X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;fp=chimeracheckcommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=cc486d3ab690fd655c1de8a22ae406eafc2c242f;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp deleted file mode 100644 index cc486d3..0000000 --- a/chimeracheckcommand.cpp +++ /dev/null @@ -1,655 +0,0 @@ -/* - * chimeracheckcommand.cpp - * Mothur - * - * Created by westcott on 3/31/10. - * Copyright 2010 Schloss Lab. All rights reserved. - * - */ - -#include "chimeracheckcommand.h" -#include "referencedb.h" - -//********************************************************************************************************************** -vector ChimeraCheckCommand::setParameters(){ - try { - 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 psvg("svg", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psvg); - CommandParameter pincrement("increment", "Number", "", "10", "", "", "",false,false); parameters.push_back(pincrement); - CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize); - CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); - CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave); - - vector myArray; - for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } - return myArray; - } - catch(exception& e) { - m->errorOut(e, "ChimeraCheckCommand", "setParameters"); - exit(1); - } -} -//********************************************************************************************************************** -string ChimeraCheckCommand::getHelpString(){ - try { - string helpString = ""; - helpString += "The chimera.check command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n"; - helpString += "This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n"; - helpString += "The chimera.check command parameters are fasta, reference, processors, ksize, increment, svg and name.\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 += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"; - helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. \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 increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n"; - helpString += "The ksize parameter allows you to input kmersize, default is 7. \n"; - helpString += "The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence, default is False.\n"; - helpString += "The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n"; - helpString += "You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n"; - helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f."; - helpString += "The chimera.check command should be in the following format: \n"; - helpString += "chimera.check(fasta=yourFastaFile, reference=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n"; - helpString += "Example: chimera.check(fasta=AD.fasta, reference=core_set_aligned,imputed.fasta, processors=4, ksize=8) \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, "ChimeraCheckCommand", "getHelpString"); - exit(1); - } -} -//********************************************************************************************************************** -ChimeraCheckCommand::ChimeraCheckCommand(){ - try { - abort = true; calledHelp = true; - setParameters(); - vector tempOutNames; - outputTypes["chimera"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand"); - exit(1); - } -} -//*************************************************************************************************************** -ChimeraCheckCommand::ChimeraCheckCommand(string option) { - try { - abort = false; calledHelp = false; - ReferenceDB* rdb = ReferenceDB::getInstance(); - - //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(); - - OptionParser parser(option); - map parameters = parser.getParameters(); - - ValidParameters validParameter("chimera.check"); - map::iterator it; - - //check to make sure all parameters are valid for command - for (it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } - } - - vector tempOutNames; - outputTypes["chimera"] = 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 { - it = parameters.find("reference"); - //user has given a template file - if(it != parameters.end()){ - string 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; } - } - } - - //check for required parameters - fastafile = validParameter.validFile(parameters, "fasta", false); - 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 - for (int i = 0; i < fastaFileNames.size(); i++) { - - 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 (!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 you can't open it, try default location - 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--; - }else { - m->setFastaFile(fastaFileNames[i]); - } - } - } - - //make sure there is at least one valid file left - if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); 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 = ""; } - - namefile = validParameter.validFile(parameters, "name", false); - if (namefile == "not found") { namefile = ""; } - 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++) { - - 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 (!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 you can't open it, try default location - 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--; - }else { - m->setNameFile(nameFileNames[i]); - } - } - } - - //make sure there is at least one valid file left - if (nameFileNames.size() != 0) { - if (nameFileNames.size() != fastaFileNames.size()) { - m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine(); - abort = true; - } - } - } - - string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } - m->setProcessors(temp); - m->mothurConvert(temp, processors); - - temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; } - save = m->isTrue(temp); - rdb->save = save; - if (save) { //clear out old references - rdb->clearMemory(); - } - - //this has to go after save so that if the user sets save=t and provides no reference we abort - templatefile = validParameter.validFile(parameters, "reference", true); - if (templatefile == "not found") { - //check for saved reference sequences - if (rdb->referenceSeqs.size() != 0) { - templatefile = "saved"; - }else { - m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required."); - m->mothurOutEndLine(); - abort = true; - } - }else if (templatefile == "not open") { abort = true; } - else { if (save) { rdb->setSavedReference(templatefile); } } - - - temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; } - m->mothurConvert(temp, ksize); - - temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; } - svg = m->isTrue(temp); - if (nameFileNames.size() != 0) { svg = true; } - - temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; } - m->mothurConvert(temp, increment); - } - } - catch(exception& e) { - m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand"); - exit(1); - } -} -//*************************************************************************************************************** - -int ChimeraCheckCommand::execute(){ - try{ - - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - for (int i = 0; i < fastaFileNames.size(); i++) { - - m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine(); - - int start = time(NULL); - - string thisNameFile = ""; - if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; } - - chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir); - - if (m->control_pressed) { delete chimera; return 0; } - - if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it - string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras"; - outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName); - - #ifdef USE_MPI - - int pid, numSeqsPerProcessor; - int tag = 2001; - vector MPIPos; - - MPI_Status status; - MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are - MPI_Comm_size(MPI_COMM_WORLD, &processors); - - MPI_File inMPI; - MPI_File outMPI; - - int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; - int inMode=MPI_MODE_RDONLY; - - char outFilename[1024]; - strcpy(outFilename, outputFileName.c_str()); - - char inFileName[1024]; - strcpy(inFileName, fastaFileNames[i].c_str()); - - 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); - - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } - - if (pid == 0) { //you are the root process - MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs - - //send file positions to all processes - for(int j = 1; j < processors; j++) { - MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD); - MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, 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; } - - - //align your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); - - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } - - //wait on chidren - for(int j = 1; j < processors; j++) { - char buf[5]; - MPI_Recv(buf, 5, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); - } - }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); - - //figure out how many sequences you have to align - numSeqsPerProcessor = numSeqs / processors; - int startIndex = pid * numSeqsPerProcessor; - if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } - - //align your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); - - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } - - //tell parent you are done. - char buf[5]; - strcpy(buf, "done"); - MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); - } - - //close files - MPI_File_close(&inMPI); - MPI_File_close(&outMPI); - MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case - #else - - - - //break up file - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) - vector positions = m->divideFile(fastaFileNames[i], processors); - - for (int s = 0; s < (positions.size()-1); s++) { - lines.push_back(new linePair(positions[s], positions[(s+1)])); - } - - if(processors == 1){ - numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]); - - if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int j = 0; j < lines.size(); j++) { delete lines[j]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } - - }else{ - processIDS.resize(0); - - numSeqs = createProcesses(outputFileName, fastaFileNames[i]); - - rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str()); - - //append output files - for(int j=1;jappendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName); - m->mothurRemove((outputFileName + toString(processIDS[j]) + ".temp")); - } - - if (m->control_pressed) { - for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); - for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); - delete chimera; - return 0; - } - } - - #else - lines.push_back(new linePair(0, 1000)); - numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]); - - if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } - #endif - #endif - delete chimera; - for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); - - m->mothurOutEndLine(); m->mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); m->mothurOutEndLine(); - m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); - - } - - m->mothurOutEndLine(); - m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } - m->mothurOutEndLine(); - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "ChimeraCheckCommand", "execute"); - exit(1); - } -} -//********************************************************************************************************************** - -int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string filename){ - try { - ofstream out; - m->openOutputFile(outputFName, out); - - ofstream out2; - - ifstream inFASTA; - m->openInputFile(filename, inFASTA); - - inFASTA.seekg(filePos->start); - - bool done = false; - int count = 0; - - while (!done) { - - if (m->control_pressed) { return 1; } - - Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); - - if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file - //find chimeras - chimera->getChimeras(candidateSeq); - - if (m->control_pressed) { delete candidateSeq; return 1; } - - //print results - chimera->print(out, out2); - } - delete candidateSeq; - - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) - unsigned long long 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(); } - - out.close(); - inFASTA.close(); - - return count; - } - catch(exception& e) { - m->errorOut(e, "ChimeraCheckCommand", "driver"); - exit(1); - } -} -//********************************************************************************************************************** -#ifdef USE_MPI -int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos){ - try { - MPI_File outAccMPI; - MPI_Status status; - int pid; - MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are - - for(int i=0;icontrol_pressed) { return 0; } - - //read next sequence - int length = MPIPos[start+i+1] - MPIPos[start+i]; - - char* buf4 = new char[length]; - MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status); - - string tempBuf = buf4; - if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); } - istringstream iss (tempBuf,istringstream::in); - delete buf4; - - Sequence* candidateSeq = new Sequence(iss); m->gobble(iss); - - if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file - //find chimeras - chimera->getChimeras(candidateSeq); - - //print results - chimera->print(outMPI, outAccMPI); - } - delete candidateSeq; - - //report progress - if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); } - } - //report progress - if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); } - - return 0; - } - catch(exception& e) { - m->errorOut(e, "ChimeraCheckCommand", "driverMPI"); - exit(1); - } -} -#endif - -/**************************************************************************************************/ - -int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) { - try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) - int process = 0; - int num = 0; - - //loop through and create all the processes you want - while (process != processors) { - int pid = fork(); - - if (pid > 0) { - 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); - - //pass numSeqs to parent - ofstream out; - string tempFile = outputFileName + toString(getpid()) + ".num.temp"; - m->openOutputFile(tempFile, out); - out << num << endl; - out.close(); - - 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 - for (int i=0;iopenInputFile(tempFile, in); - if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; } - in.close(); m->mothurRemove(tempFile); - } - - return num; -#endif - } - catch(exception& e) { - m->errorOut(e, "ChimeraCheckCommand", "createProcesses"); - exit(1); - } -} -/**************************************************************************************************/ - -