exit(1);
}
}
+//**********************************************************************************************************************
+string SubSampleCommand::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 = "subsample" + m->getExtension(inputName); }
+ else if (type == "sabund") { outputFileName = "subsample" + m->getExtension(inputName); }
+ else if (type == "name") { outputFileName = "subsample" + m->getExtension(inputName); }
+ else if (type == "group") { outputFileName = "subsample" + m->getExtension(inputName); }
+ else if (type == "list") { outputFileName = "subsample" + m->getExtension(inputName); }
+ else if (type == "rabund") { outputFileName = "subsample" + m->getExtension(inputName); }
+ else if (type == "shared") { outputFileName = "subsample" + m->getExtension(inputName); }
+ 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, "SubSampleCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
SubSampleCommand::SubSampleCommand(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile);
-
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
ofstream out;
m->openOutputFile(outputFileName, out);
if (namefile != "") {
m->mothurOut("Deconvoluting subsampled fasta file... "); m->mothurOutEndLine();
+ string outputNameFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
//use unique.seqs to create new name and fastafile
string inputString = "fasta=" + outputFileName;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
delete uniqueCommand;
m->mothurCalling = false;
- outputTypes["name"].push_back(filenames["name"][0]); outputNames.push_back(filenames["name"][0]);
- m->mothurRemove(outputFileName);
- outputFileName = filenames["fasta"][0];
-
+ m->renameFile(filenames["name"][0], outputNameFileName);
+ m->renameFile(filenames["fasta"][0], outputFileName);
+
+ outputTypes["name"].push_back(outputNameFileName); outputNames.push_back(outputNameFileName);
+
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Done."); m->mothurOutEndLine();
string groupOutputDir = outputDir;
if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); }
- string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
+ string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
ofstream outGroup;
m->openOutputFile(groupOutputFileName, outGroup);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + ".subsample" + m->getExtension(sharedfile);
-
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + getOutputFileNameTag("shared", sharedfile);
SubSample sample;
vector<string> subsampledLabels = sample.getSample(thislookup, size);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "subsample" + m->getExtension(listfile);
-
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "subsample" + m->getExtension(rabundfile);
-
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + getOutputFileNameTag("rabund", rabundfile);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "subsample" + m->getExtension(sabundfile);
-
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + getOutputFileNameTag("sabund", sabundfile);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);