X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=9d5a625308f8970888833ec7e74ec4b2e2ec32dd;hb=86c838c428a9e7d26f902f5492738241fa72c4e7;hp=4c1a0251013afcd77a7137d09be0db5b1c60ffe3;hpb=284fd95c611ccc3b1a7875c4dacfca06d1f50ed6;p=mothur.git diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp index 4c1a025..9d5a625 100644 --- a/classifyseqscommand.cpp +++ b/classifyseqscommand.cpp @@ -14,20 +14,101 @@ #include "phylosummary.h" #include "knn.h" -//********************************************************************************************************************** +//********************************************************************************************************************** +vector ClassifySeqsCommand::setParameters(){ + try { + CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy); + CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup); + CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance", "kmer", "", "", "",false,false); parameters.push_back(psearch); + CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize); + CommandParameter pmethod("method", "Multiple", "bayesian-knn", "bayesian", "", "", "",false,false); parameters.push_back(pmethod); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); + CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch); + CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch); + CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen); + CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend); + CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff); + CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pprobs); + CommandParameter piters("iters", "Number", "", "100", "", "", "",false,true); parameters.push_back(piters); + CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "",false,true); parameters.push_back(pnumwanted); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ClassifySeqsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string ClassifySeqsCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n"; + helpString += "The classify.seqs command parameters are reference, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n"; + helpString += "The reference, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"; + helpString += "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast and distance. The default is kmer.\n"; + helpString += "The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n"; + helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n"; + helpString += "The method parameter allows you to specify classification method to use. Your options are: bayesian and knn. The default is bayesian.\n"; + helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n"; + helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n"; +#ifdef USE_MPI + helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n"; +#endif + helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n"; + helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n"; + helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n"; + helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n"; + helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method. The default is 10.\n"; + helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy. The default is 0.\n"; + helpString += "The probs parameter shuts off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be shown.\n"; + helpString += "The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the bayesian method. The default is 100.\n"; + helpString += "The classify.seqs command should be in the following format: \n"; + helpString += "classify.seqs(reference=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n"; + helpString += "Example classify.seqs(fasta=amazon.fasta, reference=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n"; + helpString += "The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n"; + helpString += "The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "ClassifySeqsCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +ClassifySeqsCommand::ClassifySeqsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["taxsummary"] = tempOutNames; + outputTypes["matchdist"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** ClassifySeqsCommand::ClassifySeqsCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { - - //valid paramters for this command - string AlignArray[] = {"template","fasta","name","group","search","ksize","method","processors","taxonomy","match","mismatch","gapopen","gapextend","numwanted","cutoff","probs","iters", "outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -40,6 +121,12 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["taxsummary"] = tempOutNames; + outputTypes["matchdist"] = tempOutNames; + //if the user changes the output directory command factory will send this info to us in the output parameter outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } @@ -48,18 +135,18 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { if (inputDir == "not found"){ inputDir = ""; } else { string path; - it = parameters.find("template"); + it = parameters.find("reference"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["template"] = inputDir + it->second; } + if (path == "") { parameters["reference"] = inputDir + it->second; } } it = parameters.find("taxonomy"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["taxonomy"] = inputDir + it->second; } } @@ -67,16 +154,16 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { it = parameters.find("group"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["group"] = inputDir + it->second; } } } //check for required parameters - templateFileName = validParameter.validFile(parameters, "template", true); + templateFileName = validParameter.validFile(parameters, "reference", true); if (templateFileName == "not found") { - m->mothurOut("template is a required parameter for the classify.seqs command."); + m->mothurOut("reference is a required parameter for the classify.seqs command."); m->mothurOutEndLine(); abort = true; } @@ -84,39 +171,74 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { fastaFileName = validParameter.validFile(parameters, "fasta", false); - if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the classify.seqs command."); m->mothurOutEndLine(); abort = true; } + if (fastaFileName == "not found") { + //if there is a current fasta file, use it + string filename = m->getFastaFile(); + if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } + } else { - splitAtDash(fastaFileName, fastaFileNames); + m->splitAtDash(fastaFileName, fastaFileNames); //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 = 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 = 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() + getSimpleName(fastaFileNames[i]); - m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); - 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--; } } - 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--; + 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]; } + } + + 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; + } + } + + 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--; + } } } @@ -139,38 +261,65 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { if (namefile == "not found") { namefile = ""; } else { - splitAtDash(namefile, namefileNames); + m->splitAtDash(namefile, namefileNames); //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 = 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]; } + 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--; + } } - int ableToOpen; - ifstream in; - ableToOpen = 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() + getSimpleName(namefileNames[i]); - m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); - 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]; } } - } - in.close(); + int ableToOpen; + + ifstream in; + ableToOpen = m->openInputFile(namefileNames[i], in, "noerror"); - if (ableToOpen == 1) { - m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); abort = true; - //erase from file list - namefileNames.erase(namefileNames.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(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(); abort = true; + //erase from file list + namefileNames.erase(namefileNames.begin()+i); + i--; + } } - } } @@ -181,29 +330,43 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { groupfile = validParameter.validFile(parameters, "group", false); if (groupfile == "not found") { groupfile = ""; } else { - splitAtDash(groupfile, groupfileNames); + m->splitAtDash(groupfile, groupfileNames); //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < groupfileNames.size(); i++) { if (inputDir != "") { - string path = hasPath(groupfileNames[i]); + string path = m->hasPath(groupfileNames[i]); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { groupfileNames[i] = inputDir + groupfileNames[i]; } } int ableToOpen; ifstream in; - ableToOpen = openInputFile(groupfileNames[i], in, "noerror"); + ableToOpen = m->openInputFile(groupfileNames[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() + getSimpleName(groupfileNames[i]); + string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]); m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); groupfileNames[i] = tryPath; } } + + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]); + m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + groupfileNames[i] = tryPath; + } + } + in.close(); if (ableToOpen == 1) { @@ -227,7 +390,8 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; } convert(temp, kmerSize); - temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); convert(temp, processors); search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; } @@ -253,7 +417,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { convert(temp, cutoff); temp = validParameter.validFile(parameters, "probs", false); if (temp == "not found"){ temp = "true"; } - probs = isTrue(temp); + probs = m->isTrue(temp); temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; } convert(temp, iters); @@ -274,57 +438,16 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) { } //********************************************************************************************************************** - ClassifySeqsCommand::~ClassifySeqsCommand(){ - if (abort == false) { for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); } } - -//********************************************************************************************************************** - -void ClassifySeqsCommand::help(){ - try { - m->mothurOut("The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n"); - m->mothurOut("The classify.seqs command parameters are template, fasta, name, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n"); - m->mothurOut("The template, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); - m->mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer, blast and distance. The default is kmer.\n"); - m->mothurOut("The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n"); - m->mothurOut("The group parameter allows you add a group file so you can have the summary totals broken up by group.\n"); - m->mothurOut("The method parameter allows you to specify classification method to use. Your options are: bayesian and knn. The default is bayesian.\n"); - m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n"); - m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n"); - #ifdef USE_MPI - m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n"); - #endif - m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n"); - m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n"); - m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n"); - m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n"); - m->mothurOut("The numwanted parameter allows you to specify the number of sequence matches you want with the knn method. The default is 10.\n"); - m->mothurOut("The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy. The default is 0.\n"); - m->mothurOut("The probs parameter shuts off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be shown.\n"); - m->mothurOut("The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the bayesian method. The default is 100.\n"); - m->mothurOut("The classify.seqs command should be in the following format: \n"); - m->mothurOut("classify.seqs(template=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n"); - m->mothurOut("Example classify.seqs(fasta=amazon.fasta, template=core.filtered, method=knn, search=gotoh, ksize=8, processors=2)\n"); - m->mothurOut("The .taxonomy file consists of 2 columns: 1 = your sequence name, 2 = the taxonomy for your sequence. \n"); - m->mothurOut("The .tax.summary is a summary of the different taxonomies represented in your fasta file. \n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "ClassifySeqsCommand", "help"); - exit(1); - } -} - - //********************************************************************************************************************** int ClassifySeqsCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } if(method == "bayesian"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters); } else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted); } @@ -336,36 +459,35 @@ int ClassifySeqsCommand::execute(){ if (m->control_pressed) { delete classify; return 0; } - vector outputNames; for (int s = 0; s < fastaFileNames.size(); s++) { m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine(); - string RippedTaxName = getRootName(getSimpleName(taxonomyFileName)); - RippedTaxName = getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1)); + string RippedTaxName = m->getRootName(m->getSimpleName(taxonomyFileName)); + RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1)); if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); } RippedTaxName += "."; - if (outputDir == "") { outputDir += hasPath(fastaFileNames[s]); } - string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy"; - string tempTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "taxonomy.temp"; - string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary"; + if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); } + string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy"; + string tempTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "taxonomy.temp"; + string taxSummary = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary"; if ((method == "knn") && (search == "distance")) { - string DistName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "match.dist"; - classify->setDistName(DistName); outputNames.push_back(DistName); + string DistName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "match.dist"; + classify->setDistName(DistName); outputNames.push_back(DistName); outputTypes["matchdist"].push_back(DistName); } - outputNames.push_back(newTaxonomyFile); - outputNames.push_back(taxSummary); + outputNames.push_back(newTaxonomyFile); outputTypes["taxonomy"].push_back(newTaxonomyFile); + outputNames.push_back(taxSummary); outputTypes["taxsummary"].push_back(taxSummary); int start = time(NULL); int numFastaSeqs = 0; for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); #ifdef USE_MPI - int pid, end, numSeqsPerProcessor; + int pid, numSeqsPerProcessor; int tag = 2001; vector MPIPos; @@ -380,20 +502,11 @@ int ClassifySeqsCommand::execute(){ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; int inMode=MPI_MODE_RDONLY; - //char* outNewTax = new char[newTaxonomyFile.length()]; - //memcpy(outNewTax, newTaxonomyFile.c_str(), newTaxonomyFile.length()); - char outNewTax[1024]; strcpy(outNewTax, newTaxonomyFile.c_str()); - - //char* outTempTax = new char[tempTaxonomyFile.length()]; - //memcpy(outTempTax, tempTaxonomyFile.c_str(), tempTaxonomyFile.length()); char outTempTax[1024]; strcpy(outTempTax, tempTaxonomyFile.c_str()); - - //char* inFileName = new char[fastaFileNames[s].length()]; - //memcpy(inFileName, fastaFileNames[s].c_str(), fastaFileNames[s].length()); char inFileName[1024]; strcpy(inFileName, fastaFileNames[s].c_str()); @@ -402,15 +515,11 @@ int ClassifySeqsCommand::execute(){ MPI_File_open(MPI_COMM_WORLD, outNewTax, outMode, MPI_INFO_NULL, &outMPINewTax); MPI_File_open(MPI_COMM_WORLD, outTempTax, outMode, MPI_INFO_NULL, &outMPITempTax); - //delete outNewTax; - //delete outTempTax; - //delete inFileName; - - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; } if (pid == 0) { //you are the root process - MPIPos = setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs + MPIPos = m->setFilePosFasta(fastaFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs //send file positions to all processes for(int i = 1; i < processors; i++) { @@ -427,7 +536,7 @@ int ClassifySeqsCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; } for (int i = 1; i < processors; i++) { int done; @@ -447,7 +556,7 @@ int ClassifySeqsCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPINewTax, outMPITempTax, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPITempTax); delete classify; return 0; } int done = 0; MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); @@ -461,7 +570,7 @@ int ClassifySeqsCommand::execute(){ #else - vector positions = divideFile(fastaFileNames[s], processors); + vector positions = m->divideFile(fastaFileNames[s], processors); for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); @@ -476,16 +585,6 @@ int ClassifySeqsCommand::execute(){ numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]); - rename((newTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), newTaxonomyFile.c_str()); - rename((tempTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), tempTaxonomyFile.c_str()); - - for(int i=1;iopenInputFile(namefileNames[s], inNames); string firstCol, secondCol; while(!inNames.eof()) { - inNames >> firstCol >> secondCol; gobble(inNames); + inNames >> firstCol >> secondCol; m->gobble(inNames); vector temp; - splitAtComma(secondCol, temp); + m->splitAtComma(secondCol, temp); nameMap[firstCol] = temp; } @@ -532,18 +631,18 @@ int ClassifySeqsCommand::execute(){ PhyloSummary taxaSum(taxonomyFileName, group); - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; } + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; } if (namefile == "") { taxaSum.summarize(tempTaxonomyFile); } else { ifstream in; - openInputFile(tempTaxonomyFile, in); + m->openInputFile(tempTaxonomyFile, in); //read in users taxonomy file and add sequences to tree string name, taxon; while(!in.eof()){ - in >> name >> taxon; gobble(in); + in >> name >> taxon; m->gobble(in); itNames = nameMap.find(name); @@ -561,31 +660,31 @@ int ClassifySeqsCommand::execute(){ } remove(tempTaxonomyFile.c_str()); - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; } + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete classify; return 0; } //print summary file ofstream outTaxTree; - openOutputFile(taxSummary, outTaxTree); + m->openOutputFile(taxSummary, outTaxTree); taxaSum.print(outTaxTree); outTaxTree.close(); //output taxonomy with the unclassified bins added ifstream inTax; - openInputFile(newTaxonomyFile, inTax); + m->openInputFile(newTaxonomyFile, inTax); ofstream outTax; string unclass = newTaxonomyFile + ".unclass.temp"; - openOutputFile(unclass, outTax); + m->openOutputFile(unclass, outTax); //get maxLevel from phylotree so you know how many 'unclassified's to add int maxLevel = taxaSum.getMaxLevel(); - + //read taxfile - this reading and rewriting is done to preserve the confidence scores. string name, taxon; while (!inTax.eof()) { - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(unclass.c_str()); delete classify; return 0; } + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } remove(unclass.c_str()); delete classify; return 0; } - inTax >> name >> taxon; gobble(inTax); + inTax >> name >> taxon; m->gobble(inTax); string newTax = addUnclassifieds(taxon, maxLevel); @@ -610,6 +709,13 @@ int ClassifySeqsCommand::execute(){ m->mothurOutEndLine(); } + //set taxonomy file as new current taxonomyfile + string current = ""; + itTypes = outputTypes.find("taxonomy"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); } + } + delete classify; return 0; } @@ -653,7 +759,7 @@ string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) { int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - int process = 0; + int process = 1; int num = 0; //loop through and create all the processes you want @@ -668,29 +774,43 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, //pass numSeqs to parent ofstream out; - string tempFile = toString(getpid()) + ".temp"; - openOutputFile(tempFile, out); + string tempFile = filename + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); out << num << endl; out.close(); exit(0); - }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); } + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } } + //parent does its part + num = driver(lines[0], taxFileName, tempTaxFile, filename); + //force parent to wait until all the processes are done - for (int i=0;iopenInputFile(tempFile, in); if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; } in.close(); remove(tempFile.c_str()); } + for(int i=0;iopenOutputFileAppend(filename, output); + m->openInputFile(temp, input); while(char c = input.get()){ if(input.eof()) { break; } @@ -728,13 +848,13 @@ void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) { int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string filename){ try { ofstream outTax; - openOutputFile(taxFName, outTax); + m->openOutputFile(taxFName, outTax); ofstream outTaxSimple; - openOutputFile(tempTFName, outTaxSimple); + m->openOutputFile(tempTFName, outTaxSimple); ifstream inFASTA; - openInputFile(filename, inFASTA); + m->openInputFile(filename, inFASTA); string taxonomy; @@ -742,13 +862,14 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT bool done = false; int count = 0; - + while (!done) { if (m->control_pressed) { return 0; } - Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA); - + Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); + if (candidateSeq->getName() != "") { + taxonomy = classify->getTaxonomy(candidateSeq); if (m->control_pressed) { delete candidateSeq; return 0; } @@ -767,15 +888,20 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT } delete candidateSeq; - unsigned long int pos = inFASTA.tellg(); - if ((pos == -1) || (pos >= filePos->end)) { break; } + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + unsigned long int pos = inFASTA.tellg(); + if ((pos == -1) || (pos >= filePos->end)) { break; } + #else + if (inFASTA.eof()) { break; } + #endif //report progress if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } + } //report progress if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } - + inFASTA.close(); outTax.close(); outTaxSimple.close(); @@ -890,10 +1016,10 @@ int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){ string firstCol, secondCol; while(!iss.eof()) { - iss >> firstCol >> secondCol; gobble(iss); + iss >> firstCol >> secondCol; m->gobble(iss); vector temp; - splitAtComma(secondCol, temp); + m->splitAtComma(secondCol, temp); nameMap[firstCol] = temp; }