+++ /dev/null
-/*
- * aligncommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 5/15/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- * This version of nast does everything I think that the greengenes nast server does and then some. I have added the
- * feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment
- * method. This latter feature is perhaps most significant. nastPlus enables a user to use either a Needleman-Wunsch
- * (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm. This is significant because it
- * 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).
- *
- */
-
-#include "aligncommand.h"
-#include "referencedb.h"
-
-//**********************************************************************************************************************
-vector<string> 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 psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
- 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<string> 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 += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
- 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<string> 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;
- ReferenceDB* rdb = ReferenceDB::getInstance();
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true;}
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string, string> parameters = parser.getParameters();
-
- ValidParameters validParameter("align.seqs");
- map<string, string>::iterator it;
-
- //check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> 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("reference");
-
- //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["reference"] = inputDir + it->second; }
- }
- }
-
- 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++) {
- //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--;
- }
- }
-
- 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
- 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;
- temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found"){ temp = "8"; }
- m->mothurConvert(temp, kmerSize);
-
- temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
- m->mothurConvert(temp, match);
-
- temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
- m->mothurConvert(temp, misMatch);
-
- temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
- m->mothurConvert(temp, gapOpen);
-
- temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
- m->mothurConvert(temp, gapExtend);
-
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
- m->setProcessors(temp);
- m->mothurConvert(temp, processors);
-
- temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
- flip = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
- save = m->isTrue(temp);
- rdb->save = save;
- if (save) { //clear out old references
- rdb->clearMemory();
- }
-
- //this has to go after save so that if the user sets save=t and provides no reference we abort
- templateFileName = validParameter.validFile(parameters, "reference", true);
- if (templateFileName == "not found") {
- //check for saved reference sequences
- if (rdb->referenceSeqs.size() != 0) {
- templateFileName = "saved";
- }else {
- m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the align.seqs command.");
- m->mothurOutEndLine();
- abort = true;
- }
- }else if (templateFileName == "not open") { abort = true; }
- else { if (save) { rdb->setSavedReference(templateFileName); } }
-
- temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; }
- m->mothurConvert(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; }
-
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "AlignCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-AlignCommand::~AlignCommand(){
-
- if (abort == false) {
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- delete templateDB;
- }
-}
-//**********************************************************************************************************************
-
-int AlignCommand::execute(){
- try {
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand());
-
- for (int s = 0; s < candidateFileNames.size(); s++) {
- if (m->control_pressed) { outputTypes.clear(); return 0; }
-
- m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
-
- if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); }
- string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
- string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
- bool hasAccnos = true;
-
- int numFastaSeqs = 0;
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- int start = time(NULL);
-
-#ifdef USE_MPI
- int pid, numSeqsPerProcessor;
- int tag = 2001;
- vector<unsigned long long> 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;
- m->mothurRemove(accnosFileName);
- }
- }
-
-#else
-
- vector<unsigned long long> positions;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- 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)])); }
- #else
- if (processors == 1) {
- lines.push_back(new linePair(0, 1000));
- }else {
- positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs);
- if (positions.size() < processors) { processors = positions.size(); }
-
- //figure out how many sequences you have to process
- int numSeqsPerProcessor = numFastaSeqs / processors;
- for (int i = 0; i < processors; i++) {
- int startIndex = i * numSeqsPerProcessor;
- if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
- lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
- }
- }
- #endif
-
- if(processors == 1){
- numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
- }else{
- numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
- }
-
- if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(alignFileName); m->mothurRemove(reportFileName); outputTypes.clear(); return 0; }
-
- //delete accnos file if its blank else report to user
- if (m->isBlank(accnosFileName)) { m->mothurRemove(accnosFileName); 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();
- }
-
- //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();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
- try {
- ofstream alignmentFile;
- m->openOutputFile(alignFName, alignmentFile);
-
- ofstream accnosFile;
- m->openOutputFile(accnosFName, accnosFile);
-
- NastReport report(reportFName);
-
- ifstream inFASTA;
- m->openInputFile(filename, inFASTA);
-
- inFASTA.seekg(filePos->start);
-
- bool done = false;
- int count = 0;
-
- //moved this into driver to avoid deep copies in windows paralellized version
- Alignment* alignment;
- 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); }
- else if(align == "noalign") { alignment = new NoAlign(); }
- else {
- 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);
- }
-
- while (!done) {
-
- if (m->control_pressed) { break; }
-
- Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
- 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 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;
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- unsigned long long 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(); }
-
- }
- //report progress
- if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-
- delete alignment;
- alignmentFile.close();
- inFASTA.close();
- accnosFile.close();
-
- return count;
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "driver");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-#ifdef USE_MPI
-int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long long>& 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;
- }
-
- Alignment* alignment;
- 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); }
- else if(align == "noalign") { alignment = new NoAlign(); }
- else {
- 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);
- }
-
-
- for(int i=0;i<num;i++){
-
- if (m->control_pressed) { delete alignment; 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
-/**************************************************************************************************/
-
-int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
- try {
- int num = 0;
- processIDS.resize(0);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- int process = 1;
-
- //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){
- num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
-
- //pass numSeqs to parent
- ofstream out;
- string tempFile = alignFileName + toString(getpid()) + ".num.temp";
- m->openOutputFile(tempFile, out);
- out << num << endl;
- out.close();
-
- exit(0);
- }else {
- m->mothurOut("[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<processIDS.size();i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- vector<string> nonBlankAccnosFiles;
- if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
- else { m->mothurRemove(accnosFName); } //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(); m->mothurRemove(tempFile);
-
- appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
- m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
-
- appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
- m->mothurRemove((reportFileName + toString(processIDS[i]) + ".temp"));
-
- if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
- nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
- }else { m->mothurRemove((accnosFName + toString(processIDS[i]) + ".temp")); }
-
- }
-
- //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);
- m->mothurRemove(nonBlankAccnosFiles[h]);
- }
- }else { //recreate the accnosfile if needed
- ofstream out;
- m->openOutputFile(accnosFName, out);
- out.close();
- }
-#else
- //////////////////////////////////////////////////////////////////////////////////////////////////////
- //Windows version shared memory, so be careful when passing variables through the alignData struct.
- //Above fork() will clone, so memory is separate, but that's not the case with windows,
- //////////////////////////////////////////////////////////////////////////////////////////////////////
-
- vector<alignData*> pDataArray;
- DWORD dwThreadIdArray[processors-1];
- HANDLE hThreadArray[processors-1];
-
- //Create processor worker threads.
- for( int i=0; i<processors-1; i++ ){
- //copy templateDb
- //AlignmentDB* tempDB = new AlignmentDB(*templateDB);
-
- // Allocate memory for thread data.
- string extension = "";
- if (i != 0) { extension = toString(i) + ".temp"; }
-
- alignData* tempalign = new alignData(templateFileName, (alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
- pDataArray.push_back(tempalign);
- processIDS.push_back(i);
-
- //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
- //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
- hThreadArray[i] = CreateThread(NULL, 0, MyAlignThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
- }
-
- //need to check for line ending error
- ifstream inFASTA;
- m->openInputFile(filename, inFASTA);
- inFASTA.seekg(lines[processors-1]->start-1);
- char c = inFASTA.peek();
-
- if (c != '>') { //we need to move back
- lines[processors-1]->start--;
- }
-
- //using the main process as a worker saves time and memory
- //do my part - do last piece because windows is looking for eof
- num = driver(lines[processors-1], (alignFileName + toString(processors-1) + ".temp"), (reportFileName + toString(processors-1) + ".temp"), (accnosFName + toString(processors-1) + ".temp"), filename);
-
- //Wait until all threads have terminated.
- WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
-
- //Close all thread handles and free memory allocations.
- for(int i=0; i < pDataArray.size(); i++){
- num += pDataArray[i]->count;
- CloseHandle(hThreadArray[i]);
- delete pDataArray[i];
- }
-
- vector<string> nonBlankAccnosFiles;
- if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
- else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
-
- for (int i = 1; i < processors; i++) {
- appendAlignFiles((alignFileName + toString(i) + ".temp"), alignFileName);
- m->mothurRemove((alignFileName + toString(i) + ".temp"));
-
- appendReportFiles((reportFileName + toString(i) + ".temp"), reportFileName);
- m->mothurRemove((reportFileName + toString(i) + ".temp"));
-
- if (!(m->isBlank(accnosFName + toString(i) + ".temp"))) {
- nonBlankAccnosFiles.push_back(accnosFName + toString(i) + ".temp");
- }else { m->mothurRemove((accnosFName + toString(i) + ".temp")); }
- }
-
- //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);
- m->mothurRemove(nonBlankAccnosFiles[h]);
- }
- }else { //recreate the accnosfile if needed
- ofstream out;
- m->openOutputFile(accnosFName, out);
- out.close();
- }
-#endif
-
- return num;
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "createProcesses");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-void AlignCommand::appendAlignFiles(string temp, string filename) {
- try{
-
- ofstream output;
- ifstream input;
- m->openOutputFileAppend(filename, output);
- m->openInputFile(temp, input);
-
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
- }
-
- input.close();
- output.close();
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "appendAlignFiles");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-void AlignCommand::appendReportFiles(string temp, string filename) {
- try{
-
- ofstream output;
- ifstream 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
-
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
- }
-
- input.close();
- output.close();
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "appendReportFiles");
- exit(1);
- }
-}
-//**********************************************************************************************************************
projects / mothur.git / blobdiff