X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.cpp;h=4cec90f567c764e8770987c150b67b5ececc0d35;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=5f5435f8679a9b65bb4799dae9dff30555818d3c;hpb=f06fdb807822f8e06db003ed809c87250905cfc8;p=mothur.git diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp index 5f5435f..4cec90f 100644 --- a/removelineagecommand.cpp +++ b/removelineagecommand.cpp @@ -57,8 +57,31 @@ string RemoveLineageCommand::getHelpString(){ exit(1); } } - - +//********************************************************************************************************************** +string RemoveLineageCommand::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 = "pick" + m->getExtension(inputName); } + else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "alignreport") { outputFileName = "pick.align.report"; } + 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, "RemoveLineageCommand", "getOutputFileNameTag"); + exit(1); + } +} //********************************************************************************************************************** RemoveLineageCommand::RemoveLineageCommand(){ try { @@ -169,16 +192,19 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } + if (fastafile == "not open") { fastafile = ""; abort = true; } else if (fastafile == "not found") { fastafile = ""; } + else { m->setFastaFile(fastafile); } 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); } groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } alignfile = validParameter.validFile(parameters, "alignreport", true); if (alignfile == "not open") { abort = true; } @@ -187,14 +213,15 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { abort = true; } else if (listfile == "not found") { listfile = ""; } + else { m->setListFile(listfile); } taxfile = validParameter.validFile(parameters, "taxonomy", true); - if (taxfile == "not open") { abort = true; } + if (taxfile == "not open") { taxfile = ""; abort = true; } else if (taxfile == "not found") { taxfile = m->getTaxonomyFile(); if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); } else { m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; } - } + }else { m->setTaxonomyFile(taxfile); } string usedDups = "true"; string temp = validParameter.validFile(parameters, "dups", false); @@ -216,7 +243,12 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; } if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; } - + + if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){ + vector files; files.push_back(fastafile); files.push_back(taxfile); + parser.getNameFile(files); + } + } } @@ -243,7 +275,7 @@ int RemoveLineageCommand::execute(){ if (listfile != "") { readList(); } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } if (outputNames.size() != 0) { m->mothurOutEndLine(); @@ -293,8 +325,7 @@ int RemoveLineageCommand::readFasta(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile); ofstream out; m->openOutputFile(outputFileName, out); @@ -305,7 +336,7 @@ int RemoveLineageCommand::readFasta(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } Sequence currSeq(in); name = currSeq.getName(); @@ -339,8 +370,7 @@ int RemoveLineageCommand::readList(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile); ofstream out; m->openOutputFile(outputFileName, out); @@ -359,7 +389,7 @@ int RemoveLineageCommand::readList(){ //for each bin for (int i = 0; i < list.getNumBins(); i++) { - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } //parse out names that are in accnos file string binnames = list.get(i); @@ -410,8 +440,7 @@ int RemoveLineageCommand::readName(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(namefile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile); ofstream out; m->openOutputFile(outputFileName, out); @@ -422,7 +451,7 @@ int RemoveLineageCommand::readName(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> firstCol; in >> secondCol; @@ -488,8 +517,7 @@ int RemoveLineageCommand::readGroup(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile); ofstream out; m->openOutputFile(outputFileName, out); @@ -500,7 +528,7 @@ int RemoveLineageCommand::readGroup(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column in >> group; //read from second column @@ -531,7 +559,7 @@ int RemoveLineageCommand::readTax(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile); + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile); ofstream out; m->openOutputFile(outputFileName, out); @@ -551,14 +579,15 @@ int RemoveLineageCommand::readTax(){ if (hasConPos != string::npos) { taxonsHasConfidence[i] = true; searchTaxons[i] = getTaxons(listOfTaxons[i]); - noConfidenceTaxons[i] = removeConfidences(listOfTaxons[i]); + noConfidenceTaxons[i] = listOfTaxons[i]; + m->removeConfidences(noConfidenceTaxons[i]); } } while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column in >> tax; //read from second column @@ -573,7 +602,8 @@ int RemoveLineageCommand::readTax(){ int hasConfidences = tax.find_first_of('('); if (hasConfidences != string::npos) { - newtax = removeConfidences(tax); + newtax = tax; + m->removeConfidences(newtax); } int pos = newtax.find(noConfidenceTaxons[j]); @@ -605,7 +635,8 @@ int RemoveLineageCommand::readTax(){ string noNewTax = tax; int hasConfidences = tax.find_first_of('('); if (hasConfidences != string::npos) { - noNewTax = removeConfidences(tax); + noNewTax = tax; + m->removeConfidences(noNewTax); } int pos = noNewTax.find(noConfidenceTaxons[j]); @@ -722,36 +753,13 @@ vector< map > RemoveLineageCommand::getTaxons(string tax) { exit(1); } } -/**************************************************************************************************/ -string RemoveLineageCommand::removeConfidences(string tax) { - try { - - string taxon = ""; - int taxLength = tax.length(); - for(int i=0;ierrorOut(e, "RemoveLineageCommand", "removeConfidences"); - exit(1); - } -} //********************************************************************************************************************** //alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name int RemoveLineageCommand::readAlign(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report"; + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport"); ofstream out; m->openOutputFile(outputFileName, out); @@ -770,7 +778,7 @@ int RemoveLineageCommand::readAlign(){ out << endl; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column