X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=a4b3a79012aa5ac0d53c6ff78f541864984b42ec;hb=438aa88dbc092d9c1c80ec3fa20c8e47f97101c4;hp=94cba4a10e344f5e27593a4723adb662cb9ab458;hpb=182db2b6f1747bc1e0b8cd3eceec8751abdd31d5;p=mothur.git diff --git a/aligncommand.cpp b/aligncommand.cpp index 94cba4a..a4b3a79 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; } @@ -95,23 +95,45 @@ AlignCommand::AlignCommand(string option) { //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; + + #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(); + + #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); + } + + #endif + if (ableToOpen == 1) { m->mothurOut(candidateFileNames[i] + " 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; @@ -197,10 +219,10 @@ 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); } @@ -213,6 +235,8 @@ 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]); } @@ -224,8 +248,111 @@ int AlignCommand::execute(){ 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; + + 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[alignFileName.length()]; + strcpy(outAlignFilename, alignFileName.c_str()); + + char outReportFilename[reportFileName.length()]; + strcpy(outReportFilename, reportFileName.c_str()); + + char outAccnosFilename[accnosFileName.length()]; + strcpy(outAccnosFilename, accnosFileName.c_str()); + + char inFileName[candidateFileNames[s].length()]; + 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 = setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs + + //send file positions to all processes + MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs + MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos + + //figure out how many sequences you have to align + numSeqsPerProcessor = numFastaSeqs / processors; + if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; } + int startIndex = 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_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs + MPIPos.resize(numFastaSeqs+1); + MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions + + //figure out how many sequences you have to align + numSeqsPerProcessor = numFastaSeqs / processors; + if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; } + int startIndex = 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 -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) if(processors == 1){ ifstream inFASTA; openInputFile(candidateFileNames[s], inFASTA); @@ -234,8 +361,9 @@ int AlignCommand::execute(){ lines.push_back(new linePair(0, numFastaSeqs)); - int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); - if (exitCommand == 0) { + driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); + + if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); @@ -280,7 +408,7 @@ int AlignCommand::execute(){ lines.push_back(new linePair(startPos, numSeqsPerProcessor)); } - int exitCommand = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); + 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()); @@ -317,14 +445,14 @@ int AlignCommand::execute(){ m->mothurOutEndLine(); }else{ hasAccnos = false; } - if (exitCommand == 0) { + if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); return 0; } } -#else + #else ifstream inFASTA; openInputFile(candidateFileNames[s], inFASTA); numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); @@ -332,8 +460,9 @@ int AlignCommand::execute(){ lines.push_back(new linePair(0, numFastaSeqs)); - int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); - if (exitCommand == 0) { + driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); + + if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); @@ -350,12 +479,25 @@ 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(); @@ -391,12 +533,13 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName, openInputFile(filename, inFASTA); inFASTA.seekg(line->start); - + for(int i=0;inumSeqs;i++){ if (m->control_pressed) { return 0; } Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA); + int origNumBases = candidateSeq->getNumBases(); string originalUnaligned = candidateSeq->getUnaligned(); int numBasesNeeded = origNumBases * threshold; @@ -487,14 +630,160 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName, 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[length]; + strcpy(buf, outputString.c_str()); + + MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport); + } + + for(int i=0;icontrol_pressed) { return 0; } + //read next sequence + int length = MPIPos[start+i+1] - MPIPos[start+i]; + char buf4[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); + + 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[length]; + strcpy(buf, outputString.c_str()); + + MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos); + 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[length]; + strcpy(buf2, outputString.c_str()); + + MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign); + + outputString = report.getReport(); + + //send results to parent + length = outputString.length(); + char buf3[length]; + strcpy(buf3, outputString.c_str()); + + MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport); + + 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 exitCommand = 1; // processIDS.resize(0); //loop through and create all the processes you want @@ -573,5 +862,4 @@ void AlignCommand::appendReportFiles(string temp, string filename) { exit(1); } } - //**********************************************************************************************************************