string helpString = "";
helpString += "The shhh.seqs command reads a fasta and name file and ....\n";
helpString += "The shhh.seqs command parameters are fasta, name, group, sigma and processors.\n";
- helpString += "The fasta parameter allows you to enter the fasta file containing your potentially sequences, and is required, unless you have a valid current fasta file. \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 name parameter allows you to provide a name file associated with your fasta file. It is required. \n";
helpString += "The group parameter allows you to provide a group file. When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
else { m->setGroupFile(groupfile); }
string temp = validParameter.validFile(parameters, "sigma", false); if(temp == "not found"){ temp = "0.01"; }
- convert(temp, sigma);
-
+ m->mothurConvert(temp, sigma);
+ sigma = 1/sigma;
+
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
catch(exception& e) {
lines.push_back(linePair(startIndex, endIndex));
}
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
string inputString = "fasta=" + fastaFile + ", name=" + nameFile;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
-
+ m->mothurCalling = true;
+
Command* uniqueCommand = new DeconvoluteCommand(inputString);
uniqueCommand->execute();
map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
delete uniqueCommand;
-
+ m->mothurCalling = false;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
string newnameFile = filenames["name"][0];