#include "secondarystructurecommand.h"
#include "sequence.hpp"
+#include "counttable.h"
//**********************************************************************************************************************
-vector<string> AlignCheckCommand::getValidParameters(){
+vector<string> AlignCheckCommand::setParameters(){
try {
- string Array[] = {"fasta", "name","map", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "AlignCheckCommand", "getValidParameters");
+ m->errorOut(e, "AlignCheckCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-AlignCheckCommand::AlignCheckCommand(){
+string AlignCheckCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["aligncheck"] = tempOutNames;
+ string helpString = "";
+ helpString += "The align.check command reads a fasta file and map file as well as an optional name or count file.\n";
+ helpString += "It outputs a file containing the secondary structure matches in the .align.check file.\n";
+ helpString += "The align.check command parameters are fasta and map, both are required.\n";
+ helpString += "The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n";
+ helpString += "Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
+ m->errorOut(e, "AlignCheckCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> AlignCheckCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta","map"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCheckCommand", "getRequiredParameters");
- exit(1);
- }
+string AlignCheckCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ 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);
+ }
}
//**********************************************************************************************************************
-vector<string> AlignCheckCommand::getRequiredFiles(){
+AlignCheckCommand::AlignCheckCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["aligncheck"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "AlignCheckCommand", "getRequiredFiles");
+ m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
exit(1);
}
}
//allow user to run help
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","name","map", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = 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; }
+ }
}
//check for required parameters
else if (mapfile == "not found") { mapfile = ""; m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; }
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; m->mothurOut("You must provide an fasta file."); m->mothurOutEndLine(); abort = true; }
+ if (fastafile == "not open") { fastafile = ""; 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") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+ if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
//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 = "";
outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
-
+
+ if (countfile == "") {
+ if ((namefile == "") && (fastafile != "")){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
}
}
catch(exception& e) {
- m->errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-void AlignCheckCommand::help(){
- try {
- m->mothurOut("The align.check command reads a fasta file and map file.\n");
- m->mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n");
- m->mothurOut("The align.check command parameters are fasta and map, both are required.\n");
- m->mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n");
- m->mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCheckCommand", "help");
+ m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
exit(1);
}
}
-
//**********************************************************************************************************************
int AlignCheckCommand::execute(){
readMap();
if (namefile != "") { nameMap = m->readNames(namefile); }
+ else if (countfile != "") {
+ CountTable ct;
+ ct.readTable(countfile, false);
+ nameMap = ct.getNameMap();
+ }
if (m->control_pressed) { return 0; }
m->openInputFile(fastafile, in);
ofstream out;
- string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outfile = getOutputFileName("aligncheck",variables);
m->openOutputFile(outfile, out);
int count = 0;
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outfile); return 0; }
Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
if (haderror == 1) { m->control_pressed = true; break; }
int num = 1;
- if (namefile != "") {
+ if ((namefile != "") || (countfile != "")) {
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(seq.getName());
- if (it == nameMap.end()) { cout << "[ERROR]: " << seq.getName() << " is not in your namefile, please correct." << endl; m->control_pressed = true; }
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + seq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
else { num = it->second; }
}
in.close();
out.close();
- if (m->control_pressed) { remove(outfile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
sort(pound.begin(), pound.end());
sort(dash.begin(), dash.end());
int ptile97_5 = int(size * 0.975);
int ptile100 = size - 1;
- if (m->control_pressed) { remove(outfile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
m->mothurOutEndLine();
m->mothurOut("\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal"); m->mothurOutEndLine();
m->mothurOut("75%-tile:\t" + toString(pound[ptile75]) + "\t" + toString(dash[ptile75]) + "\t" + toString(plus[ptile75]) + "\t" + toString(equal[ptile75]) + "\t" + toString(loop[ptile75]) + "\t" + toString(tilde[ptile75]) + "\t" + toString(total[ptile75])); m->mothurOutEndLine();
m->mothurOut("97.5%-tile:\t" + toString(pound[ptile97_5]) + "\t" + toString(dash[ptile97_5]) + "\t" + toString(plus[ptile97_5]) + "\t" + toString(equal[ptile97_5]) + "\t" + toString(loop[ptile97_5]) + "\t" + toString(tilde[ptile97_5]) + "\t" + toString(total[ptile97_5])); m->mothurOutEndLine();
m->mothurOut("Maximum:\t" + toString(pound[ptile100]) + "\t" + toString(dash[ptile100]) + "\t" + toString(plus[ptile100]) + "\t" + toString(equal[ptile100]) + "\t" + toString(loop[ptile100]) + "\t" + toString(tilde[ptile100]) + "\t" + toString(total[ptile100])); m->mothurOutEndLine();
- if (namefile == "") { m->mothurOut("# of Seqs:\t" + toString(count)); m->mothurOutEndLine(); }
+ if ((namefile == "") && (countfile == "")) { m->mothurOut("# of Seqs:\t" + toString(count)); m->mothurOutEndLine(); }
else { m->mothurOut("# of unique seqs:\t" + toString(count)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(size)); m->mothurOutEndLine(); }
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outfile); m->mothurOutEndLine(); outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
m->mothurOutEndLine();
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