helpString += "The cluster.fragments command should be in the following format: \n";
helpString += "cluster.fragments(fasta=yourFastaFile, names=yourNamesFile) \n";
helpString += "Example cluster.fragments(fasta=amazon.fasta).\n";
- helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
return helpString;
}
catch(exception& e) {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (fastafile == "not open") { fastafile = ""; abort = true; }
+ else { m->setFastaFile(fastafile); }
//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); }
// ...at some point should added some additional type checking...
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not found") { namefile = ""; }
- else if (namefile == "not open") { abort = true; }
- else { readNameFile(); }
+ else if (namefile == "not open") { namefile = ""; abort = true; }
+ else { readNameFile(); m->setNameFile(namefile); }
string temp;
temp = validParameter.validFile(parameters, "diffs", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, diffs);
+ m->mothurConvert(temp, diffs);
temp = validParameter.validFile(parameters, "percent", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, percent);
+ m->mothurConvert(temp, percent);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
string newFastaFile = fileroot + "fragclust.fasta";
- string newNamesFile = fileroot + "names";
+ string newNamesFile = fileroot + "fragclust.names";
if (m->control_pressed) { return 0; }
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
- if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();