X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=064189b1423434f24e88fb05df3ad67a7ea4967f;hb=02909d6cae9963ba00dc746969a370fa8ca934fc;hp=81f8e6ab78c7dbc90d351894bd420a7d7e2cca9e;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git diff --git a/aligncommand.cpp b/aligncommand.cpp index 81f8e6a..064189b 100644 --- a/aligncommand.cpp +++ b/aligncommand.cpp @@ -12,45 +12,85 @@ * allows for a global alignment and not the local alignment provided by bLAst. Furthermore, it has the potential to * provide a better alignment because of the banding method employed by blast (I'm not sure about this). * - * to compile type: - * make - * - * for basic instructions on how to run nastPlus type: - * ./nastPlus */ #include "aligncommand.h" #include "sequence.hpp" -#include "alignment.hpp" #include "gotohoverlap.hpp" #include "needlemanoverlap.hpp" #include "blastalign.hpp" #include "noalign.hpp" -#include "database.hpp" #include "kmerdb.hpp" #include "suffixdb.hpp" #include "blastdb.hpp" -#include "distancedb.hpp" #include "nast.hpp" #include "nastreport.hpp" //********************************************************************************************************************** -AlignCommand::AlignCommand(){ + +AlignCommand::AlignCommand(string option){ try { - globaldata = GlobalData::getInstance(); - candidateFileName = globaldata->inputFileName; - templateFileName = globaldata->getTemplateFile(); - openInputFile(candidateFileName, in); - convert(globaldata->getKSize(), kmerSize); - convert(globaldata->getMatch(), match); - convert(globaldata->getMismatch(), misMatch); - convert(globaldata->getGapopen(), gapOpen); - convert(globaldata->getGapextend(), gapExtend); - distanceFileName = "????"; + // globaldata = GlobalData::getInstance(); + abort = false; + + //allow user to run help + if(option == "help") { help(); abort = true; } + + else { + + //valid paramters for this command + string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //check for required parameters + templateFileName = validParameter.validFile(parameters, "template", true); + if (templateFileName == "not found") { cout << "template is a required parameter for the align.seqs command." << endl; abort = true; } + else if (templateFileName == "not open") { abort = true; } + + candidateFileName = validParameter.validFile(parameters, "candidate", true); + if (candidateFileName == "not found") { cout << "candidate is a required parameter for the align.seqs command." << endl; 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; + temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; } + convert(temp, kmerSize); + + temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; } + convert(temp, match); + + temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; } + convert(temp, misMatch); + + temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; } + convert(temp, gapOpen); + + temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; } + convert(temp, gapExtend); + + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } + convert(temp, processors); + + search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; } + + align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; } + } + } catch(exception& e) { cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function AlignCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; @@ -64,88 +104,309 @@ AlignCommand::AlignCommand(){ //********************************************************************************************************************** -AlignCommand::~AlignCommand(){ - +AlignCommand::~AlignCommand(){ + + if (abort == false) { + for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); + delete templateDB; + delete alignment; + } +} + +//********************************************************************************************************************** + +void AlignCommand::help(){ + try { + cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n"; + cout << "The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n"; + cout << "The template and candidate parameters are required." << "\n"; + cout << "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"; + cout << "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"; + cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7." << "\n"; + cout << "The match parameter allows you to specify the bonus for having the same base. The default is 1.0." << "\n"; + cout << "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0." << "\n"; + cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0." << "\n"; + cout << "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0." << "\n"; + cout << "The align.seqs command should be in the following format: " << "\n"; + cout << "align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n"; + cout << "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"; + cout << "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n"; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the AlignCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } } + //********************************************************************************************************************** int AlignCommand::execute(){ try { - srand( (unsigned)time( NULL ) ); //needed to assign names to temporary files - - Database* templateDB; - if(globaldata->getSearch() == "kmer") { templateDB = new KmerDB(templateFileName, kmerSize); } - else if(globaldata->getSearch() == "suffix") { templateDB = new SuffixDB(templateFileName); } - else if(globaldata->getSearch() == "blast") { templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch); } - else if(globaldata->getSearch() == "distance") { templateDB = new DistanceDB(templateFileName, distanceFileName); } - else { cout << globaldata->getSearch() << " is not a valid search option. I will run the command using suffix." << endl; - templateDB = new SuffixDB(templateFileName); } - - Alignment* alignment; - if(globaldata->getAlign() == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, 3000); } - else if(globaldata->getAlign() == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000); } - else if(globaldata->getAlign() == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); } - else if(globaldata->getAlign() == "noalign") { alignment = new NoAlign(); } - else { cout << globaldata->getAlign() << " is not a valid alignment option. I will run the command using blast." << endl; - alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); } - - int numFastaSeqs=count(istreambuf_iterator(in),istreambuf_iterator(), '>'); - in.seekg(0); - - string candidateAligngmentFName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + globaldata->getSearch() + '.' + globaldata->getAlign() + ".nast.align"; - ofstream candidateAlignmentFile; - openOutputFile(candidateAligngmentFName, candidateAlignmentFile); - - string candidateReportFName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + globaldata->getSearch() + '.' + globaldata->getAlign() + ".nast.report"; - NastReport report(candidateReportFName); - - cout << "We are going to align the " << numFastaSeqs << " sequences in " << candidateFileName << "..." << endl; - cout.flush(); - + 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 { + cout << search << " is not a valid search option. I will run the command using kmer, ksize=8." << endl; kmerSize = 8; + templateDB = new KmerDB(templateFileName, kmerSize); + } + + if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, 3000); } + else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000); } + else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); } + else if(align == "noalign") { alignment = new NoAlign(); } + else { + cout << align << " is not a valid alignment option. I will run the command using needleman." << endl; + alignment = new NeedlemanOverlap(gapOpen, match, misMatch, 3000); + } + + 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); + + while(!inFASTA.eof()){ + char c = inFASTA.get(); + if(c == '>'){ positions.push_back(inFASTA.tellg()); } + while (!inFASTA.eof()) { c = inFASTA.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + } + inFASTA.close(); + + numFastaSeqs = positions.size(); + + int numSeqsPerProcessor = numFastaSeqs / processors; + + for (int i = 0; i < processors; i++) { + int startPos = positions[ i * numSeqsPerProcessor ]; + if(i == processors - 1){ + numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; + } + 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(inFASTA),istreambuf_iterator(), '>'); + inFASTA.close(); + + lines.push_back(new linePair(0, numFastaSeqs)); + + driver(lines[0], alignFileName, reportFileName); +#endif + + cout << "It took " << time(NULL) - start << " secs to align " << numFastaSeqs << " sequences" << endl; + cout << endl; + + + + return 0; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the AlignCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} - for(int i=0;istart); + + for(int i=0;inumSeqs;i++){ + + Sequence* candidateSeq = new Sequence(inFASTA); report.setCandidate(candidateSeq); - - Sequence* templateSeq = templateDB->findClosestSequence(candidateSeq); + + Sequence temp = templateDB->findClosestSequence(candidateSeq); + Sequence* templateSeq = &temp; + report.setTemplate(templateSeq); - report.setSearchParameters(globaldata->getSearch(), templateDB->getSearchScore()); - + report.setSearchParameters(search, templateDB->getSearchScore()); + Nast nast(alignment, candidateSeq, templateSeq); - report.setAlignmentParameters(globaldata->getAlign(), alignment); + report.setAlignmentParameters(align, alignment); report.setNastParameters(nast); + + alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl; + + report.print(); + + delete candidateSeq; + } + + alignmentFile.close(); + inFASTA.close(); + + return 1; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the AlignCommand class Function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the AlignCommand class function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} - candidateAlignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl; - candidateAlignmentFile.flush(); +/**************************************************************************************************/ - if((i+1) % 100 == 0){ - cout << "It has taken " << time(NULL) - start << " secs to align " << i+1 << " sequences" << endl; - } - report.print(); +void AlignCommand::createProcesses(string alignFileName, string reportFileName) { + try { +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + int process = 0; + // processIDS.resize(0); - delete candidateSeq; + //loop through and create all the processes you want + while (process != processors) { + int pid = fork(); + + if (pid > 0) { + processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later + process++; + }else if (pid == 0){ + driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp"); + exit(0); + }else { cout << "unable to spawn the necessary processes." << endl; exit(0); } } - cout << "It took " << time(NULL) - start << " secs to align " << numFastaSeqs << " sequences" << endl; - cout << endl; + //force parent to wait until all the processes are done + for (int i=0;i