X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=39408427d87d439d6cdf8e637dd656df5049becd;hb=bdb5d82e2a73829b4e1fa42656ad9bcb57e3e948;hp=8d1b40f37cd7eb9edfc708e3b9e856092de5eb5a;hpb=956cdff34f2d609a7736838b1631cd7957580b8b;p=mothur.git diff --git a/aligncommand.cpp b/aligncommand.cpp index 8d1b40f..3940842 100644 --- a/aligncommand.cpp +++ b/aligncommand.cpp @@ -27,10 +27,58 @@ //********************************************************************************************************************** - +vector AlignCommand::getValidParameters(){ + try { + string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "AlignCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector AlignCommand::getRequiredParameters(){ + try { + string AlignArray[] = {"template","candidate"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "AlignCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector AlignCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "AlignCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +AlignCommand::AlignCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["alignreport"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "AlignCommand", "AlignCommand"); + exit(1); + } +} +//********************************************************************************************************************** AlignCommand::AlignCommand(string option) { try { - abort = false; //allow user to run help @@ -45,14 +93,20 @@ AlignCommand::AlignCommand(string option) { OptionParser parser(option); map parameters = parser.getParameters(); - ValidParameters validParameter; + ValidParameters validParameter("align.seqs"); 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; } } - + + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["alignreport"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + //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 = ""; } @@ -68,7 +122,7 @@ AlignCommand::AlignCommand(string option) { //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; } } @@ -86,43 +140,51 @@ AlignCommand::AlignCommand(string option) { candidateFileName = validParameter.validFile(parameters, "candidate", false); if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true; } else { - splitAtDash(candidateFileName, candidateFileNames); + m->splitAtDash(candidateFileName, candidateFileNames); //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < candidateFileNames.size(); i++) { + //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]); + if (inputDir != "") { - string path = hasPath(candidateFileNames[i]); + string path = m->hasPath(candidateFileNames[i]); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[i]; } } int ableToOpen; ifstream in; + ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror"); + in.close(); - #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 - - if (pid == 0) { - #endif - - ableToOpen = openInputFile(candidateFileNames[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(candidateFileNames[i]); + m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + candidateFileNames[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(candidateFileNames[i]); + m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + candidateFileNames[i] = tryPath; } - - #endif + } + + if (ableToOpen == 1) { - m->mothurOut(candidateFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); + m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); //erase from file list candidateFileNames.erase(candidateFileNames.begin()+i); i--; @@ -156,7 +218,7 @@ AlignCommand::AlignCommand(string option) { convert(temp, processors); temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; } - flip = isTrue(temp); + flip = m->isTrue(temp); temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; } convert(temp, threshold); @@ -172,7 +234,6 @@ AlignCommand::AlignCommand(string option) { exit(1); } } - //********************************************************************************************************************** AlignCommand::~AlignCommand(){ @@ -189,7 +250,7 @@ AlignCommand::~AlignCommand(){ void AlignCommand::help(){ try { m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n"); - m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n"); + m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen, gapextend and processors.\n"); m->mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); m->mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n"); m->mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n"); @@ -232,17 +293,16 @@ int AlignCommand::execute(){ m->mothurOutEndLine(); alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); } - vector outputNames; for (int s = 0; s < candidateFileNames.size(); s++) { - if (m->control_pressed) { return 0; } + if (m->control_pressed) { outputTypes.clear(); return 0; } m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine(); - if (outputDir == "") { outputDir += hasPath(candidateFileNames[s]); } - string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align"; - string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report"; - string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos"; + if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); } + string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align"; + string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report"; + string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos"; bool hasAccnos = true; int numFastaSeqs = 0; @@ -252,9 +312,9 @@ int AlignCommand::execute(){ #ifdef USE_MPI int pid, end, numSeqsPerProcessor; int tag = 2001; - vector MPIPos; + vector MPIPos; MPIWroteAccnos = false; - + MPI_Status status; MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are MPI_Comm_size(MPI_COMM_WORLD, &processors); @@ -284,11 +344,11 @@ int AlignCommand::execute(){ MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport); MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; } if (pid == 0) { //you are the root process - MPIPos = setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs + MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs //send file positions to all processes for(int i = 1; i < processors; i++) { @@ -301,11 +361,10 @@ int AlignCommand::execute(){ int startIndex = pid * numSeqsPerProcessor; if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; } - //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; } for (int i = 1; i < processors; i++) { bool tempResult; @@ -327,7 +386,7 @@ int AlignCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; } MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); } @@ -356,27 +415,19 @@ int AlignCommand::execute(){ } #else - + + vector positions = m->divideFile(candidateFileNames[s], processors); + for (int i = 0; i < (positions.size()-1); i++) { + lines.push_back(new linePair(positions[i], positions[(i+1)])); + } #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) if(processors == 1){ - ifstream inFASTA; - openInputFile(candidateFileNames[s], inFASTA); - getNumSeqs(inFASTA, numFastaSeqs); - inFASTA.close(); + numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); - lines.push_back(new linePair(0, numFastaSeqs)); - - driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); - - if (m->control_pressed) { - remove(accnosFileName.c_str()); - remove(alignFileName.c_str()); - remove(reportFileName.c_str()); - return 0; - } + if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; } //delete accnos file if its blank else report to user - if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } + if (m->isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } else { m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + "."); if (!flip) { @@ -384,36 +435,10 @@ int AlignCommand::execute(){ }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); } m->mothurOutEndLine(); } - } - else{ - vector positions; + }else{ processIDS.resize(0); - ifstream inFASTA; - openInputFile(candidateFileNames[s], inFASTA); - - string input; - while(!inFASTA.eof()){ - input = getline(inFASTA); - if (input.length() != 0) { - if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } - } - } - inFASTA.close(); - - numFastaSeqs = positions.size(); - - int numSeqsPerProcessor = numFastaSeqs / processors; - - for (int i = 0; i < processors; i++) { - unsigned long int startPos = positions[ i * numSeqsPerProcessor ]; - if(i == processors - 1){ - numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; - } - lines.push_back(new linePair(startPos, numSeqsPerProcessor)); - } - - createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); + numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str()); rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str()); @@ -430,7 +455,7 @@ int AlignCommand::execute(){ vector nonBlankAccnosFiles; //delete blank accnos files generated with multiple processes for(int i=0;iisBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) { nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp"); }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); } } @@ -450,32 +475,15 @@ int AlignCommand::execute(){ m->mothurOutEndLine(); }else{ hasAccnos = false; } - if (m->control_pressed) { - remove(accnosFileName.c_str()); - remove(alignFileName.c_str()); - remove(reportFileName.c_str()); - return 0; - } + if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; } } #else - ifstream inFASTA; - openInputFile(candidateFileNames[s], inFASTA); - getNumSeqs(inFASTA, numFastaSeqs); - inFASTA.close(); + numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); - lines.push_back(new linePair(0, numFastaSeqs)); - - driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); - - if (m->control_pressed) { - remove(accnosFileName.c_str()); - remove(alignFileName.c_str()); - remove(reportFileName.c_str()); - return 0; - } + if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; } //delete accnos file if its blank else report to user - if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } + if (m->isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } else { m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + "."); if (!flip) { @@ -495,9 +503,9 @@ int AlignCommand::execute(){ if (pid == 0) { //only one process should output to screen #endif - outputNames.push_back(alignFileName); - outputNames.push_back(reportFileName); - if (hasAccnos) { outputNames.push_back(accnosFileName); } + outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName); + outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName); + if (hasAccnos) { outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); } #ifdef USE_MPI } @@ -524,27 +532,31 @@ int AlignCommand::execute(){ //********************************************************************************************************************** -int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){ +int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){ try { ofstream alignmentFile; - openOutputFile(alignFName, alignmentFile); + m->openOutputFile(alignFName, alignmentFile); ofstream accnosFile; - openOutputFile(accnosFName, accnosFile); + m->openOutputFile(accnosFName, accnosFile); NastReport report(reportFName); ifstream inFASTA; - openInputFile(filename, inFASTA); + m->openInputFile(filename, inFASTA); - inFASTA.seekg(line->start); + inFASTA.seekg(filePos->start); + + bool done = false; + int count = 0; - for(int i=0;inumSeqs;i++){ + while (!done) { if (m->control_pressed) { return 0; } - Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA); - + Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); + report.setCandidate(candidateSeq); + int origNumBases = candidateSeq->getNumBases(); string originalUnaligned = candidateSeq->getUnaligned(); int numBasesNeeded = origNumBases * threshold; @@ -556,10 +568,11 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName, Sequence temp = templateDB->findClosestSequence(candidateSeq); Sequence* templateSeq = &temp; - + float searchScore = templateDB->getSearchScore(); Nast* nast = new Nast(alignment, candidateSeq, templateSeq); + Sequence* copy; Nast* nast2; @@ -571,9 +584,10 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName, //if there is a possibility that this sequence should be reversed if (candidateSeq->getNumBases() < numBasesNeeded) { - string wasBetter = ""; + string wasBetter = ""; //if the user wants you to try the reverse if (flip) { + //get reverse compliment copy = new Sequence(candidateSeq->getName(), originalUnaligned); copy->reverseComplement(); @@ -593,8 +607,9 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName, delete nast; nast = nast2; needToDeleteCopy = true; + wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement."; }else{ - wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence."; + wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence."; delete nast2; delete copy; } @@ -604,7 +619,6 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName, accnosFile << candidateSeq->getName() << wasBetter << endl; } - report.setCandidate(candidateSeq); report.setTemplate(templateSeq); report.setSearchParameters(search, searchScore); report.setAlignmentParameters(align, alignment); @@ -615,20 +629,30 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName, report.print(); delete nast; if (needToDeleteCopy) { delete copy; } + + 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(toString(i+1)); m->mothurOutEndLine(); } + if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } + } //report progress - if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine(); } + if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } alignmentFile.close(); inFASTA.close(); accnosFile.close(); - return 1; + return count; } catch(exception& e) { m->errorOut(e, "AlignCommand", "driver"); @@ -637,7 +661,7 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName, } //********************************************************************************************************************** #ifdef USE_MPI -int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector& MPIPos){ +int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector& MPIPos){ try { string outputString = ""; MPI_Status statusReport; @@ -669,7 +693,7 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align int length = MPIPos[start+i+1] - MPIPos[start+i]; char* buf4 = new char[length]; - memcpy(buf4, outputString.c_str(), length); + //memcpy(buf4, outputString.c_str(), length); MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status); @@ -678,9 +702,12 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align delete buf4; if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); } - istringstream iss (tempBuf,istringstream::in); + istringstream iss (tempBuf,istringstream::in); + Sequence* candidateSeq = new Sequence(iss); + report.setCandidate(candidateSeq); + int origNumBases = candidateSeq->getNumBases(); string originalUnaligned = candidateSeq->getUnaligned(); int numBasesNeeded = origNumBases * threshold; @@ -729,6 +756,7 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align delete nast; nast = nast2; needToDeleteCopy = true; + wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement."; }else{ wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence."; delete nast2; @@ -750,7 +778,6 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align MPIWroteAccnos = true; } - report.setCandidate(candidateSeq); report.setTemplate(templateSeq); report.setSearchParameters(search, searchScore); report.setAlignmentParameters(align, alignment); @@ -802,7 +829,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; - int exitCommand = 1; + int num = 0; // processIDS.resize(0); //loop through and create all the processes you want @@ -813,9 +840,21 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s 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){ - exitCommand = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename); + num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename); + + //pass numSeqs to parent + ofstream out; + string tempFile = alignFileName + 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 @@ -824,7 +863,15 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s wait(&temp); } - return exitCommand; + for (int i = 0; i < processIDS.size(); i++) { + ifstream in; + string tempFile = alignFileName + 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) { @@ -832,7 +879,6 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s exit(1); } } - /**************************************************************************************************/ void AlignCommand::appendAlignFiles(string temp, string filename) { @@ -840,8 +886,8 @@ void AlignCommand::appendAlignFiles(string temp, string filename) { ofstream output; ifstream input; - openOutputFileAppend(filename, output); - openInputFile(temp, input); + m->openOutputFileAppend(filename, output); + m->openInputFile(temp, input); while(char c = input.get()){ if(input.eof()) { break; } @@ -863,8 +909,8 @@ void AlignCommand::appendReportFiles(string temp, string filename) { ofstream output; ifstream input; - openOutputFileAppend(filename, output); - openInputFile(temp, input); + m->openOutputFileAppend(filename, output); + m->openInputFile(temp, input); while (!input.eof()) { char c = input.get(); if (c == 10 || c == 13){ break; } } // get header line