X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitabundcommand.cpp;h=bc1cdb3ecfaa8ca528b88c2534e40c61263aacef;hb=5b72d1cf3fa48730e5bb70d59cced1e43e1fe424;hp=8131fa9195f6b8d939b27891605dd862d618964b;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp index 8131fa9..bc1cdb3 100644 --- a/splitabundcommand.cpp +++ b/splitabundcommand.cpp @@ -56,7 +56,30 @@ string SplitAbundCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string SplitAbundCommand::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 = "fasta"; } + else if (type == "list") { outputFileName = "list"; } + else if (type == "name") { outputFileName = "names"; } + else if (type == "group") { outputFileName = "groups"; } + else if (type == "accnos") { outputFileName = "accnos"; } + 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, "SplitAbundCommand", "getOutputFileNameTag"); + exit(1); + } +} //********************************************************************************************************************** SplitAbundCommand::SplitAbundCommand(){ try { @@ -434,11 +457,11 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag) { ofstream aout; ofstream rout; - string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare.list"; + string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare." + getOutputFileNameTag("list"); m->openOutputFile(rare, rout); outputNames.push_back(rare); outputTypes["list"].push_back(rare); - string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund.list"; + string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund." + getOutputFileNameTag("list"); m->openOutputFile(abund, aout); outputNames.push_back(abund); outputTypes["list"].push_back(abund); @@ -476,10 +499,12 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag) { temp2 = new ofstream; filehandles[Groups[i]+".abund"] = temp2; - m->openOutputFile(fileroot + Groups[i] + tag + ".rare.list", *(filehandles[Groups[i]+".rare"])); - m->openOutputFile(fileroot + Groups[i] + tag + ".abund.list", *(filehandles[Groups[i]+".abund"])); - outputNames.push_back(fileroot + Groups[i] + tag + ".rare.list"); outputTypes["list"].push_back(fileroot + Groups[i] + tag + ".rare.list"); - outputNames.push_back(fileroot + Groups[i] + tag + ".abund.list"); outputTypes["list"].push_back(fileroot + Groups[i] + tag + ".abund.list"); + string rareGroupFileName = fileroot + Groups[i] + tag + ".rare." + getOutputFileNameTag("list"); + string abundGroupFileName = fileroot + Groups[i] + tag + ".abund." + getOutputFileNameTag("list"); + m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"])); + m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"])); + outputNames.push_back(rareGroupFileName); outputTypes["list"].push_back(rareGroupFileName); + outputNames.push_back(abundGroupFileName); outputTypes["list"].push_back(abundGroupFileName); } map groupVector; @@ -642,11 +667,11 @@ int SplitAbundCommand::writeNames() { //namefile ofstream aout; ofstream rout; - string rare = outputDir + m->getRootName(m->getSimpleName(namefile)) + "rare.names"; + string rare = outputDir + m->getRootName(m->getSimpleName(namefile)) + "rare." + getOutputFileNameTag("name"); m->openOutputFile(rare, rout); outputNames.push_back(rare); outputTypes["name"].push_back(rare); - string abund = outputDir + m->getRootName(m->getSimpleName(namefile)) + "abund.names"; + string abund = outputDir + m->getRootName(m->getSimpleName(namefile)) + "abund." + getOutputFileNameTag("name"); m->openOutputFile(abund, aout); outputNames.push_back(abund); outputTypes["name"].push_back(abund); @@ -677,8 +702,10 @@ int SplitAbundCommand::writeNames() { //namefile temp2 = new ofstream; filehandles[Groups[i]+".abund"] = temp2; - m->openOutputFile(fileroot + Groups[i] + ".rare.names", *(filehandles[Groups[i]+".rare"])); - m->openOutputFile(fileroot + Groups[i] + ".abund.names", *(filehandles[Groups[i]+".abund"])); + string rareGroupFileName = fileroot + Groups[i] + ".rare." + getOutputFileNameTag("name"); + string abundGroupFileName = fileroot + Groups[i] + ".abund." + getOutputFileNameTag("name"); + m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"])); + m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"])); } for (map::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) { @@ -714,7 +741,7 @@ int SplitAbundCommand::writeNames() { //namefile for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { (*(filehandles[it3->first])).close(); - outputNames.push_back(fileroot + it3->first + ".names"); outputTypes["name"].push_back(fileroot + it3->first + ".names"); + outputNames.push_back(fileroot + it3->first + "." + getOutputFileNameTag("name")); outputTypes["name"].push_back(fileroot + it3->first + "." + getOutputFileNameTag("name")); delete it3->second; } } @@ -739,7 +766,7 @@ int SplitAbundCommand::writeAccnos(string tag) { ofstream rout; - string rare = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag + "rare.accnos"; + string rare = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag + "rare." + getOutputFileNameTag("accnos"); m->openOutputFile(rare, rout); outputNames.push_back(rare); outputTypes["accnos"].push_back(rare); @@ -748,7 +775,7 @@ int SplitAbundCommand::writeAccnos(string tag) { } rout.close(); - string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag + "abund.accnos"; + string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag + "abund." + getOutputFileNameTag("accnos"); m->openOutputFile(abund, aout); outputNames.push_back(abund); outputTypes["accnos"].push_back(abund); @@ -770,8 +797,8 @@ int SplitAbundCommand::writeAccnos(string tag) { temp2 = new ofstream; filehandles[Groups[i]+".abund"] = temp2; - m->openOutputFile(fileroot + tag + Groups[i] + ".rare.accnos", *(filehandles[Groups[i]+".rare"])); - m->openOutputFile(fileroot + tag + Groups[i] + ".abund.accnos", *(filehandles[Groups[i]+".abund"])); + m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".rare"])); + m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".abund"])); } //write rare @@ -795,7 +822,7 @@ int SplitAbundCommand::writeAccnos(string tag) { //close files for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { (*(filehandles[it3->first])).close(); - outputNames.push_back(fileroot + tag + it3->first + ".accnos"); outputTypes["accnos"].push_back(fileroot + tag + it3->first + ".accnos"); + outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos")); outputTypes["accnos"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos")); delete it3->second; } } @@ -818,11 +845,12 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile ofstream aout; ofstream rout; - string rare = outputDir + m->getRootName(m->getSimpleName(groupfile)) + tag + "rare.groups"; + string rare = outputDir + m->getRootName(m->getSimpleName(groupfile)) + tag + "rare." + getOutputFileNameTag("group"); m->openOutputFile(rare, rout); outputNames.push_back(rare); outputTypes["group"].push_back(rare); - string abund = outputDir + m->getRootName(m->getSimpleName(groupfile)) + tag + "abund.groups"; + string abund = outputDir + m->getRootName(m->getSimpleName(groupfile)) + tag + "abund." + getOutputFileNameTag("group"); +; m->openOutputFile(abund, aout); outputNames.push_back(abund); outputTypes["group"].push_back(abund); @@ -862,8 +890,8 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile temp2 = new ofstream; filehandles[Groups[i]+".abund"] = temp2; - m->openOutputFile(fileroot + tag + Groups[i] + ".rare.groups", *(filehandles[Groups[i]+".rare"])); - m->openOutputFile(fileroot + tag + Groups[i] + ".abund.groups", *(filehandles[Groups[i]+".abund"])); + m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".rare"])); + m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".abund"])); } for (map::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) { @@ -889,7 +917,7 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { (*(filehandles[it3->first])).close(); - outputNames.push_back(fileroot + tag + it3->first + ".groups"); outputTypes["group"].push_back(fileroot + tag + it3->first + ".groups"); + outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group")); outputTypes["group"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group")); delete it3->second; } } @@ -912,11 +940,11 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile ofstream aout; ofstream rout; - string rare = outputDir + m->getRootName(m->getSimpleName(fastafile)) + tag + "rare.fasta"; + string rare = outputDir + m->getRootName(m->getSimpleName(fastafile)) + tag + "rare." + getOutputFileNameTag("fasta"); m->openOutputFile(rare, rout); outputNames.push_back(rare); outputTypes["fasta"].push_back(rare); - string abund = outputDir + m->getRootName(m->getSimpleName(fastafile)) + tag + "abund.fasta"; + string abund = outputDir + m->getRootName(m->getSimpleName(fastafile)) + tag + "abund." + getOutputFileNameTag("fasta"); m->openOutputFile(abund, aout); outputNames.push_back(abund); outputTypes["fasta"].push_back(abund); @@ -963,8 +991,8 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile temp2 = new ofstream; filehandles[Groups[i]+".abund"] = temp2; - m->openOutputFile(fileroot + tag + Groups[i] + ".rare.fasta", *(filehandles[Groups[i]+".rare"])); - m->openOutputFile(fileroot + tag + Groups[i] + ".abund.fasta", *(filehandles[Groups[i]+".abund"])); + m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".rare"])); + m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".abund"])); } //open input file @@ -1009,7 +1037,7 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { (*(filehandles[it3->first])).close(); - outputNames.push_back(fileroot + tag + it3->first + ".fasta"); outputTypes["fasta"].push_back(fileroot + tag + it3->first + ".fasta"); + outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta")); outputTypes["fasta"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta")); delete it3->second; } }