X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=15bf954f301b3585cbb595f28832d316842b199e;hb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;hp=dbdd4a9eeca506fab01005f2cf752452beb8310a;hpb=df41d90a9611eab75d0516e2654ed8580f8df24c;p=mothur.git diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp index dbdd4a9..15bf954 100644 --- a/chimeraslayercommand.cpp +++ b/chimeraslayercommand.cpp @@ -9,68 +9,114 @@ #include "chimeraslayercommand.h" #include "chimeraslayer.h" +#include "deconvolutecommand.h" //********************************************************************************************************************** -vector ChimeraSlayerCommand::getValidParameters(){ +vector ChimeraSlayerCommand::setParameters(){ try { - string AlignArray[] = {"fasta", "processors", "window", "template","numwanted", "ksize", "match","mismatch", - "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" }; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + 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 pwindow("window", "Number", "", "50", "", "", "",false,false); parameters.push_back(pwindow); + CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize); + CommandParameter pmatch("match", "Number", "", "5.0", "", "", "",false,false); parameters.push_back(pmatch); + 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 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 pinclude("include", "Multiple", "greater-greaterequal-all", "greater", "", "", "",false,false); parameters.push_back(pinclude); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); + CommandParameter prealign("realign", "Boolean", "", "F", "", "", "",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 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); + 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, "ChimeraSlayerCommand", "getValidParameters"); + m->errorOut(e, "ChimeraSlayerCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -ChimeraSlayerCommand::ChimeraSlayerCommand(){ +string ChimeraSlayerCommand::getHelpString(){ try { - vector tempOutNames; - outputTypes["chimera"] = tempOutNames; - outputTypes["accnos"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand"); - exit(1); - } -} -//********************************************************************************************************************** -vector ChimeraSlayerCommand::getRequiredParameters(){ - try { - string AlignArray[] = {"template","fasta"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); - return myArray; + 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 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"; + helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n"; + helpString += "The include parameter is used when template=self and allows you to choose which sequences will make up the \"template\". Options are greater, greaterequal and all, default=greater, meaning sequences with greater abundance than the query sequence. \n"; + helpString += "The processors parameter allows you to specify how many processors you would like 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 trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest piece, default=F. \n"; + helpString += "The split parameter allows you to check both pieces of non-chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n"; + helpString += "The window parameter allows you to specify the window size for searching for chimeras, default=50. \n"; + helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n"; + helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n"; + helpString += "The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n"; + helpString += "The match parameter allows you to reward matched bases in blast search, default is 5. \n"; + 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 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 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"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "ChimeraSlayerCommand", "getRequiredParameters"); + m->errorOut(e, "ChimeraSlayerCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector ChimeraSlayerCommand::getRequiredFiles(){ +ChimeraSlayerCommand::ChimeraSlayerCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + outputTypes["fasta"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "ChimeraSlayerCommand", "getRequiredFiles"); + m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand"); exit(1); } } //*************************************************************************************************************** ChimeraSlayerCommand::ChimeraSlayerCommand(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 Array[] = {"fasta", "processors", "window", "template","numwanted", "ksize", "match","mismatch", - "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -86,26 +132,20 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { vector tempOutNames; outputTypes["chimera"] = tempOutNames; outputTypes["accnos"] = tempOutNames; + outputTypes["fasta"] = tempOutNames; //if the user changes the input directory command factory will send this info to us in the output parameter string inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; } - else { - string path; - it = parameters.find("template"); - //user has given a template file - if(it != parameters.end()){ - 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; } - } - } - - + //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", false); - if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; } - else { + if (fastafile == "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 { m->splitAtDash(fastafile, fastaFileNames); //go through files and make sure they are good, if not, then disregard them @@ -155,19 +195,96 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { } //make sure there is at least one valid file left - if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; } + if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; } + } + + + //check for required parameters + bool hasName = true; + namefile = validParameter.validFile(parameters, "name", false); + if (namefile == "not found") { namefile = ""; hasName = false; } + else { + 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 = 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--; + } + } + + //make sure there is at least one valid file left + if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; } } + if (hasName && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of namefiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; } + //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 = ""; } - - templatefile = validParameter.validFile(parameters, "template", true); - if (templatefile == "not open") { abort = true; } - else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template 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 = "1"; } + + + string path; + it = parameters.find("reference"); + //user has given a template file + if(it != parameters.end()){ + if (it->second == "self") { templatefile = "self"; } + else { + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["reference"] = inputDir + it->second; } + + 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; } + } + } + + string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); convert(temp, processors); + includeAbunds = validParameter.validFile(parameters, "include", false); if (includeAbunds == "not found") { includeAbunds = "greater"; } + if ((includeAbunds != "greater") && (includeAbunds != "greaterequal") && (includeAbunds != "all")) { includeAbunds = "greater"; m->mothurOut("Invalid include setting. options are greater, greaterequal or all. using greater."); m->mothurOutEndLine(); } + temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; } convert(temp, ksize); @@ -201,6 +318,12 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "f"; } realign = m->isTrue(temp); + temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; } + trim = m->isTrue(temp); + + 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"; } temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; } @@ -220,57 +343,12 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { exit(1); } } -//********************************************************************************************************************** - -void ChimeraSlayerCommand::help(){ - try { - - m->mothurOut("The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n"); - m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n"); - m->mothurOut("The chimera.slayer command parameters are fasta, template, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign, - m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n"); - m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n"); - m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n"); - m->mothurOut("The processors parameter allows you to specify how many processors you would like 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 window parameter allows you to specify the window size for searching for chimeras, default=50. \n"); - m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n"); - m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n"); - m->mothurOut("The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n"); - m->mothurOut("The match parameter allows you to reward matched bases in blast search, default is 5. \n"); - m->mothurOut("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"); - m->mothurOut("The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n"); - m->mothurOut("The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n"); - m->mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n"); - m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n"); - m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n"); - m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n"); - m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n"); - m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n"); - m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. \n"); - m->mothurOut("The chimera.slayer command should be in the following format: \n"); - m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n"); - m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \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, "ChimeraSlayerCommand", "help"); - exit(1); - } -} - -//*************************************************************************************************************** - -ChimeraSlayerCommand::~ChimeraSlayerCommand(){ /* do nothing */ } - //*************************************************************************************************************** int ChimeraSlayerCommand::execute(){ try{ - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } for (int s = 0; s < fastaFileNames.size(); s++) { @@ -278,11 +356,40 @@ int ChimeraSlayerCommand::execute(){ int start = time(NULL); - chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign); + if (templatefile != "self") { //you want to run slayer with a refernce template + chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign); + }else { + if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one + chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFileNames[s], search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign); + }else { + + m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine(); + + //use unique.seqs to create new name and fastafile + string inputString = "fasta=" + fastaFileNames[s]; + m->mothurOut("/******************************************/"); m->mothurOutEndLine(); + m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); + + Command* uniqueCommand = new DeconvoluteCommand(inputString); + uniqueCommand->execute(); + + map > filenames = uniqueCommand->getOutputFiles(); + + delete uniqueCommand; + + m->mothurOut("/******************************************/"); m->mothurOutEndLine(); + + string nameFile = filenames["name"][0]; + fastaFileNames[s] = filenames["fasta"][0]; + chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFile, search, includeAbunds, 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 - string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras"; + string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera"; string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.accnos"; + string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.fasta"; if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } @@ -294,7 +401,7 @@ int ChimeraSlayerCommand::execute(){ templateSeqsLength = chimera->getLength(); #ifdef USE_MPI - int pid, end, numSeqsPerProcessor; + int pid, numSeqsPerProcessor; int tag = 2001; vector MPIPos; @@ -305,6 +412,7 @@ int ChimeraSlayerCommand::execute(){ MPI_File inMPI; MPI_File outMPI; MPI_File outMPIAccnos; + MPI_File outMPIFasta; int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; int inMode=MPI_MODE_RDONLY; @@ -314,6 +422,9 @@ int ChimeraSlayerCommand::execute(){ char outAccnosFilename[1024]; strcpy(outAccnosFilename, accnosFileName.c_str()); + + char outFastaFilename[1024]; + strcpy(outFastaFilename, trimFastaFileName.c_str()); char inFileName[1024]; strcpy(inFileName, fastaFileNames[s].c_str()); @@ -321,8 +432,9 @@ int ChimeraSlayerCommand::execute(){ MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI); MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos); + if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); } - if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); 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; } if (pid == 0) { //you are the root process m->mothurOutEndLine(); @@ -353,9 +465,9 @@ int ChimeraSlayerCommand::execute(){ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } //do your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); - if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); 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; } + 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); @@ -368,15 +480,16 @@ int ChimeraSlayerCommand::execute(){ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } //do your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); - if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); 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 MPI_File_close(&inMPI); MPI_File_close(&outMPI); - MPI_File_close(&outMPIAccnos); + MPI_File_close(&outMPIAccnos); + if (trim) { MPI_File_close(&outMPIFasta); } MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else @@ -396,17 +509,18 @@ int ChimeraSlayerCommand::execute(){ //break up file #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) if(processors == 1){ - numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); + numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName); - if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } }else{ processIDS.resize(0); - numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName); + numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName); rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str()); rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str()); + if (trim) { rename((trimFastaFileName + toString(processIDS[0]) + ".temp").c_str(), trimFastaFileName.c_str()); } //append output files for(int i=1;icontrol_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } + if (trim) { + for(int i=1;iappendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName); + remove((trimFastaFileName + toString(processIDS[i]) + ".temp").c_str()); + } + } + + if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } } #else - numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); + numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName); - if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } #endif @@ -443,10 +564,25 @@ int ChimeraSlayerCommand::execute(){ outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName); outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); + if (trim) { outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); } m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); } + //set accnos file as new current accnosfile + string current = ""; + itTypes = outputTypes.find("accnos"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); } + } + + if (trim) { + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } + } + } + m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } @@ -462,7 +598,7 @@ int ChimeraSlayerCommand::execute(){ } //********************************************************************************************************************** -int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos){ +int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos, string fasta){ try { ofstream out; m->openOutputFile(outputFName, out); @@ -470,6 +606,9 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f ofstream out2; m->openOutputFile(accnos, out2); + ofstream out3; + if (trim) { m->openOutputFile(fasta, out3); } + ifstream inFASTA; m->openInputFile(filename, inFASTA); @@ -480,9 +619,10 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f while (!done) { - if (m->control_pressed) { return 1; } + if (m->control_pressed) { out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1; } 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 @@ -493,11 +633,58 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f chimera->getChimeras(candidateSeq); if (m->control_pressed) { delete candidateSeq; return 1; } - - //print results - chimera->print(out, out2); + + //if you are not chimeric, then check each half + data_results wholeResults = chimera->getResults(); + + //determine if we need to split + bool isChimeric = false; + + if (wholeResults.flag == "yes") { + string chimeraFlag = "no"; + if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR) + || + (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; } + + + if (chimeraFlag == "yes") { + if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; } + } + } + + if ((!isChimeric) && trimera) { + + //split sequence in half by bases + string leftQuery, rightQuery; + Sequence tempSeq(candidateSeq->getName(), candidateAligned); + divideInHalf(tempSeq, leftQuery, rightQuery); + + //run chimeraSlayer on each piece + Sequence* left = new Sequence(candidateSeq->getName(), leftQuery); + Sequence* right = new Sequence(candidateSeq->getName(), rightQuery); + + //find chimeras + chimera->getChimeras(left); + data_results leftResults = chimera->getResults(); + + chimera->getChimeras(right); + data_results rightResults = chimera->getResults(); + + //if either piece is chimeric then report + Sequence* trimmed = chimera->print(out, out2, leftResults, rightResults); + if (trim) { trimmed->printSequence(out3); delete trimmed; } + + delete left; delete right; + + }else { //already chimeric + //print results + Sequence* trimmed = chimera->print(out, out2); + if (trim) { trimmed->printSequence(out3); delete trimmed; } + } + + } - count++; + count++; } delete candidateSeq; @@ -516,6 +703,7 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f out.close(); out2.close(); + if (trim) { out3.close(); } inFASTA.close(); return count; @@ -527,7 +715,7 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f } //********************************************************************************************************************** #ifdef USE_MPI -int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector& MPIPos){ +int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector& MPIPos){ try { MPI_Status status; int pid; @@ -550,6 +738,7 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil delete buf4; Sequence* candidateSeq = new Sequence(iss); m->gobble(iss); + string candidateAligned = candidateSeq->getAligned(); if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file @@ -561,9 +750,77 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil chimera->getChimeras(candidateSeq); if (m->control_pressed) { delete candidateSeq; return 1; } - //cout << "about to print" << endl; - //print results - bool isChimeric = chimera->print(outMPI, outAccMPI); + + //if you are not chimeric, then check each half + data_results wholeResults = chimera->getResults(); + + //determine if we need to split + bool isChimeric = false; + + if (wholeResults.flag == "yes") { + string chimeraFlag = "no"; + if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR) + || + (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; } + + + if (chimeraFlag == "yes") { + if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; } + } + } + + if ((!isChimeric) && trimera) { + //split sequence in half by bases + string leftQuery, rightQuery; + Sequence tempSeq(candidateSeq->getName(), candidateAligned); + divideInHalf(tempSeq, leftQuery, rightQuery); + + //run chimeraSlayer on each piece + Sequence* left = new Sequence(candidateSeq->getName(), leftQuery); + Sequence* right = new Sequence(candidateSeq->getName(), rightQuery); + + //find chimeras + chimera->getChimeras(left); + data_results leftResults = chimera->getResults(); + + chimera->getChimeras(right); + data_results rightResults = chimera->getResults(); + + //if either piece is chimeric then report + Sequence* trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults); + if (trim) { + string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n"; + delete trimmed; + + //write to accnos file + int length = outputString.length(); + char* buf2 = new char[length]; + memcpy(buf2, outputString.c_str(), length); + + MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status); + delete buf2; + } + + delete left; delete right; + + }else { + //print results + Sequence* trimmed = chimera->print(outMPI, outAccMPI); + + if (trim) { + string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n"; + delete trimmed; + + //write to accnos file + int length = outputString.length(); + char* buf2 = new char[length]; + memcpy(buf2, outputString.c_str(), length); + + MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status); + delete buf2; + } + } + } } delete candidateSeq; @@ -586,7 +843,7 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil /**************************************************************************************************/ -int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos) { +int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta) { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; @@ -600,7 +857,7 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later process++; }else if (pid == 0){ - num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp"); + num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp"); //pass numSeqs to parent ofstream out; @@ -610,7 +867,11 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename 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); + } } //force parent to wait until all the processes are done @@ -638,4 +899,42 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename /**************************************************************************************************/ +int ChimeraSlayerCommand::divideInHalf(Sequence querySeq, string& leftQuery, string& rightQuery) { + try { + + string queryUnAligned = querySeq.getUnaligned(); + int numBases = int(queryUnAligned.length() * 0.5); + + string queryAligned = querySeq.getAligned(); + leftQuery = querySeq.getAligned(); + rightQuery = querySeq.getAligned(); + + int baseCount = 0; + int leftSpot = 0; + for (int i = 0; i < queryAligned.length(); i++) { + //if you are a base + if (isalpha(queryAligned[i])) { + baseCount++; + } + + //if you have half + if (baseCount >= numBases) { leftSpot = i; break; } //first half + } + + //blank out right side + for (int i = leftSpot; i < leftQuery.length(); i++) { leftQuery[i] = '.'; } + + //blank out left side + for (int i = 0; i < leftSpot; i++) { rightQuery[i] = '.'; } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayerCommand", "divideInHalf"); + exit(1); + } +} + +/**************************************************************************************************/