X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=subsamplecommand.cpp;h=35441013919fbfe55452532e735b5bd1d7673f2f;hb=8e67e9de1b200106bea5a468ac02125954656499;hp=717b1d3231c20368a2d23e9b86d52a6707f03b12;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp index 717b1d3..3544101 100644 --- a/subsamplecommand.cpp +++ b/subsamplecommand.cpp @@ -63,6 +63,33 @@ string SubSampleCommand::getHelpString(){ exit(1); } } +//********************************************************************************************************************** +string SubSampleCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::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 { @@ -479,8 +506,7 @@ int SubSampleCommand::getSubSampleFasta() { 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); @@ -528,6 +554,7 @@ int SubSampleCommand::getSubSampleFasta() { 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(); @@ -542,10 +569,11 @@ int SubSampleCommand::getSubSampleFasta() { 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(); @@ -558,7 +586,7 @@ int SubSampleCommand::getSubSampleFasta() { 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); @@ -639,34 +667,13 @@ int SubSampleCommand::getNames() { int SubSampleCommand::readNames() { try { - ifstream in; - m->openInputFile(namefile, in); - - string thisname, repnames; - map >::iterator it; - - while(!in.eof()){ - - if (m->control_pressed) { in.close(); return 0; } - - in >> thisname; m->gobble(in); //read from first column - in >> repnames; //read from second column - - it = nameMap.find(thisname); - if (it == nameMap.end()) { - - vector splitRepNames; - m->splitAtComma(repnames, splitRepNames); - - nameMap[thisname] = splitRepNames; - for (int i = 0; i < splitRepNames.size(); i++) { names.push_back(splitRepNames[i]); } - - }else{ m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine(); } - - m->gobble(in); - } - in.close(); - + nameMap.clear(); + m->readNames(namefile, nameMap); + + //save names of all sequences + map >::iterator it; + for (it = nameMap.begin(); it != nameMap.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { names.push_back((it->second)[i]); } } + return 0; } @@ -801,8 +808,7 @@ int SubSampleCommand::processShared(vector& thislookup) { 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 subsampledLabels = sample.getSample(thislookup, size); @@ -840,8 +846,7 @@ int SubSampleCommand::getSubSampleList() { 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); @@ -1185,8 +1190,7 @@ int SubSampleCommand::getSubSampleRabund() { 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); @@ -1340,8 +1344,7 @@ int SubSampleCommand::getSubSampleSabund() { 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);