#include "deconvolutecommand.h"
/**************************************************************************************/
-DeconvoluteCommand::DeconvoluteCommand(string option) {
+DeconvoluteCommand::DeconvoluteCommand(string option) {
try {
abort = false;
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
//check for required parameters
inFastaName = validParameter.validFile(parameters, "fasta", true);
if (inFastaName == "not open") { abort = true; }
- else if (inFastaName == "not found") { inFastaName = ""; mothurOut("fasta is a required parameter for the unique.seqs command."); mothurOutEndLine(); abort = true; }
+ else if (inFastaName == "not found") { inFastaName = ""; m->mothurOut("fasta is a required parameter for the unique.seqs command."); 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 += hasPath(inFastaName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it
}
oldNameMapFName = validParameter.validFile(parameters, "name", true);
}
catch(exception& e) {
- errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+ m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
exit(1);
}
}
void DeconvoluteCommand::help(){
try {
- mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
- mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n");
- mothurOut("If the sequence is unique the second column will just contain its name. \n");
- mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
- mothurOut("The unique.seqs command should be in the following format: \n");
- mothurOut("unique.seqs(fasta=yourFastaFile) \n");
+ m->mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
+ m->mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n");
+ m->mothurOut("If the sequence is unique the second column will just contain its name. \n");
+ m->mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
+ m->mothurOut("The unique.seqs command should be in the following format: \n");
+ m->mothurOut("unique.seqs(fasta=yourFastaFile) \n");
}
catch(exception& e) {
- errorOut(e, "DeconvoluteCommand", "help");
+ m->errorOut(e, "DeconvoluteCommand", "help");
exit(1);
}
}
if (abort == true) { return 0; }
//prepare filenames and open files
- string outNameFile = outputDir + getRootName(getSimpleName(inFastaName)) + "names";
- string outFastaFile = outputDir + getRootName(getSimpleName(inFastaName)) + "unique" + getExtension(inFastaName);
+ string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
+ string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
FastaMap fastamap;
if(oldNameMapFName == "") { fastamap.readFastaFile(inFastaName); }
else { fastamap.readFastaFile(inFastaName, oldNameMapFName); }
+ if (m->control_pressed) { return 0; }
+
fastamap.printCondensedFasta(outFastaFile);
fastamap.printNamesFile(outNameFile);
+ if (m->control_pressed) { remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outFastaFile); m->mothurOutEndLine();
+ m->mothurOut(outNameFile); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+
+
return 0;
}
catch(exception& e) {
- errorOut(e, "DeconvoluteCommand", "execute");
+ m->errorOut(e, "DeconvoluteCommand", "execute");
exit(1);
}
}