X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=5da0ee8d0f091b8ce07acdedd48d2069e53ec1e9;hb=220dc345e493cddc569521111ce32ac4d965ab7f;hp=3f70e2d3733a2d40da2012d8ba31bff61c768b9b;hpb=284fd95c611ccc3b1a7875c4dacfca06d1f50ed6;p=mothur.git diff --git a/aligncommand.cpp b/aligncommand.cpp index 3f70e2d..5da0ee8 100644 --- a/aligncommand.cpp +++ b/aligncommand.cpp @@ -25,22 +25,88 @@ #include "nast.hpp" #include "nastreport.hpp" - //********************************************************************************************************************** - +vector AlignCommand::setParameters(){ + try { + CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate); + CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate); + CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch); + CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize); + CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch); + CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign); + CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch); + CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen); + CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); + CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip); + CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "AlignCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string AlignCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file."; + helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors."; + helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta."; + helpString += "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."; + helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman."; + helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8."; + helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0."; + helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0."; + helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0."; + helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0."; + helpString += "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."; + helpString += "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."; + helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported."; + helpString += "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."; + helpString += "The align.seqs command should be in the following format:"; + helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)"; + helpString += "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)"; + helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile)."; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "AlignCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +AlignCommand::AlignCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + 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; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true;} + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - - //valid paramters for this command - string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -52,7 +118,13 @@ AlignCommand::AlignCommand(string option) { 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 = ""; } @@ -64,61 +136,98 @@ AlignCommand::AlignCommand(string option) { else { string path; - it = parameters.find("template"); + it = parameters.find("reference"); //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; } + if (path == "") { parameters["reference"] = inputDir + it->second; } } } //check for required parameters - templateFileName = validParameter.validFile(parameters, "template", true); + templateFileName = validParameter.validFile(parameters, "reference", true); if (templateFileName == "not found") { - m->mothurOut("template is a required parameter for the align.seqs command."); + m->mothurOut("reference is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true; }else if (templateFileName == "not open") { 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 { - splitAtDash(candidateFileName, candidateFileNames); + candidateFileName = validParameter.validFile(parameters, "fasta", false); + if (candidateFileName == "not found") { + //if there is a current fasta file, use it + string filename = m->getFastaFile(); + if (filename != "") { candidateFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current fastafile and the candidate parameter is required."); 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++) { - if (inputDir != "") { - string path = 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, "noerror"); - - //if you can't open it, try default location - if (ableToOpen == 1) { - if (m->getDefaultPath() != "") { //default path is set - string tryPath = m->getDefaultPath() + getSimpleName(candidateFileNames[i]); - m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); - candidateFileNames[i] = tryPath; + //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]); + + bool ignore = false; + if (candidateFileNames[i] == "current") { + candidateFileNames[i] = m->getFastaFile(); + if (candidateFileNames[i] != "") { m->mothurOut("Using " + candidateFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; + //erase from file list + candidateFileNames.erase(candidateFileNames.begin()+i); + i--; } } - in.close(); - - 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--; - } + if (!ignore) { + + 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 output 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--; + }else { + m->setFastaFile(candidateFileNames[i]); + } + } } //make sure there is at least one valid file left @@ -143,18 +252,22 @@ AlignCommand::AlignCommand(string option) { 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"; } + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); 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); search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; } + if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; } align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; } + if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; } + } } @@ -163,9 +276,7 @@ AlignCommand::AlignCommand(string option) { exit(1); } } - //********************************************************************************************************************** - AlignCommand::~AlignCommand(){ if (abort == false) { @@ -174,42 +285,11 @@ AlignCommand::~AlignCommand(){ delete alignment; } } - -//********************************************************************************************************************** - -void AlignCommand::help(){ - try { - m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n"); - m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n"); - m->mothurOut("The 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) { - m->errorOut(e, "AlignCommand", "help"); - exit(1); - } -} - - //********************************************************************************************************************** int AlignCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch); int longestBase = templateDB->getLongestBase(); @@ -223,17 +303,16 @@ int AlignCommand::execute(){ m->mothurOutEndLine(); alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); } - vector outputNames; for (int s = 0; s < candidateFileNames.size(); s++) { - if (m->control_pressed) { return 0; } + if (m->control_pressed) { outputTypes.clear(); return 0; } m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine(); - if (outputDir == "") { outputDir += hasPath(candidateFileNames[s]); } - string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align"; - string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report"; - string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos"; + if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); } + string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align"; + string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report"; + string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos"; bool hasAccnos = true; int numFastaSeqs = 0; @@ -241,7 +320,7 @@ int AlignCommand::execute(){ int start = time(NULL); #ifdef USE_MPI - int pid, end, numSeqsPerProcessor; + int pid, numSeqsPerProcessor; int tag = 2001; vector MPIPos; MPIWroteAccnos = false; @@ -275,11 +354,11 @@ int AlignCommand::execute(){ MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport); MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; } if (pid == 0) { //you are the root process - MPIPos = setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs + MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs //send file positions to all processes for(int i = 1; i < processors; i++) { @@ -295,7 +374,7 @@ int AlignCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; } for (int i = 1; i < processors; i++) { bool tempResult; @@ -317,7 +396,7 @@ int AlignCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIAlign); MPI_File_close(&outMPIReport); MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; } MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); } @@ -346,75 +425,25 @@ int AlignCommand::execute(){ } #else - vector positions = divideFile(candidateFileNames[s], processors); - + + 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; } - 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(); - } }else{ - processIDS.resize(0); - 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()); - - //append alignment and report files - for(int i=1;i nonBlankAccnosFiles; - //delete blank accnos files generated with multiple processes - for(int i=0;imothurOut("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{ hasAccnos = false; } - - 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]); + #endif - if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); return 0; } + if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; } //delete accnos file if its blank else report to user - if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } + if (m->isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } else { m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + "."); if (!flip) { @@ -422,8 +451,6 @@ int AlignCommand::execute(){ }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); } m->mothurOutEndLine(); } - - #endif #endif @@ -434,9 +461,9 @@ int AlignCommand::execute(){ if (pid == 0) { //only one process should output to screen #endif - outputNames.push_back(alignFileName); - outputNames.push_back(reportFileName); - if (hasAccnos) { outputNames.push_back(accnosFileName); } + outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName); + outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName); + if (hasAccnos) { outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); } #ifdef USE_MPI } @@ -447,6 +474,12 @@ int AlignCommand::execute(){ m->mothurOutEndLine(); } + //set align file as new current fastafile + string currentFasta = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); } + } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -466,15 +499,15 @@ int AlignCommand::execute(){ 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(filePos->start); @@ -485,8 +518,9 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam if (m->control_pressed) { return 0; } - Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA); - + Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); + report.setCandidate(candidateSeq); + int origNumBases = candidateSeq->getNumBases(); string originalUnaligned = candidateSeq->getUnaligned(); int numBasesNeeded = origNumBases * threshold; @@ -498,10 +532,11 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam Sequence temp = templateDB->findClosestSequence(candidateSeq); Sequence* templateSeq = &temp; - + float searchScore = templateDB->getSearchScore(); Nast* nast = new Nast(alignment, candidateSeq, templateSeq); + Sequence* copy; Nast* nast2; @@ -516,6 +551,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam string wasBetter = ""; //if the user wants you to try the reverse if (flip) { + //get reverse compliment copy = new Sequence(candidateSeq->getName(), originalUnaligned); copy->reverseComplement(); @@ -547,7 +583,6 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam accnosFile << candidateSeq->getName() << wasBetter << endl; } - report.setCandidate(candidateSeq); report.setTemplate(templateSeq); report.setSearchParameters(search, searchScore); report.setAlignmentParameters(align, alignment); @@ -563,8 +598,12 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam } delete candidateSeq; - unsigned long int pos = inFASTA.tellg(); - if ((pos == -1) || (pos >= filePos->end)) { break; } + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + unsigned long int pos = inFASTA.tellg(); + if ((pos == -1) || (pos >= filePos->end)) { break; } + #else + if (inFASTA.eof()) { break; } + #endif //report progress if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } @@ -631,7 +670,8 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align 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; @@ -680,6 +720,7 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align delete nast; nast = nast2; needToDeleteCopy = true; + wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement."; }else{ wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence."; delete nast2; @@ -701,7 +742,6 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align MPIWroteAccnos = true; } - report.setCandidate(candidateSeq); report.setTemplate(templateSeq); report.setSearchParameters(search, searchScore); report.setAlignmentParameters(align, alignment); @@ -752,7 +792,8 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align 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); @@ -768,27 +809,63 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s //pass numSeqs to parent ofstream out; - string tempFile = toString(getpid()) + ".temp"; - openOutputFile(tempFile, out); + string tempFile = alignFileName + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); out << num << endl; out.close(); exit(0); - }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); } + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } } + //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 = toString(processIDS[i]) + ".temp"; - openInputFile(tempFile, 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; @@ -806,8 +883,8 @@ 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; } @@ -829,8 +906,8 @@ 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