}
}
//**********************************************************************************************************************
+string SplitGroupCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ 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 = "fasta"; }
+ else if (type == "name") { outputFileName = "names"; }
+ 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, "SplitGroupCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(){
try {
abort = true; calledHelp = true;
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
//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(groupfile); }
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
- string newFasta = fastafileRoot + Groups[i] + ".fasta";
- string newName = namefileRoot + Groups[i] + ".names";
+ string newFasta = fastafileRoot + Groups[i] + "." + getOutputFileNameTag("fasta");
+ string newName = namefileRoot + Groups[i] + "." + getOutputFileNameTag("name");
parser->getSeqs(Groups[i], newFasta, false);
outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);