X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=a422c8883ea9f172fe076961fa7705cb548e767e;hb=15dfbabd5aa00c468a43f1f99cb73b2ebc5b5e3f;hp=1a9c1fb5ca3d56896e605803bd98d472428f9f01;hpb=64581f6d0e63e67d4e119601bea695ebb3f52a13;p=mothur.git diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp index 1a9c1fb..a422c88 100644 --- a/chimeraslayercommand.cpp +++ b/chimeraslayercommand.cpp @@ -23,15 +23,15 @@ vector ChimeraSlayerCommand::setParameters(){ CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "",false,false); parameters.push_back(pmismatch); CommandParameter pminsim("minsim", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminsim); CommandParameter pmincov("mincov", "Number", "", "70", "", "", "",false,false); parameters.push_back(pmincov); - CommandParameter pminsnp("minsnp", "Number", "", "100", "", "", "",false,false); parameters.push_back(pminsnp); + CommandParameter pminsnp("minsnp", "Number", "", "10", "", "", "",false,false); parameters.push_back(pminsnp); CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs); - CommandParameter psearch("search", "Multiple", "kmer-blast-distance", "distance", "", "", "",false,false); parameters.push_back(psearch); + CommandParameter psearch("search", "Multiple", "kmer-blast", "blast", "", "", "",false,false); parameters.push_back(psearch); CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); - CommandParameter prealign("realign", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prealign); + CommandParameter prealign("realign", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(prealign); CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim); CommandParameter psplit("split", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psplit); CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "",false,false); parameters.push_back(pnumwanted); - CommandParameter piters("iters", "Number", "", "100", "", "", "",false,false); parameters.push_back(piters); + CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters); CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "",false,false); parameters.push_back(pdivergence); CommandParameter pparents("parents", "Number", "", "3", "", "", "",false,false); parameters.push_back(pparents); CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement); @@ -53,7 +53,7 @@ string ChimeraSlayerCommand::getHelpString(){ string helpString = ""; helpString += "The chimera.slayer command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n"; helpString += "This command was modeled after the chimeraSlayer written by the Broad Institute.\n"; - helpString += "The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"; //realign, + helpString += "The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment, numwanted, and realign.\n"; helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n"; helpString += "The name parameter allows you to provide a name file, if you are using template=self. \n"; helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n"; @@ -72,13 +72,13 @@ string ChimeraSlayerCommand::getHelpString(){ helpString += "The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n"; helpString += "The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n"; helpString += "The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n"; - helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n"; + helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=1000.\n"; helpString += "The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n"; helpString += "The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n"; helpString += "The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n"; - helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n"; - helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n"; - helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. \n"; + helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n"; + helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are blast, and kmer, default blast. \n"; + helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true. \n"; helpString += "The chimera.slayer command should be in the following format: \n"; helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n"; helpString += "Example: chimera.slayer(fasta=AD.align, reference=core_set_aligned.imputed.fasta, search=kmer) \n"; @@ -112,6 +112,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -148,47 +149,63 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < fastaFileNames.size(); i++) { - if (inputDir != "") { - string path = m->hasPath(fastaFileNames[i]); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; } - } - - int ableToOpen; - ifstream in; - ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror"); - - //if you can't open it, try default location - if (ableToOpen == 1) { - if (m->getDefaultPath() != "") { //default path is set - string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]); - m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - fastaFileNames[i] = tryPath; + bool ignore = false; + if (fastaFileNames[i] == "current") { + fastaFileNames[i] = m->getFastaFile(); + if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; } } - if (ableToOpen == 1) { - if (m->getOutputDir() != "") { //default path is set - string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]); - m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - fastaFileNames[i] = tryPath; + if (!ignore) { + + if (inputDir != "") { + string path = m->hasPath(fastaFileNames[i]); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; } } - } - - in.close(); + + int ableToOpen; + ifstream in; + + ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror"); - if (ableToOpen == 1) { - m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); - //erase from file list - fastaFileNames.erase(fastaFileNames.begin()+i); - i--; + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getDefaultPath() != "") { //default path is set + string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; + } + } + + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; + } + } + + in.close(); + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; + } } } @@ -206,47 +223,63 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < nameFileNames.size(); i++) { - if (inputDir != "") { - string path = m->hasPath(nameFileNames[i]); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; } - } - - int ableToOpen; - ifstream in; - - ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror"); - //if you can't open it, try default location - if (ableToOpen == 1) { - if (m->getDefaultPath() != "") { //default path is set - string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]); - m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - nameFileNames[i] = tryPath; + bool ignore = false; + if (nameFileNames[i] == "current") { + nameFileNames[i] = m->getNameFile(); + if (nameFileNames[i] != "") { m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true; + //erase from file list + nameFileNames.erase(nameFileNames.begin()+i); + i--; } } - if (ableToOpen == 1) { - if (m->getOutputDir() != "") { //default path is set - string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]); - m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - nameFileNames[i] = tryPath; + if (!ignore) { + + if (inputDir != "") { + string path = m->hasPath(nameFileNames[i]); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; } + } + + int ableToOpen; + ifstream in; + + ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror"); + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getDefaultPath() != "") { //default path is set + string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]); + m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + nameFileNames[i] = tryPath; + } + } + + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]); + m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + nameFileNames[i] = tryPath; + } + } + + in.close(); + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + nameFileNames.erase(nameFileNames.begin()+i); + i--; } - } - - in.close(); - - if (ableToOpen == 1) { - m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); - //erase from file list - nameFileNames.erase(nameFileNames.begin()+i); - i--; } } @@ -272,9 +305,10 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { templatefile = validParameter.validFile(parameters, "reference", true); if (templatefile == "not open") { abort = true; } - else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; } + else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.slayer command, unless and namefile is given."); m->mothurOutEndLine(); abort = true; } } - } + }else if (hasName) { templatefile = "self"; } + else { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; } string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); @@ -304,13 +338,13 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; } convert(temp, minBS); - temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "100"; } + temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; } convert(temp, minSNP); temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; } convert(temp, parents); - temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "f"; } + temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "t"; } realign = m->isTrue(temp); temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; } @@ -319,9 +353,9 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { temp = validParameter.validFile(parameters, "split", false); if (temp == "not found") { temp = "f"; } trimera = m->isTrue(temp); - search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; } + search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "blast"; } - temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; } + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } convert(temp, iters); temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; } @@ -330,7 +364,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; } convert(temp, numwanted); - if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; } + if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; } } } catch(exception& e) { @@ -342,7 +376,6 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { int ChimeraSlayerCommand::execute(){ try{ - if (abort == true) { if (calledHelp) { return 0; } return 2; } for (int s = 0; s < fastaFileNames.size(); s++) { @@ -381,12 +414,12 @@ int ChimeraSlayerCommand::execute(){ //sort fastafile by abundance, returns new sorted fastafile name m->mothurOut("Sorting fastafile according to abundance..."); cout.flush(); - fastaFileNames[s] = sortFastaFile(fastaFileNames[s], nameFile); + map priority = sortFastaFile(fastaFileNames[s], nameFile); m->mothurOut("Done."); m->mothurOutEndLine(); if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } - chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign); + chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign); } if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it @@ -456,36 +489,45 @@ int ChimeraSlayerCommand::execute(){ MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs - //send file positions to all processes - for(int i = 1; i < processors; i++) { - MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); - MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + if (templatefile != "self") { //if template=self we can only use 1 processor + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } } - //figure out how many sequences you have to align numSeqsPerProcessor = numSeqs / processors; int startIndex = pid * numSeqsPerProcessor; if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } - + + if (templatefile == "self") { //if template=self we can only use 1 processor + startIndex = 0; + numSeqsPerProcessor = numSeqs; + } + //do your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); delete chimera; return 0; } }else{ //you are a child process - MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); - MPIPos.resize(numSeqs+1); - MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + if (templatefile != "self") { //if template=self we can only use 1 processor + MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + MPIPos.resize(numSeqs+1); + MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); - //figure out how many sequences you have to align - numSeqsPerProcessor = numSeqs / processors; - int startIndex = pid * numSeqsPerProcessor; - if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } + //figure out how many sequences you have to align + numSeqsPerProcessor = numSeqs / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } - //do your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); + //do your part + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); - if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + + } } //close files @@ -626,7 +668,7 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); string candidateAligned = candidateSeq->getAligned(); - + if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file if (candidateSeq->getAligned().length() != templateSeqsLength) { @@ -689,7 +731,6 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f } count++; } - delete candidateSeq; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) unsigned long int pos = inFASTA.tellg(); @@ -698,6 +739,7 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f if (inFASTA.eof()) { break; } #endif + delete candidateSeq; //report progress if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } } @@ -939,9 +981,9 @@ int ChimeraSlayerCommand::divideInHalf(Sequence querySeq, string& leftQuery, str } } /**************************************************************************************************/ - -string ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) { +map ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) { try { + map nameAbund; //read through fastafile and store info map seqs; @@ -950,7 +992,7 @@ string ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) { while (!in.eof()) { - if (m->control_pressed) { in.close(); return ""; } + if (m->control_pressed) { in.close(); return nameAbund; } Sequence seq(in); m->gobble(in); seqs[seq.getName()] = seq.getAligned(); @@ -962,10 +1004,10 @@ string ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) { vector nameMapCount; int error = m->readNames(nameFile, nameMapCount, seqs); - if (m->control_pressed) { return ""; } + if (m->control_pressed) { return nameAbund; } - if (error == 1) { m->control_pressed = true; return ""; } - if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return ""; } + if (error == 1) { m->control_pressed = true; return nameAbund; } + if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return nameAbund; } sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes); @@ -976,12 +1018,13 @@ string ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) { //print new file in order of for (int i = 0; i < nameMapCount.size(); i++) { out << ">" << nameMapCount[i].name << endl << nameMapCount[i].seq << endl; + nameAbund[nameMapCount[i].name] = nameMapCount[i].numIdentical; } out.close(); rename(newFasta.c_str(), fastaFile.c_str()); - return fastaFile; + return nameAbund; } catch(exception& e) {