X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;fp=chimeraccodecommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=fc98e0fc45c3b576a3e2420ac415c016266b4c1c;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp deleted file mode 100644 index fc98e0f..0000000 --- a/chimeraccodecommand.cpp +++ /dev/null @@ -1,666 +0,0 @@ -/* - * 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); - } -} -//********************************************************************************************************************** -