X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=7bed27f7725f78425a3c2e8f61f528b24b00c830;hb=85bf2e965f12d609c751763883b2224e6951eeba;hp=d672fc3df2a405a1057781dacd84c4a9f2b50d6f;hpb=3abb236c602eb168ee112f080b563ebe2c705029;p=mothur.git diff --git a/aligncommand.cpp b/aligncommand.cpp index d672fc3..7bed27f 100644 --- a/aligncommand.cpp +++ b/aligncommand.cpp @@ -22,57 +22,179 @@ #include "blastalign.hpp" #include "noalign.hpp" -#include "kmerdb.hpp" -#include "suffixdb.hpp" -#include "blastdb.hpp" - #include "nast.hpp" #include "nastreport.hpp" //********************************************************************************************************************** - -AlignCommand::AlignCommand(string option){ +vector AlignCommand::getValidParameters(){ try { - // globaldata = GlobalData::getInstance(); - abort = false; - + 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; calledHelp = true; + 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; calledHelp = false; + //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true;} else { //valid paramters for this command - string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors"}; + string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"}; vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); 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 (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + 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 = ""; } + + + //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("template"); + + //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["template"] = inputDir + it->second; } + } + } + //check for required parameters templateFileName = validParameter.validFile(parameters, "template", true); + if (templateFileName == "not found") { - mothurOut("template is a required parameter for the align.seqs command."); - mothurOutEndLine(); + m->mothurOut("template is a required parameter for the align.seqs command."); + m->mothurOutEndLine(); abort = true; - } - else if (templateFileName == "not open") { abort = true; } + }else if (templateFileName == "not open") { abort = true; } - candidateFileName = validParameter.validFile(parameters, "candidate", true); - if (candidateFileName == "not found") { - mothurOut("candidate is a required parameter for the align.seqs command."); - mothurOutEndLine(); - abort = true; + 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 { + 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 = 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(); + + //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; + } + } + + //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; + } + } + + + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + candidateFileNames.erase(candidateFileNames.begin()+i); + i--; + } + + } + + //make sure there is at least one valid file left + if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; } } - else if (candidateFileName == "not open") { abort = true; } - + //check for optional parameter and set defaults // ...at some point should added some additional type checking... string temp; @@ -94,6 +216,12 @@ AlignCommand::AlignCommand(string option){ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } convert(temp, processors); + temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; } + flip = m->isTrue(temp); + + temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; } + convert(temp, threshold); + search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; } align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; } @@ -101,11 +229,10 @@ AlignCommand::AlignCommand(string option){ } catch(exception& e) { - errorOut(e, "AlignCommand", "AlignCommand"); + m->errorOut(e, "AlignCommand", "AlignCommand"); exit(1); } } - //********************************************************************************************************************** AlignCommand::~AlignCommand(){ @@ -121,23 +248,27 @@ AlignCommand::~AlignCommand(){ void AlignCommand::help(){ try { - mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n"); - mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n"); - mothurOut("The template and candidate parameters are required.\n"); - 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"); - 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"); - mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7.\n"); - mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n"); - mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n"); - mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0.\n"); - mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0.\n"); - mothurOut("The align.seqs command should be in the following format: \n"); - mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n"); - mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n"); - mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n"); + 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, 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"); + m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n"); + m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n"); + m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n"); + m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n"); + m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n"); + m->mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold. The default is false.\n"); + m->mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\n"); + m->mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n"); + m->mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n"); + m->mothurOut("The align.seqs command should be in the following format: \n"); + m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n"); + m->mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n"); } catch(exception& e) { - errorOut(e, "AlignCommand", "help"); + m->errorOut(e, "AlignCommand", "help"); exit(1); } } @@ -147,19 +278,9 @@ void AlignCommand::help(){ int AlignCommand::execute(){ try { - if (abort == true) { return 0; } - - if(search == "kmer") { templateDB = new KmerDB(templateFileName, kmerSize); } - else if(search == "suffix") { templateDB = new SuffixDB(templateFileName); } - else if(search == "blast") { templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch); } - else { - mothurOut(search + " is not a valid search option. I will run the command using kmer, ksize=8."); - mothurOutEndLine(); - kmerSize = 8; - - templateDB = new KmerDB(templateFileName, kmerSize); - } - + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + 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); } @@ -167,147 +288,496 @@ int AlignCommand::execute(){ else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); } else if(align == "noalign") { alignment = new NoAlign(); } else { - mothurOut(align + " is not a valid alignment option. I will run the command using needleman."); - mothurOutEndLine(); + m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman."); + m->mothurOutEndLine(); alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); } - string alignFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align"; - string reportFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align.report"; - - int numFastaSeqs = 0; - int start = time(NULL); - -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - if(processors == 1){ - ifstream inFASTA; - openInputFile(candidateFileName, inFASTA); - numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); - inFASTA.close(); - - lines.push_back(new linePair(0, numFastaSeqs)); - - driver(lines[0], alignFileName, reportFileName); - - } - else{ - vector positions; - processIDS.resize(0); - - ifstream inFASTA; - openInputFile(candidateFileName, inFASTA); - - string input; - while(!inFASTA.eof()){ - input = getline(inFASTA); - if (input.length() != 0) { - if(input[0] == '>'){ int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } - } - } - inFASTA.close(); + for (int s = 0; s < candidateFileNames.size(); s++) { + if (m->control_pressed) { outputTypes.clear(); return 0; } - numFastaSeqs = positions.size(); + m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine(); - int numSeqsPerProcessor = numFastaSeqs / processors; + 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; - for (int i = 0; i < processors; i++) { - int startPos = positions[ i * numSeqsPerProcessor ]; - if(i == processors - 1){ - numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; + 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, 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[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); outputTypes.clear(); 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); outputTypes.clear(); 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); outputTypes.clear(); 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()); + } } - lines.push_back(new linePair(startPos, numSeqsPerProcessor)); - } - createProcesses(alignFileName, reportFileName); - - rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str()); - rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str()); - - for(int i=1;i 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]); + }else{ + numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); } + #else + numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); + #endif + + 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 (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) { + 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(); + } + +#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); 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 + } + #endif + + m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences."); + m->mothurOutEndLine(); + m->mothurOutEndLine(); } -#else - ifstream inFASTA; - openInputFile(candidateFileName, inFASTA); - numFastaSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); - inFASTA.close(); - - lines.push_back(new linePair(0, numFastaSeqs)); - driver(lines[0], alignFileName, reportFileName); -#endif - - mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences."); - mothurOutEndLine(); - mothurOutEndLine(); + 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) { - errorOut(e, "AlignCommand", "execute"); + m->errorOut(e, "AlignCommand", "execute"); exit(1); } } //********************************************************************************************************************** -int AlignCommand::driver(linePair* line, string alignFName, string reportFName){ +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; + m->openOutputFile(accnosFName, accnosFile); + NastReport report(reportFName); ifstream inFASTA; - openInputFile(candidateFileName, inFASTA); + m->openInputFile(filename, inFASTA); - inFASTA.seekg(line->start); + inFASTA.seekg(filePos->start); - for(int i=0;inumSeqs;i++){ - - Sequence* candidateSeq = new Sequence(inFASTA); - report.setCandidate(candidateSeq); + bool done = false; + int count = 0; - Sequence temp = templateDB->findClosestSequence(candidateSeq); - Sequence* templateSeq = &temp; + while (!done) { - report.setTemplate(templateSeq); - report.setSearchParameters(search, templateDB->getSearchScore()); + if (m->control_pressed) { return 0; } - Nast nast(alignment, candidateSeq, templateSeq); - - report.setAlignmentParameters(align, alignment); + Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); + report.setCandidate(candidateSeq); - report.setNastParameters(nast); + 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; + wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement."; + }else{ + wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence."; + delete nast2; + delete copy; + } + } + + //create accnos file with names + accnosFile << candidateSeq->getName() << wasBetter << endl; + } + + report.setTemplate(templateSeq); + report.setSearchParameters(search, searchScore); + report.setAlignmentParameters(align, alignment); + report.setNastParameters(*nast); + + alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl; + + report.print(); + delete nast; + if (needToDeleteCopy) { delete copy; } + + count++; + } + delete candidateSeq; - alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl; + #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.print(); + //report progress + if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } - delete candidateSeq; } + //report progress + if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } alignmentFile.close(); inFASTA.close(); + accnosFile.close(); - return 1; + return count; } catch(exception& e) { - errorOut(e, "AlignCommand", "driver"); + 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); + report.setCandidate(candidateSeq); + + 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; + 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; + 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.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 /**************************************************************************************************/ -void AlignCommand::createProcesses(string alignFileName, string reportFileName) { +int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - int process = 0; + processIDS.resize(0); + int process = 1; + int num = 0; // processIDS.resize(0); //loop through and create all the processes you want @@ -318,24 +788,77 @@ void AlignCommand::createProcesses(string alignFileName, string reportFileName) 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){ - driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp"); + 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 { mothurOut("unable to spawn the necessary processes."); 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); + } } + //do my part + num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename); + //force parent to wait until all the processes are done for (int i=0;i nonBlankAccnosFiles; + if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); } + else { remove(accnosFName.c_str()); } //remove so other files can be renamed to it + + 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()); + + appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName); + remove((alignFileName + toString(processIDS[i]) + ".temp").c_str()); + + appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName); + remove((reportFileName + toString(processIDS[i]) + ".temp").c_str()); + + if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) { + nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp"); + }else { remove((accnosFName + toString(processIDS[i]) + ".temp").c_str()); } + + } + + //append accnos files + if (nonBlankAccnosFiles.size() != 0) { + rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str()); + + for (int h=1; h < nonBlankAccnosFiles.size(); h++) { + appendAlignFiles(nonBlankAccnosFiles[h], accnosFName); + remove(nonBlankAccnosFiles[h].c_str()); + } + }else { //recreate the accnosfile if needed + ofstream out; + m->openOutputFile(accnosFName, out); + out.close(); + } + + return num; #endif } catch(exception& e) { - errorOut(e, "AlignCommand", "createProcesses"); + m->errorOut(e, "AlignCommand", "createProcesses"); exit(1); } } - /**************************************************************************************************/ void AlignCommand::appendAlignFiles(string temp, string filename) { @@ -343,8 +866,8 @@ 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; } @@ -355,20 +878,19 @@ void AlignCommand::appendAlignFiles(string temp, string filename) { output.close(); } catch(exception& e) { - errorOut(e, "AlignCommand", "appendAlignFiles"); + m->errorOut(e, "AlignCommand", "appendAlignFiles"); exit(1); } } - -/**************************************************************************************************/ +//********************************************************************************************************************** void AlignCommand::appendReportFiles(string temp, string filename) { try{ 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 @@ -381,9 +903,8 @@ void AlignCommand::appendReportFiles(string temp, string filename) { output.close(); } catch(exception& e) { - errorOut(e, "AlignCommand", "appendReportFiles"); + m->errorOut(e, "AlignCommand", "appendReportFiles"); exit(1); } } - //**********************************************************************************************************************