#include "inputdata.h"
//**********************************************************************************************************************
-vector<string> ConsensusSeqsCommand::getValidParameters(){
+vector<string> ConsensusSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta", "list", "name", "label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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 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);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "getValidParameters");
+ m->errorOut(e, "ConsensusSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-ConsensusSeqsCommand::ConsensusSeqsCommand(){
+string ConsensusSeqsCommand::getHelpString(){
try {
- abort = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["summary"] = tempOutNames;
+ string helpString = "";
+ helpString += "The consensus.seqs command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.\n";
+ helpString += "The consensus.seqs command parameters are fasta, list, name, cutoff and label.\n";
+ helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
+ helpString += "The list parameter allows you to enter a your list file. \n";
+ helpString += "The name parameter allows you to enter a names file associated with the fasta file. \n";
+ helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
+ helpString += "The cutoff parameter allows you set a percentage of sequences that support the base. For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences.\n";
+ helpString += "The consensus.seqs command should be in the following format: \n";
+ helpString += "consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n";
+ helpString += "Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
+ m->errorOut(e, "ConsensusSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> ConsensusSeqsCommand::getRequiredParameters(){
+string ConsensusSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
try {
- string Array[] = {"fasta", "list"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ 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 = "cons.fasta"; }
+ else if (type == "name") { outputFileName = "cons.names"; }
+ 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", "getRequiredParameters");
+ m->errorOut(e, "ConsensusSeqsCommand", "getOutputFileNameTag");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> ConsensusSeqsCommand::getRequiredFiles(){
+ConsensusSeqsCommand::ConsensusSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "DegapSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "ConsensusSeqsCommand", "ConsensusSeqsCommand");
exit(1);
}
}
//***************************************************************************************************************
ConsensusSeqsCommand::ConsensusSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta","list","name","label", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the consensus.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
- else if (namefile == "not found") { namefile = ""; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
+ else { m->setListFile(listfile); }
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else { allLines = 1; }
}
+ string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
+ m->mothurConvert(temp, cutoff);
+
//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); }
-
+
+ if (namefile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
catch(exception& e) {
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ConsensusSeqsCommand::help(){
- try {
- m->mothurOut("The consensus.seqs command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.\n");
- m->mothurOut("The consensus.seqs command parameters are fasta, list, name and label.\n");
- m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n");
- m->mothurOut("The list parameter allows you to enter a your list file. \n");
- m->mothurOut("The name parameter allows you to enter a names file associated with the fasta file. \n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n");
- m->mothurOut("The consensus.seqs command should be in the following format: \n");
- m->mothurOut("consensus.seqs(fasta=yourFastaFile, list=yourListFile) \n");
- m->mothurOut("Example: consensus.seqs(fasta=abrecovery.align, list=abrecovery.fn.list) \n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "ConsensusSeqsCommand", "help");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-ConsensusSeqsCommand::~ConsensusSeqsCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int ConsensusSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
readFasta();
if (listfile == "") {
ofstream outSummary;
- string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.summary";
+ string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
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)) + "cons.fasta";
+ string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
m->openOutputFile(outputFastaFile, outFasta);
outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
int seqLength = 0;
for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
- if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
string seq = fastaMap[it->second];
seqs.push_back(seq);
//get counts
for (int j = 0; j < seqLength; j++) {
- if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
int numDots = 0;
}
char conBase = '.';
- if (numDots != seqs.size()) { conBase = getBase(counts); }
+ if (numDots != seqs.size()) { conBase = getBase(counts, seqs.size()); }
consSeq += conBase;
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete list; delete input; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete list; delete input; return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } if (list != NULL) { delete list; } delete input; return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
try{
ofstream outSummary;
- string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + ".cons.summary";
+ string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("summary");
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() + ".cons.names";
+ string outputNameFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("name");
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() + ".cons.fasta";
+ string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + list->getLabel() + getOutputFileNameTag("fasta");
m->openOutputFile(outputFastaFile, outFasta);
outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
}
char conBase = '.';
- if (numDots != seqs.size()) { conBase = getBase(counts); }
+ if (numDots != seqs.size()) { conBase = getBase(counts, seqs.size()); }
consSeq += conBase;
}
//***************************************************************************************************************
-char ConsensusSeqsCommand::getBase(vector<int> counts){ //A,T,G,C,Gap
+char ConsensusSeqsCommand::getBase(vector<int> counts, int size){ //A,T,G,C,Gap
try{
/* A = adenine
* C = cytosine
char conBase = 'N';
+ //zero out counts that don't make the cutoff
+ float percentage = (100.0 - cutoff) / 100.0;
+ int zeroCutoff = percentage * size;
+
+ for (int i = 0; i < counts.size(); i++) {
+ if (counts[i] < zeroCutoff) { counts[i] = 0; }
+ }
+
//any
if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) { conBase = 'n'; }
//any no gap
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] != 0) && (counts[4] == 0)) { conBase = 'C'; }
//only gap
else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) { conBase = '-'; }
+ //cutoff removed all counts
+ else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) { conBase = 'N'; }
else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
return conBase;
int ConsensusSeqsCommand::readNames(){
try{
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string thisname, repnames;
- map<string, string>::iterator it;
-
- bool error = false;
-
- while(!in.eof()){
-
- if (m->control_pressed) { break; }
-
- in >> thisname; m->gobble(in); //read from first column
- in >> repnames; //read from second column
-
- it = nameMap.find(thisname);
+ map<string, string> temp;
+ map<string, string>::iterator it;
+ bool error = false;
+
+ m->readNames(namefile, temp); //use central buffered read
+
+ for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end(); itTemp++) {
+ string thisname, repnames;
+ thisname = itTemp->first;
+ repnames = itTemp->second;
+
+ it = nameMap.find(thisname);
if (it != nameMap.end()) { //then this sequence was in the fastafile
-
+ nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
+
vector<string> splitRepNames;
m->splitAtComma(repnames, splitRepNames);
- nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
}else{ m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
-
- m->gobble(in);
- }
-
- in.close();
-
+ }
+
if (error) { m->control_pressed = true; }
return 0;
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