X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;h=457eaf314bf304fe3d7f9e5eec67509f07236a35;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=3d3c9aea99401c492676e210173d7b397e205a70;hpb=0c78e45408d8c099bc51579225ebfc227f7523b2;p=mothur.git diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp index 3d3c9ae..457eaf3 100644 --- a/chimeraccodecommand.cpp +++ b/chimeraccodecommand.cpp @@ -10,24 +10,72 @@ #include "chimeraccodecommand.h" #include "ccode.h" +//********************************************************************************************************************** +vector ChimeraCcodeCommand::getValidParameters(){ + try { + string AlignArray[] = {"fasta", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir" }; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCcodeCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +ChimeraCcodeCommand::ChimeraCcodeCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + outputTypes["mapinfo"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector ChimeraCcodeCommand::getRequiredParameters(){ + try { + string AlignArray[] = {"template","fasta"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCcodeCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ChimeraCcodeCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCcodeCommand", "getRequiredFiles"); + exit(1); + } +} //*************************************************************************************************************** - ChimeraCcodeCommand::ChimeraCcodeCommand(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", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir", }; + string Array[] = {"fasta", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir" }; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); map parameters = parser.getParameters(); - ValidParameters validParameter; + ValidParameters validParameter("chimera.ccode"); map::iterator it; //check to make sure all parameters are valid for command @@ -35,6 +83,11 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + outputTypes["mapinfo"] = tempOutNames; + outputTypes["accnos"] = 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 = ""; } @@ -43,7 +96,7 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { it = parameters.find("template"); //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; } } @@ -53,12 +106,12 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { fastafile = validParameter.validFile(parameters, "fasta", false); if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; } else { - splitAtDash(fastafile, fastaFileNames); + 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++) { if (inputDir != "") { - string path = hasPath(fastaFileNames[i]); + 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]; } } @@ -66,30 +119,36 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { int ableToOpen; ifstream in; - #ifdef USE_MPI - int pid; - MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running - MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror"); - if (pid == 0) { - #endif - - ableToOpen = openInputFile(fastaFileNames[i], in); - in.close(); + //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; + } + } - #ifdef USE_MPI - for (int j = 1; j < processors; j++) { - MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); - } - }else{ - MPI_Status status; - MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + //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; } - - #endif - + } + + in.close(); + if (ableToOpen == 1) { - m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); //erase from file list fastaFileNames.erase(fastaFileNames.begin()+i); i--; @@ -101,10 +160,7 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { } //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 = ""; - outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it - } + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } templatefile = validParameter.validFile(parameters, "template", true); if (templatefile == "not open") { abort = true; } @@ -114,20 +170,20 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { if (maskfile == "not found") { maskfile = ""; } else if (maskfile != "default") { if (inputDir != "") { - string path = hasPath(maskfile); + string path = m->hasPath(maskfile); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { maskfile = inputDir + maskfile; } } ifstream in; - int ableToOpen = openInputFile(maskfile, in); + int ableToOpen = m->openInputFile(maskfile, in); if (ableToOpen == 1) { abort = true; } in.close(); } string temp; temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; } - filter = isTrue(temp); + filter = m->isTrue(temp); temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; } convert(temp, processors); @@ -184,7 +240,7 @@ ChimeraCcodeCommand::~ChimeraCcodeCommand(){ /* do nothing */ } int ChimeraCcodeCommand::execute(){ try{ - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } for (int s = 0; s < fastaFileNames.size(); s++) { @@ -201,24 +257,25 @@ int ChimeraCcodeCommand::execute(){ if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; } templateSeqsLength = chimera->getLength(); + if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it string outputFileName, accnosFileName; if (maskfile != "") { - outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras"; - accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos"; + outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras"; + accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos"; }else { - outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "ccode.chimeras"; - accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "ccode.accnos"; + outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ccode.chimeras"; + accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ccode.accnos"; } - string mapInfo = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "mapinfo"; + string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "mapinfo"; - if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } + if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); return 0; } #ifdef USE_MPI - int pid, end, numSeqsPerProcessor; + int pid, numSeqsPerProcessor; int tag = 2001; - vector MPIPos; + vector MPIPos; MPI_Status status; MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are @@ -244,7 +301,7 @@ int ChimeraCcodeCommand::execute(){ 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 (m->control_pressed) { 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) { 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()); } outputTypes.clear(); delete chimera; return 0; } if (pid == 0) { //you are the root process string outTemp = "For full window mapping info refer to " + mapInfo + "\n\n"; @@ -257,7 +314,7 @@ int ChimeraCcodeCommand::execute(){ MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status); delete buf2; - MPIPos = setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs + MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs //send file positions to all processes for(int i = 1; i < processors; i++) { @@ -274,7 +331,7 @@ int ChimeraCcodeCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; } }else{ //you are a child process MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); @@ -290,7 +347,7 @@ int ChimeraCcodeCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); - if (m->control_pressed) { 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) { 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()); } outputTypes.clear(); delete chimera; return 0; } } //close files @@ -302,85 +359,51 @@ int ChimeraCcodeCommand::execute(){ #else ofstream outHeader; - string tempHeader = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + "ccode.chimeras.tempHeader"; - openOutputFile(tempHeader, outHeader); + string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + "ccode.chimeras.tempHeader"; + m->openOutputFile(tempHeader, outHeader); outHeader << "For full window mapping info refer to " << mapInfo << endl << endl; outHeader.close(); + 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)])); + } + //break up file #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) if(processors == 1){ - ifstream inFASTA; - openInputFile(fastaFileNames[s], inFASTA); - getNumSeqs(inFASTA, numSeqs); - inFASTA.close(); - - lines.push_back(new linePair(0, numSeqs)); + + numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); - driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); - - if (m->control_pressed) { - 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) { 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]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } }else{ - vector positions; processIDS.resize(0); - ifstream inFASTA; - openInputFile(fastaFileNames[s], inFASTA); - - string input; - while(!inFASTA.eof()){ - input = getline(inFASTA); - if (input.length() != 0) { - if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } - } - } - inFASTA.close(); - - numSeqs = positions.size(); - - int numSeqsPerProcessor = numSeqs / processors; - - for (int i = 0; i < processors; i++) { - long int startPos = positions[ i * numSeqsPerProcessor ]; - if(i == processors - 1){ - numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; - } - lines.push_back(new linePair(startPos, numSeqsPerProcessor)); - } - - - createProcesses(outputFileName, fastaFileNames[s], accnosFileName); + numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName); rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str()); rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str()); //append output files for(int i=1;iappendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName); remove((outputFileName + toString(processIDS[i]) + ".temp").c_str()); } //append output files for(int i=1;iappendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName); remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); } if (m->control_pressed) { remove(outputFileName.c_str()); remove(accnosFileName.c_str()); - for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } + for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; @@ -389,27 +412,13 @@ int ChimeraCcodeCommand::execute(){ } #else - ifstream inFASTA; - openInputFile(fastaFileNames[s], inFASTA); - getNumSeqs(inFASTA, numSeqs); - inFASTA.close(); - lines.push_back(new linePair(0, numSeqs)); - - driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); + numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); - if (m->control_pressed) { - 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) { 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]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } #endif - appendFiles(outputFileName, tempHeader); + m->appendFiles(outputFileName, tempHeader); remove(outputFileName.c_str()); rename(tempHeader.c_str(), outputFileName.c_str()); @@ -417,15 +426,23 @@ int ChimeraCcodeCommand::execute(){ delete chimera; - outputNames.push_back(outputFileName); - outputNames.push_back(mapInfo); - outputNames.push_back(accnosFileName); - + outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName); + outputNames.push_back(mapInfo); outputTypes["mapinfo"].push_back(mapInfo); + outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); + for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); 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); } + } + m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } @@ -441,24 +458,27 @@ int ChimeraCcodeCommand::execute(){ } //********************************************************************************************************************** -int ChimeraCcodeCommand::driver(linePair* line, string outputFName, string filename, string accnos){ +int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string filename, string accnos){ try { ofstream out; - openOutputFile(outputFName, out); + m->openOutputFile(outputFName, out); ofstream out2; - openOutputFile(accnos, out2); + m->openOutputFile(accnos, out2); ifstream inFASTA; - openInputFile(filename, inFASTA); + m->openInputFile(filename, inFASTA); - inFASTA.seekg(line->start); - - for(int i=0;inumSeqs;i++){ + inFASTA.seekg(filePos->start); + + bool done = false; + int count = 0; + + while (!done) { if (m->control_pressed) { return 1; } - Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA); + Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file @@ -473,20 +493,28 @@ int ChimeraCcodeCommand::driver(linePair* line, string outputFName, string filen //print results chimera->print(out, out2); } + count++; } delete candidateSeq; + #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((i+1) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine(); } + if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } } //report progress - if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine(); } + if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } out.close(); out2.close(); inFASTA.close(); - return 0; + return count; } catch(exception& e) { m->errorOut(e, "ChimeraCcodeCommand", "driver"); @@ -495,7 +523,7 @@ int ChimeraCcodeCommand::driver(linePair* line, string outputFName, string filen } //********************************************************************************************************************** #ifdef USE_MPI -int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector& MPIPos){ +int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector& MPIPos){ try { MPI_Status status; @@ -518,7 +546,7 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File istringstream iss (tempBuf,istringstream::in); delete buf4; - Sequence* candidateSeq = new Sequence(iss); gobble(iss); + Sequence* candidateSeq = new Sequence(iss); m->gobble(iss); if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file @@ -531,7 +559,7 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File if (m->control_pressed) { delete candidateSeq; return 1; } //print results - bool isChimeric = chimera->print(outMPI, outAccMPI); + chimera->print(outMPI, outAccMPI); } } delete candidateSeq; @@ -558,7 +586,7 @@ int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; - // processIDS.resize(0); + int num = 0; //loop through and create all the processes you want while (process != processors) { @@ -568,9 +596,21 @@ int ChimeraCcodeCommand::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){ - 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"); + + //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("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 @@ -579,7 +619,15 @@ int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, wait(&temp); } - return 0; + for (int i = 0; i < processIDS.size(); i++) { + ifstream in; + string tempFile = outputFileName + toString(processIDS[i]) + ".num.temp"; + m->openInputFile(tempFile, in); + if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; } + in.close(); remove(tempFile.c_str()); + } + + return num; #endif } catch(exception& e) {