
- outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos")); outputTypes["accnos"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos"));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = it3->first;
+ outputNames.push_back(getOutputFileName("accnos",variables)); outputTypes["accnos"].push_back(getOutputFileName("accnos",variables));
delete it3->second;
}
}
ofstream aout;
ofstream rout;
- string rare = outputDir + m->getRootName(m->getSimpleName(groupfile)) + tag + "rare." + getOutputFileNameTag("group");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ string rare = getOutputFileName("group",variables);
m->openOutputFile(rare, rout);
outputNames.push_back(rare); outputTypes["group"].push_back(rare);
- string abund = outputDir + m->getRootName(m->getSimpleName(groupfile)) + tag + "abund." + getOutputFileNameTag("group");
+ variables["[tag2]"] = "abund";
+ string abund = getOutputFileName("group",variables);
;
m->openOutputFile(abund, aout);
outputNames.push_back(abund); outputTypes["group"].push_back(abund);
temp2 = new ofstream;
filehandles[Groups[i]+".abund"] = temp2;
- m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".rare"]));
- m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".abund"]));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ variables["[group]"] = Groups[i];
+ m->openOutputFile(getOutputFileName("group",variables), *(filehandles[Groups[i]+".rare"]));
+ variables["[tag2]"] = "abund";
+ m->openOutputFile(getOutputFileName("group",variables), *(filehandles[Groups[i]+".abund"]));
}
for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
(*(filehandles[it3->first])).close();
- outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group")); outputTypes["group"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group"));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = it3->first;
+ outputNames.push_back(getOutputFileName("group",variables)); outputTypes["group"].push_back(getOutputFileName("group",variables));
delete it3->second;
}
}
ofstream aout;
ofstream rout;
- string rare = outputDir + m->getRootName(m->getSimpleName(fastafile)) + tag + "rare." + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ string rare = getOutputFileName("fasta",variables);
m->openOutputFile(rare, rout);
outputNames.push_back(rare); outputTypes["fasta"].push_back(rare);
- string abund = outputDir + m->getRootName(m->getSimpleName(fastafile)) + tag + "abund." + getOutputFileNameTag("fasta");
+ variables["[tag2]"] = "abund";
+ string abund = getOutputFileName("fasta",variables);
m->openOutputFile(abund, aout);
outputNames.push_back(abund); outputTypes["fasta"].push_back(abund);
temp2 = new ofstream;
filehandles[Groups[i]+".abund"] = temp2;
- m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".rare"]));
- m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".abund"]));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ variables["[group]"] = Groups[i];
+ m->openOutputFile(getOutputFileName("fasta",variables), *(filehandles[Groups[i]+".rare"]));
+ variables["[tag2]"] = "abund";
+ m->openOutputFile(getOutputFileName("fasta",variables), *(filehandles[Groups[i]+".abund"]));
}
//open input file
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
(*(filehandles[it3->first])).close();
- outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta")); outputTypes["fasta"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta"));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = it3->first;
+ outputNames.push_back(getOutputFileName("fasta",variables)); outputTypes["fasta"].push_back(getOutputFileName("fasta",variables));
delete it3->second;
}
}
vector<string> setParameters();
string getCommandName() { return "split.abund"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Split.abund"; }
string getDescription() { return "split a list, name, group or fasta file based on abundance"; }
//**********************************************************************************************************************
vector<string> SplitGroupCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "CountGroup", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "CountGroup", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "CountGroup", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "CountGroup", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SplitGroupCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SplitGroupCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "fasta"; }
- else if (type == "name") { outputFileName = "names"; }
- else if (type == "count") { outputFileName = "count_table"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SplitGroupCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],[group],fasta"; }
+ else if (type == "name") { pattern = "[filename],[group],names"; }
+ else if (type == "count") { pattern = "[filename],[group],count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitGroupCommand", "getOutputPattern");
+ exit(1);
+ }
}
+
//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(){
try {
m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
- string newFasta = fastafileRoot + Groups[i] + "." + getOutputFileNameTag("fasta");
- string newName = namefileRoot + Groups[i] + "." + getOutputFileNameTag("name");
+ map<string, string> variables;
+ variables["[filename]"] = fastafileRoot;
+ variables["[group]"] = Groups[i];
+
+ string newFasta = getOutputFileName("fasta",variables);
+ variables["[filename]"] = namefileRoot;
+ string newName = getOutputFileName("name",variables);
parser->getSeqs(Groups[i], newFasta, false);
outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);
for (int i=0; i<Groups.size(); i++) {
temp = new ofstream;
ffiles[Groups[i]] = temp;
- string newFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + Groups[i] + "." + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[group]"] = Groups[i];
+ string newFasta = getOutputFileName("fasta",variables);
outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);
m->openOutputFile(newFasta, (*temp));
temp = new ofstream;
cfiles[Groups[i]] = temp;
- string newCount = outputDir + m->getRootName(m->getSimpleName(countfile)) + Groups[i] + "." + getOutputFileNameTag("count");
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+ string newCount = getOutputFileName("count",variables);
m->openOutputFile(newCount, (*temp));
outputNames.push_back(newCount); outputTypes["count"].push_back(newCount);
(*temp) << "Representative_Sequence\ttotal\t" << Groups[i] << endl;
vector<string> setParameters();
string getCommandName() { return "split.group"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
string getDescription() { return "split a name or fasta file by group"; }
else { options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff); }
if (outputDir != "") { options += ", outputdir=" + outputDir; }
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
Command* command = new DistanceCommand(options);
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
command->execute();
delete command;
for (int i = 0; i < Groups.size(); i++) {
if (m->inUsersGroups(Groups[i], m->getGroups())) {
if (m->control_pressed) { break; }
- cout << Groups[i] << endl;
+
int thisSize = ct->getGroupCount(Groups[i]);
if (thisSize >= size) {
//**********************************************************************************************************************
vector<string> SubSampleCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(plist);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pshared);
- CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(psabund);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
- CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none","fasta",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FLSSR", "none","list",false,false,true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none","shared",false,false,true); parameters.push_back(pshared);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none","rabund",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none","sabund",false,false); parameters.push_back(psabund);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(psize);
+ CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(ppersample);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SubSampleCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SubSampleCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "sabund") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "list") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "rabund") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "shared") { outputFileName = "subsample" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "sabund") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "name") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "group") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "count") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "list") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "shared") { pattern = "[filename],[distance],subsample,[extension]"; }
+ else if (type == "rabund") { pattern = "[filename],subsample,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
SubSampleCommand::SubSampleCommand(){
try {
string countOutputDir = outputDir;
if (outputDir == "") { countOutputDir += m->hasPath(countfile); }
- string countOutputFileName = countOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string countOutputFileName = getOutputFileName("count", variables);
outputTypes["count"].push_back(countOutputFileName); outputNames.push_back(countOutputFileName);
sampledCt.printTable(countOutputFileName);
}
string countOutputDir = outputDir;
if (outputDir == "") { countOutputDir += m->hasPath(countfile); }
- string countOutputFileName = countOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string countOutputFileName = getOutputFileName("count", variables);
outputTypes["count"].push_back(countOutputFileName); outputNames.push_back(countOutputFileName);
sampledCt.printTable(countOutputFileName);
}
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
if (namefile != "") {
m->mothurOut("Deconvoluting subsampled fasta file... "); m->mothurOutEndLine();
-
- string outputNameFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputNameFileName = getOutputFileName("name", variables);
//use unique.seqs to create new name and fastafile
string inputString = "fasta=" + outputFileName;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
string groupOutputDir = outputDir;
if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); }
- string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = groupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string groupOutputFileName = getOutputFileName("group", variables);
ofstream outGroup;
m->openOutputFile(groupOutputFileName, outGroup);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + "." +getOutputFileNameTag("shared", sharedfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
+ variables["[distance]"] = thislookup[0]->getLabel();
+ string outputFileName = getOutputFileName("shared", variables);
SubSample sample;
vector<string> subsampledLabels = sample.getSample(thislookup, size);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
string countOutputDir = outputDir;
if (outputDir == "") { countOutputDir += m->hasPath(countfile); }
- string countOutputFileName = countOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string countOutputFileName = getOutputFileName("count", variables);
outputTypes["count"].push_back(countOutputFileName); outputNames.push_back(countOutputFileName);
sampledCt.printTable(countOutputFileName);
}
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + getOutputFileNameTag("rabund", rabundfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile));
+ variables["[extension]"] = m->getExtension(rabundfile);
+ string outputFileName = getOutputFileName("rabund", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + getOutputFileNameTag("sabund", sabundfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile));
+ variables["[extension]"] = m->getExtension(sabundfile);
+ string outputFileName = getOutputFileName("sabund", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
vector<string> setParameters();
string getCommandName() { return "sub.sample"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sub.sample"; }
string getDescription() { return "get a sampling of sequences from a list, shared, rabund, sabund or fasta file"; }
//**********************************************************************************************************************
vector<string> SummaryCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
- CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false,true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false); parameters.push_back(psabund);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false,true); parameters.push_back(pshared);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psize);
+ CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SummaryCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SummaryCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "summary") { outputFileName = "summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],summary-[filename],[tag],summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
SummaryCommand::SummaryCommand(){
else { subsample = false; subsampleSize = -1; }
}
- if (subsample == false) { iters = 1; }
+ if (subsample == false) { iters = 0; }
else {
//if you did not set a samplesize and are not using a sharedfile
if ((subsampleSize == -1) && (format != "sharedfile")) { m->mothurOut("[ERROR]: If you want to subsample with a list, rabund or sabund file, you must provide the sample size. You can do this by setting subsample=yourSampleSize.\n"); abort=true; }
numLines = 0;
numCols = 0;
- string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + getOutputFileNameTag("summary");
- string fileNameAve = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "ave-std." + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+ string fileNameRoot = getOutputFileName("summary",variables);
+ variables["[tag]"] = "ave-std";
+ string fileNameAve = getOutputFileName("summary",variables);
outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
if (inputFileNames.size() > 1) {
vector<string> setParameters();
string getCommandName() { return "summary.single"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
string getDescription() { return "generate summary file that has the calculator value for each line in the OTU data"; }
//**********************************************************************************************************************
vector<string> SummaryQualCommand::setParameters(){
try {
- CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqual);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pqual);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SummaryQualCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SummaryQualCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "summary") { outputFileName = "qual.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryQualCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],qual.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
SummaryQualCommand::SummaryQualCommand(){
if (m->control_pressed) { return 0; }
//print summary file
- string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qualfile));
+ string summaryFile = getOutputFileName("summary",variables);
printQual(summaryFile, position, averageQ, scores);
if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
vector<string> setParameters();
string getCommandName() { return "summary.qual"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
string getDescription() { return "summarize the quality of a set of sequences"; }
//**********************************************************************************************************************
vector<string> SummarySharedCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
- CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdistance);
- CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","phylip",false,false); parameters.push_back(psubsample);
+ CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "","phylip",false,false); parameters.push_back(pdistance);
+ CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SummarySharedCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SummarySharedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "summary") { outputFileName = "shared.summary"; }
- else if (type == "phylip") { outputFileName = "dist"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SummarySharedCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],summary-[filename],[tag],summary"; }
+ else if (type == "phylip") { pattern = "[filename],[calc],[distance],[outputtag],[tag2],dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummarySharedCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
SummarySharedCommand::SummarySharedCommand(){
else { subsample = false; }
}
- if (subsample == false) { iters = 1; }
+ if (subsample == false) { iters = 0; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
if (abort == true) { if (calledHelp) { return 0; } return 2; }
ofstream outputFileHandle, outAll;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ string outputFileName = getOutputFileName("summary",variables);
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) { return 0; }
outputFileHandle.close();
//create file and put column headers for multiple groups file
- string outAllFileName = ((m->getRootName(sharedfile)) + "multiple." + getOutputFileNameTag("summary"));
+ variables["[tag]"]= "multiple";
+ string outAllFileName = getOutputFileName("summary",variables);
if (mult == true) {
m->openOutputFile(outAllFileName, outAll);
outputNames.push_back(outAllFileName);
matrix[column][row] = dist;
}
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + "." + getOutputFileNameTag("phylip");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[calc]"] = sumCalculators[i]->getName();
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[outputtag]"] = output;
+ string distFileName = getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outDist;
m->openOutputFile(distFileName, outDist);
stdmatrix[column][row] = stdDist;
}
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".ave." + getOutputFileNameTag("phylip");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[calc]"] = sumCalculators[i]->getName();
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[outputtag]"] = output;
+ variables["[tag2]"] = "ave";
+ string distFileName = getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outAve;
m->openOutputFile(distFileName, outAve);
outAve.close();
- distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".std." + getOutputFileNameTag("phylip");
+ variables["[tag2]"] = "std";
+ distFileName = getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outSTD;
m->openOutputFile(distFileName, outSTD);
vector<string> setParameters();
string getCommandName() { return "summary.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
string getDescription() { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
//**********************************************************************************************************************
vector<string> SummaryTaxCommand::setParameters(){
try {
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(preftaxonomy);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(ptaxonomy);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(preftaxonomy);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string SummaryTaxCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SummaryTaxCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "summary") { outputFileName = "tax.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryTaxCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "summary") { pattern = "[filename],tax.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryTaxCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
SummaryTaxCommand::SummaryTaxCommand(){
//print summary file
ofstream outTaxTree;
- string summaryFile = outputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("summary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(taxfile));
+ string summaryFile = getOutputFileName("summary",variables);
m->openOutputFile(summaryFile, outTaxTree);
taxaSum->print(outTaxTree);
outTaxTree.close();
vector<string> setParameters();
string getCommandName() { return "summary.tax"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
string getDescription() { return "summarize the taxonomies of a set of sequences"; }
//**********************************************************************************************************************
vector<string> SystemCommand::setParameters(){
try {
- CommandParameter pcommand("command", "String", "", "", "", "", "",false,false); parameters.push_back(pcommand);
+ CommandParameter pcommand("command", "String", "", "", "", "", "","",false,false); parameters.push_back(pcommand);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
vector<string> setParameters();
string getCommandName() { return "system"; }
string getCommandCategory() { return "General"; }
- string getOutputFileNameTag(string, string) { return ""; }
string getHelpString();
+ string getOutputPattern(string){ return ""; }
string getCitation() { return "http://www.mothur.org/wiki/System"; }
string getDescription() { return "execute system commands from within mothur"; }
c = filehandle.get();
//k = c;
//cout << k << endl;
- while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
name += c;
c = filehandle.get();
//k = c;
}
//cout << "name = " << name << endl;
- m->Treenames.push_back(name);
+ if (name != "\r" ) {
+ m->Treenames.push_back(name); } //cout << m->Treenames.size() << '\t' << name << endl;
+
filehandle.putback(c);
//k = c;
//cout << " after putback" << k << endl;
//**********************************************************************************************************************
vector<string> TreeGroupCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "countcolumn",false,false); parameters.push_back(pcount);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName-countcolumn",false,false); parameters.push_back(pcolumn);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
- CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false,true); parameters.push_back(pshared);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "countcolumn","",false,false); parameters.push_back(pcount);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName-countcolumn","tree",false,false); parameters.push_back(pcolumn);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
//CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string TreeGroupCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string TreeGroupCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "tree") { outputFileName = "tre"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "tree") { pattern = "[filename],[calc],[distance],[tag],tre-[filename],tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TreeGroupCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
TreeGroupCommand::TreeGroupCommand(){
if (m->control_pressed) { return 0; }
//create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("tree");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ string outputFile = getOutputFileName("tree",variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
Tree* newTree = createTree(matrix);
}
//create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave." + getOutputFileNameTag("tree");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ variables["[calc]"] = treeCalculators[i]->getName();
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[tag]"] = "ave";
+ string outputFile = getOutputFileName("tree",variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
//creates tree from similarity matrix and write out file
if (m->control_pressed) { break; }
//create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all." + getOutputFileNameTag("tree");
+ //create a new filename
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ variables["[calc]"] = treeCalculators[i]->getName();
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[tag]"] = "all";
+ string outputFile = getOutputFileName("tree",variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
ofstream outAll;
Tree* conTree = consensus.getTree(trees);
//create a new filename
- string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons." + getOutputFileNameTag("tree");
+ variables["[tag]"] = "cons";
+ string conFile = getOutputFileName("tree",variables);
outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile);
ofstream outTree;
m->openOutputFile(conFile, outTree);
}
//create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + getOutputFileNameTag("tree");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ variables["[calc]"] = treeCalculators[i]->getName();
+ variables["[distance]"] = thisLookup[0]->getLabel();
+ variables["[tag]"] = "";
+ string outputFile = getOutputFileName("tree",variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
//creates tree from similarity matrix and write out file
vector<string> setParameters();
string getCommandName() { return "tree.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
string getDescription() { return "generate a tree file that describes the dissimilarity among groups"; }
//**********************************************************************************************************************
vector<string> TrimFlowsCommand::setParameters(){
try {
- CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pflow);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
- CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
- CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
- CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
- CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
- CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
- CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
- CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
- CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
- CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
- CommandParameter porder("order", "String", "", "TACG", "", "", "",false,false); parameters.push_back(porder);
- CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfasta);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow",false,true,true); parameters.push_back(pflow);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(poligos);
+ CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "","",false,false); parameters.push_back(pmaxhomop);
+ CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pmaxflows);
+ CommandParameter pminflows("minflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pminflows);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter psignal("signal", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(psignal);
+ CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "","",false,false); parameters.push_back(pnoise);
+ CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(pallfiles);
+ CommandParameter porder("order", "String", "", "TACG", "", "", "","",false,false); parameters.push_back(porder);
+ CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfasta);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string TrimFlowsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string TrimFlowsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "flow") { outputFileName = "flow"; }
- else if (type == "fasta") { outputFileName = "flow.fasta"; }
- else if (type == "file") { outputFileName = "flow.files"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimFlowsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "flow") { pattern = "[filename],[tag],flow"; }
+ else if (type == "fasta") { pattern = "[filename],flow.fasta"; }
+ else if (type == "file") { pattern = "[filename],flow.files"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimFlowsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim." + getOutputFileNameTag("flow");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string fastaFileName = getOutputFileName("fasta",variables);
+ if(fasta){ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); }
+
+ variables["[tag]"] = "trim";
+ string trimFlowFileName = getOutputFileName("flow",variables);
outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
- string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap." + getOutputFileNameTag("flow");;
+ variables["[tag]"] = "scrap";
+ string scrapFlowFileName = getOutputFileName("flow",variables);
outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
- string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
- if(fasta){
- outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
- }
+
vector<unsigned long long> flowFilePos;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(allFiles){
set<string> namesAlreadyProcessed;
- flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
+ variables["[tag]"] = "";
+ flowFilesFileName = getOutputFileName("file",variables);
m->openOutputFile(flowFilesFileName, output);
for(int i=0;i<barcodePrimerComboFileNames.size();i++){
output.close();
}
else{
- flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file");
+ variables["[tag]"] = "";
+ flowFilesFileName = getOutputFileName("file",variables);
m->openOutputFile(flowFilesFileName, output);
output << m->getFullPathName(trimFlowFileName) << endl;
string comboGroupName = "";
string fileName = "";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+
if(primerName == ""){
comboGroupName = barcodeNameVector[itBar->second];
- fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
+ variables["[tag]"] = comboGroupName;
+ fileName = getOutputFileName("flow", variables);
}
else{
if(barcodeName == ""){
else{
comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
}
- fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
+ variables["[tag]"] = comboGroupName;
+ fileName = getOutputFileName("flow", variables);
}
outFlowFileNames[itBar->second][itPrimer->second] = fileName;
vector<string> setParameters();
string getCommandName() { return "trim.flows"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
string getDescription() { return "trim.flows"; }
//**********************************************************************************************************************
vector<string> TrimSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
- CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
- CommandParameter pmaxhomop("maxhomop", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxhomop);
- CommandParameter pminlength("minlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pminlength);
- CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
- CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
- CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
- CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
- CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
- CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pallfiles);
- CommandParameter pkeepforward("keepforward", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepforward);
- CommandParameter pqtrim("qtrim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqtrim);
- CommandParameter pqthreshold("qthreshold", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqthreshold);
- CommandParameter pqaverage("qaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqaverage);
- CommandParameter prollaverage("rollaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(prollaverage);
- CommandParameter pqwindowaverage("qwindowaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqwindowaverage);
- CommandParameter pqstepsize("qstepsize", "Number", "", "1", "", "", "",false,false); parameters.push_back(pqstepsize);
- CommandParameter pqwindowsize("qwindowsize", "Number", "", "50", "", "", "",false,false); parameters.push_back(pqwindowsize);
- CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "",false,false); parameters.push_back(pkeepfirst);
- CommandParameter premovelast("removelast", "Number", "", "0", "", "", "",false,false); parameters.push_back(premovelast);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","qfile",false,false,true); parameters.push_back(pqfile);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(pflip);
+ CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxambig);
+ CommandParameter pmaxhomop("maxhomop", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxhomop);
+ CommandParameter pminlength("minlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pminlength);
+ CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxlength);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles);
+ CommandParameter pkeepforward("keepforward", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkeepforward);
+ CommandParameter pqtrim("qtrim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pqtrim);
+ CommandParameter pqthreshold("qthreshold", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pqthreshold);
+ CommandParameter pqaverage("qaverage", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pqaverage);
+ CommandParameter prollaverage("rollaverage", "Number", "", "0", "", "", "","",false,false); parameters.push_back(prollaverage);
+ CommandParameter pqwindowaverage("qwindowaverage", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pqwindowaverage);
+ CommandParameter pqstepsize("qstepsize", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pqstepsize);
+ CommandParameter pqwindowsize("qwindowsize", "Number", "", "50", "", "", "","",false,false); parameters.push_back(pqwindowsize);
+ CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pkeepfirst);
+ CommandParameter premovelast("removelast", "Number", "", "0", "", "", "","",false,false); parameters.push_back(premovelast);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string TrimSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string TrimSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "qfile") { outputFileName = "qual"; }
- else if (type == "fasta") { outputFileName = "fasta"; }
- else if (type == "group") { outputFileName = "groups"; }
- else if (type == "name") { outputFileName = "names"; }
- else if (type == "count") { outputFileName = "count_table"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "qfile") { pattern = "[filename],[tag],qual"; }
+ else if (type == "fasta") { pattern = "[filename],[tag],fasta"; }
+ else if (type == "group") { pattern = "[filename],groups"; }
+ else if (type == "name") { pattern = "[filename],[tag],names"; }
+ else if (type == "count") { pattern = "[filename],count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
-
//**********************************************************************************************************************
TrimSeqsCommand::TrimSeqsCommand(){
vector<vector<string> > qualFileNames;
vector<vector<string> > nameFileNames;
- string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
+ variables["[tag]"] = "trim";
+ string trimSeqFile = getOutputFileName("fasta",variables);
+ string trimQualFile = getOutputFileName("qfile",variables);
outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
-
- string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("fasta");
+
+ variables["[tag]"] = "scrap";
+ string scrapSeqFile = getOutputFileName("fasta",variables);
+ string scrapQualFile = getOutputFileName("qfile",variables);
outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
- string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("qfile");
- string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("qfile");
-
if (qFileName != "") {
outputNames.push_back(trimQualFile);
outputNames.push_back(scrapQualFile);
outputTypes["qfile"].push_back(scrapQualFile);
}
- string trimNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "trim." + getOutputFileNameTag("name");
- string scrapNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "scrap." + getOutputFileNameTag("name");
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFile));
+ variables["[tag]"] = "trim";
+ string trimNameFile = getOutputFileName("name",variables);
+ variables["[tag]"] = "scrap";
+ string scrapNameFile = getOutputFileName("name",variables);
if (nameFile != "") {
m->readNames(nameFile, nameMap);
outputTypes["name"].push_back(scrapNameFile);
}
- string trimCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + "trim." + getOutputFileNameTag("count");
- string scrapCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + "scrap." + getOutputFileNameTag("count");
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[tag]"] = "trim";
+ string trimCountFile = getOutputFileName("count",variables);
+ variables["[tag]"] = "scrap";
+ string scrapCountFile = getOutputFileName("count",variables);
if (countfile != "") {
CountTable ct;
if(oligoFile != ""){
createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
if ((createGroup) && (countfile == "")){
- outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + getOutputFileNameTag("group");
+ map<string, string> myvariables;
+ myvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
+ outputGroupFileName = getOutputFileName("group",myvariables);
outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
}
}
m->openInputFile(it->first, in);
ofstream out;
- string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first));
- if (countfile == "") { thisGroupName += getOutputFileNameTag("group"); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); }
- else { thisGroupName += getOutputFileNameTag("count"); outputNames.push_back(thisGroupName); outputTypes["count"].push_back(thisGroupName); }
+ map<string, string> myvariables;
+ myvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(it->first));
+ string thisGroupName = "";
+ if (countfile == "") { thisGroupName = getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); }
+ else { thisGroupName = getOutputFileName("count",variables); outputNames.push_back(thisGroupName); outputTypes["count"].push_back(thisGroupName); }
m->openOutputFile(thisGroupName, out);
if (countfile != "") { out << "Representative_Sequence\ttotal\t" << it->second << endl; }
ofstream temp;
- fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
+ variables["[tag]"] = comboGroupName;
+ fastaFileName = getOutputFileName("fasta", variables);
if (uniqueNames.count(fastaFileName) == 0) {
outputNames.push_back(fastaFileName);
outputTypes["fasta"].push_back(fastaFileName);
m->openOutputFile(fastaFileName, temp); temp.close();
if(qFileName != ""){
- qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qFileName));
+ qualFileName = getOutputFileName("qfile", variables);
if (uniqueNames.count(qualFileName) == 0) {
outputNames.push_back(qualFileName);
outputTypes["qfile"].push_back(qualFileName);
}
if(nameFile != ""){
- nameFileName = outputDir + m->getRootName(m->getSimpleName(nameFile)) + comboGroupName + ".names";
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFile));
+ nameFileName = getOutputFileName("name", variables);
if (uniqueNames.count(nameFileName) == 0) {
outputNames.push_back(nameFileName);
outputTypes["name"].push_back(nameFileName);
vector<string> setParameters();
string getCommandName() { return "trim.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
string getDescription() { return "provides the preprocessing features needed to screen and sort pyrosequences"; }
//**********************************************************************************************************************
vector<string> UnifracUnweightedCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter prandom("random", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prandom);
- CommandParameter pdistance("distance", "Multiple", "column-lt-square-phylip", "column", "", "", "",false,false); parameters.push_back(pdistance);
- CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
- CommandParameter pconsensus("consensus", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pconsensus);
- CommandParameter proot("root", "Boolean", "F", "", "", "", "",false,false); parameters.push_back(proot);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","unweighted-uwsummary",false,true,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter prandom("random", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(prandom);
+ CommandParameter pdistance("distance", "Multiple", "column-lt-square-phylip", "column", "", "", "","phylip-column",false,false); parameters.push_back(pdistance);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter pconsensus("consensus", "Boolean", "", "F", "", "", "","tree",false,false); parameters.push_back(pconsensus);
+ CommandParameter proot("root", "Boolean", "F", "", "", "", "","",false,false); parameters.push_back(proot);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string UnifracUnweightedCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
-
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "unweighted") { outputFileName = "unweighted"; }
- else if (type == "uwsummary") { outputFileName = "uwsummary"; }
- else if (type == "phylip") { outputFileName = "dist"; }
- else if (type == "column") { outputFileName = "dist"; }
- else if (type == "tree") { outputFileName = "tre"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "UnifracUnweightedCommand", "getOutputFileNameTag");
- exit(1);
- }
+string UnifracUnweightedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+ if (type == "unweighted") { pattern = "[filename],unweighted-[filename],[tag],unweighted"; }
+ else if (type == "uwsummary") { pattern = "[filename],uwsummary"; }
+ else if (type == "phylip") { pattern = "[filename],[tag],[tag2],dist"; }
+ else if (type == "column") { pattern = "[filename],[tag],[tag2],dist"; }
+ else if (type == "tree") { pattern = "[filename],[tag],[tag2],tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracUnweightedCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
UnifracUnweightedCommand::UnifracUnweightedCommand(){
try {
ct = T[0]->getCountTable();
delete reader;
- sumFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("uwsummary");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ sumFile = getOutputFileName("uwsummary",variables);
outputNames.push_back(sumFile); outputTypes["uwsummary"].push_back(sumFile);
m->openOutputFile(sumFile, outSum);
counter = 0;
if (random) {
- output = new ColumnFile(outputDir + m->getSimpleName(treefile) + toString(i+1) + "." + getOutputFileNameTag("unweighted"), itersString);
- outputNames.push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + "." + getOutputFileNameTag("unweighted"));
- outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + "." + getOutputFileNameTag("unweighted"));
+ variables["[filename]"] = outputDir + m->getSimpleName(treefile);
+ variables["[tag]"] = toString(i+1);
+ string unFileName = getOutputFileName("unweighted", variables);
+ output = new ColumnFile(unFileName, itersString);
+ outputNames.push_back(unFileName); outputTypes["unweighted"].push_back(unFileName);
}
CountTable* newCt = new CountTable();
//uses method of setting groups to doNotIncludeMe
+ int sampleTime = 0;
+ if (m->debug) { sampleTime = time(NULL); }
SubSample sample;
Tree* subSampleTree = sample.getSample(T[i], ct, newCt, subsampleSize);
+ if (m->debug) { m->mothurOut("[DEBUG]: iter " + toString(thisIter) + " took " + toString(time(NULL) - sampleTime) + " seconds to sample tree.\n"); }
+
//call new weighted function
vector<double> iterData; iterData.resize(numComp,0);
Unweighted thisUnweighted(includeRoot);
}
}
- string aveFileName = outputDir + m->getSimpleName(treefile) + toString(treeNum+1) + ".unweighted.ave." + getOutputFileNameTag("phylip");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ variables["[tag]"] = toString(treeNum+1);
+ variables["[tag2]"] = "unweighted.ave";
+ string aveFileName = getOutputFileName("phylip",variables);
if (outputForm != "column") { outputNames.push_back(aveFileName); outputTypes["phylip"].push_back(aveFileName); }
else { outputNames.push_back(aveFileName); outputTypes["column"].push_back(aveFileName); }
ofstream out;
m->openOutputFile(aveFileName, out);
- string stdFileName = outputDir + m->getSimpleName(treefile) + toString(treeNum+1) + ".unweighted.std." + getOutputFileNameTag("phylip");
+ variables["[tag2]"] = "unweighted.std";
+ string stdFileName = getOutputFileName("phylip",variables);
if (outputForm != "column") { outputNames.push_back(stdFileName); outputTypes["phylip"].push_back(stdFileName); }
else { outputNames.push_back(stdFileName); outputTypes["column"].push_back(stdFileName); }
ofstream outStd;
Tree* conTree = con.getTree(newTrees);
//create a new filename
- string conFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".unweighted.cons." + getOutputFileNameTag("tree");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ variables["[tag]"] = toString(treeNum+1);
+ variables["[tag2]"] = "unweighted.cons";
+ string conFile = getOutputFileName("tree",variables);
outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile);
ofstream outTree;
m->openOutputFile(conFile, outTree);
vector<Tree*> trees;
//create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".unweighted.all." + getOutputFileNameTag("tree");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ variables["[tag]"] = toString(treeNum+1);
+ variables["[tag2]"] = "unweighted.all";
+ string outputFile = getOutputFileName("tree",variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
ofstream outAll;
void UnifracUnweightedCommand::createPhylipFile(int i) {
try {
string phylipFileName;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getSimpleName(treefile);
+ variables["[tag]"] = toString(i+1);
if ((outputForm == "lt") || (outputForm == "square")) {
- phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.phylip." + getOutputFileNameTag("phylip");
+ variables["[tag2]"] = "unweighted.phylip";
+ phylipFileName = getOutputFileName("phylip",variables);
outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName);
}else { //column
- phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.column." + getOutputFileNameTag("column");
+ variables["[tag2]"] = "unweighted.column";
+ phylipFileName = getOutputFileName("column",variables);
outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName);
}
vector<string> setParameters();
string getCommandName() { return "unifrac.unweighted"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-35. \nhttp://www.mothur.org/wiki/Unifrac.unweighted"; }
string getDescription() { return "generic tests that describes whether two or more communities have the same structure"; }
//**********************************************************************************************************************
vector<string> UnifracWeightedCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
- CommandParameter pconsensus("consensus", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pconsensus);
- CommandParameter prandom("random", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prandom);
- CommandParameter pdistance("distance", "Multiple", "column-lt-square-phylip", "column", "", "", "",false,false); parameters.push_back(pdistance);
- CommandParameter proot("root", "Boolean", "F", "", "", "", "",false,false); parameters.push_back(proot);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","weighted-wsummary",false,true,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter pconsensus("consensus", "Boolean", "", "F", "", "", "","tree",false,false); parameters.push_back(pconsensus);
+ CommandParameter prandom("random", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(prandom);
+ CommandParameter pdistance("distance", "Multiple", "column-lt-square-phylip", "column", "", "", "","phylip-column",false,false); parameters.push_back(pdistance);
+ CommandParameter proot("root", "Boolean", "F", "", "", "", "","",false,false); parameters.push_back(proot);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string UnifracWeightedCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string UnifracWeightedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+ if (type == "weighted") { pattern = "[filename],weighted-[filename],[tag],weighted"; }
+ else if (type == "wsummary") { pattern = "[filename],wsummary"; }
+ else if (type == "phylip") { pattern = "[filename],[tag],[tag2],dist"; }
+ else if (type == "column") { pattern = "[filename],[tag],[tag2],dist"; }
+ else if (type == "tree") { pattern = "[filename],[tag],[tag2],tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "weighted") { outputFileName = "weighted"; }
- else if (type == "wsummary") { outputFileName = "wsummary"; }
- else if (type == "phylip") { outputFileName = "dist"; }
- else if (type == "column") { outputFileName = "dist"; }
- else if (type == "tree") { outputFileName = "tre"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "UnifracWeightedCommand", "getOutputFileNameTag");
- exit(1);
- }
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
UnifracWeightedCommand::UnifracWeightedCommand(){
delete reader;
if (m->control_pressed) { delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; } return 0; }
-
- sumFile = outputDir + m->getSimpleName(treefile) + getOutputFileNameTag("wsummary");
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getSimpleName(treefile);
+ sumFile = getOutputFileName("wsummary",variables);
m->openOutputFile(sumFile, outSum);
outputNames.push_back(sumFile); outputTypes["wsummary"].push_back(sumFile);
vector<double> randomData; randomData.resize(numComp,0); //weighted score info for random trees. data[0] = weightedscore AB, data[1] = weightedscore AC...
if (random) {
- output = new ColumnFile(outputDir + m->getSimpleName(treefile) + toString(i+1) + "." + getOutputFileNameTag("weighted"), itersString);
- outputNames.push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + "." + getOutputFileNameTag("weighted"));
- outputTypes["weighted"].push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + "." + getOutputFileNameTag("weighted"));
+ variables["[filename]"] = outputDir + m->getSimpleName(treefile);
+ variables["[tag]"] = toString(i+1);
+ string wFileName = getOutputFileName("weighted", variables);
+ output = new ColumnFile(wFileName, itersString);
+ outputNames.push_back(wFileName); outputTypes["wweighted"].push_back(wFileName);
}
userData = weighted.getValues(T[i], processors, outputDir); //userData[0] = weightedscore
}
}
- string aveFileName = outputDir + m->getSimpleName(treefile) + toString(treeNum+1) + ".weighted.ave." + getOutputFileNameTag("phylip");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getSimpleName(treefile);
+ variables["[tag]"] = toString(treeNum+1);
+ variables["[tag2]"] = "weighted.ave";
+ string aveFileName = getOutputFileName("phylip",variables);
if (outputForm != "column") { outputNames.push_back(aveFileName); outputTypes["phylip"].push_back(aveFileName); }
else { outputNames.push_back(aveFileName); outputTypes["column"].push_back(aveFileName); }
ofstream out;
m->openOutputFile(aveFileName, out);
- string stdFileName = outputDir + m->getSimpleName(treefile) + toString(treeNum+1) + ".weighted.std." + getOutputFileNameTag("phylip");
+ variables["[tag2]"] = "weighted.std";
+ string stdFileName = getOutputFileName("phylip",variables);
if (outputForm != "column") { outputNames.push_back(stdFileName); outputTypes["phylip"].push_back(stdFileName); }
else { outputNames.push_back(stdFileName); outputTypes["column"].push_back(stdFileName); }
ofstream outStd;
Tree* conTree = con.getTree(newTrees);
//create a new filename
- string conFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".weighted.cons." + getOutputFileNameTag("tree");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ variables["[tag]"] = toString(treeNum+1);
+ variables["[tag2]"] = "weighted.cons";
+ string conFile = getOutputFileName("tree",variables);
outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile);
ofstream outTree;
m->openOutputFile(conFile, outTree);
vector<Tree*> trees;
//create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(treeNum+1) + ".weighted.all." + getOutputFileNameTag("tree");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ variables["[tag]"] = toString(treeNum+1);
+ variables["[tag2]"] = "weighted.all";
+ string outputFile = getOutputFileName("tree",variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
ofstream outAll;
//for each tree
for (int i = 0; i < T.size(); i++) {
- string phylipFileName;
- if ((outputForm == "lt") || (outputForm == "square")) {
- phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".weighted.phylip." + getOutputFileNameTag("phylip");
- outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName);
- }else { //column
- phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".weighted.column." + getOutputFileNameTag("column");
- outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName);
- }
+ string phylipFileName;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getSimpleName(treefile);
+ variables["[tag]"] = toString(i+1);
+ if ((outputForm == "lt") || (outputForm == "square")) {
+ variables["[tag2]"] = "weighted.phylip";
+ phylipFileName = getOutputFileName("phylip",variables);
+ outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName);
+ }else { //column
+ variables["[tag2]"] = "weighted.column";
+ phylipFileName = getOutputFileName("column",variables);
+ outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName);
+ }
+
ofstream out;
m->openOutputFile(phylipFileName, out);
vector<string> setParameters();
string getCommandName() { return "unifrac.weighted"; }
string getCommandCategory() { return "Hypothesis Testing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Lozupone CA, Hamady M, Kelley ST, Knight R (2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-85. \nhttp://www.mothur.org/wiki/Unifrac.weighted"; }
string getDescription() { return "generic tests that describes whether two or more communities have the same structure"; }
//**********************************************************************************************************************
vector<string> VennCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcalc("calc", "String", "", "", "", "", "",false,false); parameters.push_back(pcalc);
- CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnseqs);
- CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
- CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppermute);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcalc("calc", "String", "", "", "", "", "","",false,false); parameters.push_back(pcalc);
+ CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnseqs);
+ CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
+ CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppermute);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-
-string VennCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string VennCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "svg") { outputFileName = "svg"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "VennCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "svg") { pattern = "[filename],svg"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
vector<string> setParameters();
string getCommandName() { return "venn"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Venn"; }
string getDescription() { return "generates a Venn diagram from data provided in a shared file"; }
projects / mothur.git / commitdiff