X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;fp=chimeraccodecommand.cpp;h=fc98e0fc45c3b576a3e2420ac415c016266b4c1c;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp new file mode 100644 index 0000000..fc98e0f --- /dev/null +++ b/chimeraccodecommand.cpp @@ -0,0 +1,666 @@ +/* + * chimeraccodecommand.cpp + * Mothur + * + * Created by westcott on 3/30/10. + * Copyright 2010 Schloss Lab. All rights reserved. + * + */ + +#include "chimeraccodecommand.h" +#include "ccode.h" +#include "referencedb.h" +//********************************************************************************************************************** +vector ChimeraCcodeCommand::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 pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter); + CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow); + CommandParameter pnumwanted("numwanted", "Number", "", "20", "", "", "",false,false); parameters.push_back(pnumwanted); + CommandParameter pmask("mask", "String", "", "", "", "", "",false,false); parameters.push_back(pmask); + 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, "ChimeraCcodeCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string ChimeraCcodeCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The chimera.ccode command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n"; + helpString += "This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n"; + helpString += "The chimera.ccode command parameters are fasta, reference, filter, mask, processors, window and numwanted.\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 filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \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 mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n"; + helpString += "The window parameter allows you to specify the window size for searching for chimeras. \n"; + helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\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.ccode command should be in the following format: \n"; + helpString += "chimera.ccode(fasta=yourFastaFile, reference=yourTemplate) \n"; + helpString += "Example: chimera.ccode(fasta=AD.align, reference=core_set_aligned.imputed.fasta) \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, "ChimeraCcodeCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +ChimeraCcodeCommand::ChimeraCcodeCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + outputTypes["mapinfo"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand"); + exit(1); + } +} +//*************************************************************************************************************** +ChimeraCcodeCommand::ChimeraCcodeCommand(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.ccode"); + 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; + 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 = ""; } + else { + string path; + it = parameters.find("reference"); + //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["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 = ""; } + + maskfile = validParameter.validFile(parameters, "mask", false); + if (maskfile == "not found") { maskfile = ""; } + else if (maskfile != "default") { + if (inputDir != "") { + 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 = 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 = m->isTrue(temp); + + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + m->mothurConvert(temp, processors); + + temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; } + m->mothurConvert(temp, window); + + temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "20"; } + m->mothurConvert(temp, numwanted); + + 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); } } + + + } + } + catch(exception& e) { + m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand"); + exit(1); + } +} +//*************************************************************************************************************** +int ChimeraCcodeCommand::execute(){ + try{ + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + for (int s = 0; s < fastaFileNames.size(); s++) { + + m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine(); + + int start = time(NULL); + + //set user options + if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); } + + chimera = new Ccode(fastaFileNames[s], templatefile, filter, maskfile, window, numwanted, outputDir); + + //is your template aligned? + 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 + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras"; + accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos"; + }else { + outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ccode.chimeras"; + accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ccode.accnos"; + } + + string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "mapinfo"; + + if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); return 0; } + + #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; + MPI_File outMPIAccnos; + + int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; + int inMode=MPI_MODE_RDONLY; + + char outFilename[1024]; + strcpy(outFilename, outputFileName.c_str()); + + char outAccnosFilename[1024]; + strcpy(outAccnosFilename, accnosFileName.c_str()); + + char inFileName[1024]; + strcpy(inFileName, fastaFileNames[s].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); + 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++) { m->mothurRemove(outputNames[j]); } 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"; + + //print header + int length = outTemp.length(); + char* buf2 = new char[length]; + memcpy(buf2, outTemp.c_str(), length); + + MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status); + delete buf2; + + MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs + + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } + + //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, outMPIAccnos, MPIPos); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } + + }else{ //you are a child process + MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + MPIPos.resize(numSeqs+1); + MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + + //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, 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++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } + } + + //close files + MPI_File_close(&inMPI); + MPI_File_close(&outMPI); + MPI_File_close(&outMPIAccnos); + + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case + + #else + ofstream 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(); + + + + //break up file + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + 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)])); + } + + if(processors == 1){ + + numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); + + if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } + + }else{ + processIDS.resize(0); + + 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); + m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp")); + } + + //append output files + for(int i=1;iappendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName); + m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp")); + } + + if (m->control_pressed) { + m->mothurRemove(outputFileName); + m->mothurRemove(accnosFileName); + for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); + for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); + delete chimera; + return 0; + } + + } + + #else + lines.push_back(new linePair(0, 1000)); + numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); + + if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } + + #endif + + m->appendFiles(outputFileName, tempHeader); + + m->mothurRemove(outputFileName); + rename(tempHeader.c_str(), outputFileName.c_str()); + #endif + + delete chimera; + + 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(); } + m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ChimeraCcodeCommand", "execute"); + exit(1); + } +} +//********************************************************************************************************************** + +int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string filename, string accnos){ + try { + ofstream out; + m->openOutputFile(outputFName, out); + + ofstream out2; + m->openOutputFile(accnos, 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 + + if (candidateSeq->getAligned().length() != templateSeqsLength) { + m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine(); + }else{ + //find chimeras + chimera->getChimeras(candidateSeq); + + if (m->control_pressed) { delete candidateSeq; return 1; } + + //print results + chimera->print(out, out2); + } + count++; + } + 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(); + out2.close(); + inFASTA.close(); + + return count; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCcodeCommand", "driver"); + exit(1); + } +} +//********************************************************************************************************************** +#ifdef USE_MPI +int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector& MPIPos){ + try { + + 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 + + if (candidateSeq->getAligned().length() != templateSeqsLength) { + m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine(); + }else{ + //find chimeras + chimera->getChimeras(candidateSeq); + + if (m->control_pressed) { delete candidateSeq; return 1; } + + //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, "ChimeraCcodeCommand", "driverMPI"); + exit(1); + } +} +#endif + +/**************************************************************************************************/ + +int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) { + 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, 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("[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, "ChimeraCcodeCommand", "createProcesses"); + exit(1); + } +} +//********************************************************************************************************************** +