X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=5aabeef9437bd9f5fdd90f6b785e52065afc3115;hb=0c764f30117bc3ae41413e12071070330c3d6a3d;hp=94cba4a10e344f5e27593a4723adb662cb9ab458;hpb=182db2b6f1747bc1e0b8cd3eceec8751abdd31d5;p=mothur.git diff --git a/aligncommand.cpp b/aligncommand.cpp index 94cba4a..5aabeef 100644 --- a/aligncommand.cpp +++ b/aligncommand.cpp @@ -32,7 +32,7 @@ AlignCommand::AlignCommand(string option) { try { abort = false; - + //allow user to run help if(option == "help") { help(); abort = true; } @@ -45,7 +45,7 @@ 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 @@ -68,7 +68,7 @@ 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; } } @@ -86,32 +86,47 @@ 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 = openInputFile(candidateFileNames[i], in); + + ableToOpen = m->openInputFile(candidateFileNames[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(candidateFileNames[i]); + m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ableToOpen = m->openInputFile(tryPath, in, "noerror"); + candidateFileNames[i] = tryPath; + } + } + in.close(); + 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--; } - in.close(); + } //make sure there is at least one valid file left if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; } } - + //check for optional parameter and set defaults // ...at some point should added some additional type checking... string temp; @@ -134,7 +149,7 @@ 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); @@ -197,10 +212,10 @@ void AlignCommand::help(){ int AlignCommand::execute(){ try { if (abort == true) { return 0; } - + templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch); int longestBase = templateDB->getLongestBase(); - + if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); } else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); } else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); } @@ -213,37 +228,139 @@ int AlignCommand::execute(){ vector outputNames; for (int s = 0; s < candidateFileNames.size(); s++) { + if (m->control_pressed) { 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; for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); int start = time(NULL); + +#ifdef USE_MPI + int pid, end, numSeqsPerProcessor; + int tag = 2001; + vector MPIPos; + MPIWroteAccnos = false; -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - if(processors == 1){ - ifstream inFASTA; - openInputFile(candidateFileNames[s], inFASTA); - numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); - inFASTA.close(); - - lines.push_back(new linePair(0, numFastaSeqs)); - - int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); - if (exitCommand == 0) { - remove(accnosFileName.c_str()); - remove(alignFileName.c_str()); - remove(reportFileName.c_str()); - return 0; + 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 outMPIAlign; + MPI_File outMPIReport; + MPI_File outMPIAccnos; + + int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; + int inMode=MPI_MODE_RDONLY; + + char outAlignFilename[1024]; + strcpy(outAlignFilename, alignFileName.c_str()); + + char outReportFilename[1024]; + strcpy(outReportFilename, reportFileName.c_str()); + + char outAccnosFilename[1024]; + strcpy(outAccnosFilename, accnosFileName.c_str()); + + char inFileName[1024]; + strcpy(inFileName, candidateFileNames[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, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign); + 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 (pid == 0) { //you are the root process + + MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs + + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } + + //figure out how many sequences you have to align + numSeqsPerProcessor = numFastaSeqs / processors; + 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; } + + for (int i = 1; i < processors; i++) { + bool tempResult; + MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status); + if (tempResult != 0) { MPIWroteAccnos = true; } + } + }else{ //you are a child process + MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + MPIPos.resize(numFastaSeqs+1); + MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + + + //figure out how many sequences you have to align + numSeqsPerProcessor = numFastaSeqs / processors; + 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; } + + MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); + } + + //close files + MPI_File_close(&inMPI); + MPI_File_close(&outMPIAlign); + MPI_File_close(&outMPIReport); + MPI_File_close(&outMPIAccnos); + + //delete accnos file if blank + if (pid == 0) { + //delete accnos file if its blank else report to user + if (MPIWroteAccnos) { + m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + "."); + if (!flip) { + m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); + }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); } + m->mothurOutEndLine(); + }else { + //MPI_Info info; + //MPI_File_delete(outAccnosFilename, info); + hasAccnos = false; + remove(accnosFileName.c_str()); + } } +#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){ + 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; } + //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) { @@ -251,36 +368,10 @@ 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] == '>'){ 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++) { - long int startPos = positions[ i * numSeqsPerProcessor ]; - if(i == processors - 1){ - numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; - } - lines.push_back(new linePair(startPos, numSeqsPerProcessor)); - } - - int exitCommand = 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()); @@ -297,7 +388,7 @@ 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()); } } @@ -317,31 +408,15 @@ int AlignCommand::execute(){ m->mothurOutEndLine(); }else{ hasAccnos = false; } - if (exitCommand == 0) { - remove(accnosFileName.c_str()); - remove(alignFileName.c_str()); - remove(reportFileName.c_str()); - return 0; - } - } -#else - ifstream inFASTA; - openInputFile(candidateFileNames[s], inFASTA); - numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); - inFASTA.close(); - - lines.push_back(new linePair(0, numFastaSeqs)); - - int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); - if (exitCommand == 0) { - 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()); return 0; } } + #else + 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; } //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) { @@ -350,12 +425,25 @@ int AlignCommand::execute(){ m->mothurOutEndLine(); } -#endif - + #endif + +#endif + + + #ifdef USE_MPI + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + 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); } - + + #ifdef USE_MPI + } + #endif + m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); @@ -377,26 +465,30 @@ 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); - - for(int i=0;inumSeqs;i++){ + inFASTA.seekg(filePos->start); + + bool done = false; + int count = 0; + + while (!done) { if (m->control_pressed) { return 0; } - Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA); + Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); + int origNumBases = candidateSeq->getNumBases(); string originalUnaligned = candidateSeq->getUnaligned(); int numBasesNeeded = origNumBases * threshold; @@ -423,7 +515,7 @@ 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 @@ -445,8 +537,9 @@ 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; } @@ -467,34 +560,202 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName, report.print(); delete nast; if (needToDeleteCopy) { delete copy; } + + count++; } delete candidateSeq; + unsigned long int pos = inFASTA.tellg(); + if ((pos == -1) || (pos >= filePos->end)) { break; } + //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"); exit(1); } } +//********************************************************************************************************************** +#ifdef USE_MPI +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; + MPI_Status statusAlign; + MPI_Status statusAccnos; + MPI_Status status; + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + NastReport report; + + if (pid == 0) { + outputString = report.getHeaders(); + int length = outputString.length(); + + char* buf = new char[length]; + memcpy(buf, outputString.c_str(), length); + + MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport); + + delete buf; + } + + 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]; + //memcpy(buf4, outputString.c_str(), length); + + MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status); + + string tempBuf = buf4; + + delete buf4; + + if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); } + + istringstream iss (tempBuf,istringstream::in); + + Sequence* candidateSeq = new Sequence(iss); + + int origNumBases = candidateSeq->getNumBases(); + string originalUnaligned = candidateSeq->getUnaligned(); + int numBasesNeeded = origNumBases * threshold; + + if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file + if (candidateSeq->getUnaligned().length() > alignment->getnRows()) { + alignment->resize(candidateSeq->getUnaligned().length()+1); + } + + Sequence temp = templateDB->findClosestSequence(candidateSeq); + Sequence* templateSeq = &temp; + + float searchScore = templateDB->getSearchScore(); + + Nast* nast = new Nast(alignment, candidateSeq, templateSeq); + Sequence* copy; + + Nast* nast2; + bool needToDeleteCopy = false; //this is needed in case you have you enter the ifs below + //since nast does not make a copy of hte sequence passed, and it is used by the reporter below + //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place + //so this bool tells you if you need to delete it + + //if there is a possibility that this sequence should be reversed + if (candidateSeq->getNumBases() < numBasesNeeded) { + + string wasBetter = ""; + //if the user wants you to try the reverse + if (flip) { + //get reverse compliment + copy = new Sequence(candidateSeq->getName(), originalUnaligned); + copy->reverseComplement(); + + //rerun alignment + Sequence temp2 = templateDB->findClosestSequence(copy); + Sequence* templateSeq2 = &temp2; + + searchScore = templateDB->getSearchScore(); + + nast2 = new Nast(alignment, copy, templateSeq2); + + //check if any better + if (copy->getNumBases() > candidateSeq->getNumBases()) { + candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better + templateSeq = templateSeq2; + delete nast; + nast = nast2; + needToDeleteCopy = true; + }else{ + wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence."; + delete nast2; + delete copy; + } + } + + //create accnos file with names + outputString = candidateSeq->getName() + wasBetter + "\n"; + + //send results to parent + int length = outputString.length(); + + char* buf = new char[length]; + memcpy(buf, outputString.c_str(), length); + + MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos); + delete buf; + MPIWroteAccnos = true; + } + + report.setCandidate(candidateSeq); + report.setTemplate(templateSeq); + report.setSearchParameters(search, searchScore); + report.setAlignmentParameters(align, alignment); + report.setNastParameters(*nast); + + outputString = ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n"; + + //send results to parent + int length = outputString.length(); + char* buf2 = new char[length]; + memcpy(buf2, outputString.c_str(), length); + + MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign); + + delete buf2; + + outputString = report.getReport(); + + //send results to parent + length = outputString.length(); + char* buf3 = new char[length]; + memcpy(buf3, outputString.c_str(), length); + + MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport); + + delete buf3; + delete nast; + if (needToDeleteCopy) { delete copy; } + } + delete candidateSeq; + + //report progress + if((i+1) % 100 == 0){ cout << (toString(i+1)) << endl; } + } + //report progress + if((num) % 100 != 0){ cout << (toString(num)) << endl; } + + return 1; + } + catch(exception& e) { + m->errorOut(e, "AlignCommand", "driverMPI"); + exit(1); + } +} +#endif /**************************************************************************************************/ int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; - int exitCommand; + int num = 0; // processIDS.resize(0); //loop through and create all the processes you want @@ -505,7 +766,15 @@ 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); } } @@ -516,7 +785,15 @@ 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) { @@ -524,7 +801,6 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s exit(1); } } - /**************************************************************************************************/ void AlignCommand::appendAlignFiles(string temp, string filename) { @@ -532,8 +808,8 @@ 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; } @@ -555,8 +831,8 @@ 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 @@ -573,5 +849,4 @@ void AlignCommand::appendReportFiles(string temp, string filename) { exit(1); } } - //**********************************************************************************************************************