X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=chimerapintailcommand.cpp;h=a8d2d65c6c3752fcc7ca9737e505c32850d62f7b;hb=03acfa01ede71b107817966fcf27cd728038b3c9;hp=5818ab22c0bfc3e0245372de038e4c43d95a2289;hpb=050220fe7822cc660615972a0054cf4a83eefbe4;p=mothur.git diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp index 5818ab2..a8d2d65 100644 --- a/chimerapintailcommand.cpp +++ b/chimerapintailcommand.cpp @@ -10,14 +10,61 @@ #include "chimerapintailcommand.h" #include "pintail.h" +//********************************************************************************************************************** +vector ChimeraPintailCommand::getValidParameters(){ + try { + string AlignArray[] = {"fasta","filter","processors","window" ,"increment","template","conservation","quantile","mask","outputdir","inputdir"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraPintailCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +ChimeraPintailCommand::ChimeraPintailCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ChimeraPintailCommand", "ChimeraPintailCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector ChimeraPintailCommand::getRequiredParameters(){ + try { + string AlignArray[] = {"template","fasta"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraPintailCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ChimeraPintailCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraPintailCommand", "getRequiredFiles"); + exit(1); + } +} //*************************************************************************************************************** - ChimeraPintailCommand::ChimeraPintailCommand(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 { //valid paramters for this command @@ -35,6 +82,10 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + //if the user changes the input directory command factory will send this info to us in the output parameter inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; } @@ -43,7 +94,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { it = parameters.find("template"); //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; } } @@ -51,7 +102,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { it = parameters.find("conservation"); //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["conservation"] = inputDir + it->second; } } @@ -59,7 +110,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { it = parameters.find("quantile"); //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["quantile"] = inputDir + it->second; } } @@ -70,12 +121,12 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { fastafile = validParameter.validFile(parameters, "fasta", false); if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.pintail command."); m->mothurOutEndLine(); abort = true; } else { - splitAtDash(fastafile, fastaFileNames); + m->splitAtDash(fastafile, fastaFileNames); //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < fastaFileNames.size(); i++) { if (inputDir != "") { - string path = hasPath(fastaFileNames[i]); + string path = m->hasPath(fastaFileNames[i]); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; } } @@ -83,38 +134,33 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { int ableToOpen; ifstream in; - #ifdef USE_MPI - int pid; - MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running - MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are - - if (pid == 0) { - #endif - - ableToOpen = openInputFile(fastaFileNames[i], in, "noerror"); + ableToOpen = m->openInputFile(fastaFileNames[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(fastaFileNames[i]); + string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]); m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); fastaFileNames[i] = tryPath; } } - in.close(); - #ifdef USE_MPI - for (int j = 1; j < processors; j++) { - MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); - } - }else{ - MPI_Status status; - MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; } - - #endif + } + in.close(); + if (ableToOpen == 1) { m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); //erase from file list @@ -129,7 +175,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { string temp; temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; } - filter = isTrue(temp); + filter = m->isTrue(temp); temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; } convert(temp, processors); @@ -144,23 +190,46 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { if (maskfile == "not found") { maskfile = ""; } else if (maskfile != "default") { if (inputDir != "") { - string path = hasPath(maskfile); + string path = m->hasPath(maskfile); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { maskfile = inputDir + maskfile; } } ifstream in; - int ableToOpen = openInputFile(maskfile, in); - if (ableToOpen == 1) { abort = true; } + int ableToOpen = m->openInputFile(maskfile, in, "no error"); + if (ableToOpen == 1) { + if (m->getDefaultPath() != "") { //default path is set + string tryPath = m->getDefaultPath() + m->getSimpleName(maskfile); + m->mothurOut("Unable to open " + maskfile + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + maskfile = tryPath; + } + } + + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(maskfile); + m->mothurOut("Unable to open " + maskfile + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + maskfile = tryPath; + } + } + in.close(); + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + maskfile + "."); m->mothurOutEndLine(); + abort = true; + } } //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 = ""; - outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it - } + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } templatefile = validParameter.validFile(parameters, "template", true); if (templatefile == "not open") { abort = true; } @@ -171,13 +240,22 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { else if (consfile == "not found") { consfile = ""; //check for consfile - string tempConsFile = getRootName(inputDir + getSimpleName(templatefile)) + "freq"; + string tempConsFile = m->getRootName(inputDir + m->getSimpleName(templatefile)) + "freq"; ifstream FileTest(tempConsFile.c_str()); if(FileTest){ - bool GoodFile = checkReleaseVersion(FileTest, m->getVersion()); + bool GoodFile = m->checkReleaseVersion(FileTest, m->getVersion()); if (GoodFile) { m->mothurOut("I found " + tempConsFile + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); consfile = tempConsFile; FileTest.close(); } + }else { + string tempConsFile = m->getDefaultPath() + m->getRootName(m->getSimpleName(templatefile)) + "freq"; + ifstream FileTest2(tempConsFile.c_str()); + if(FileTest2){ + bool GoodFile = m->checkReleaseVersion(FileTest2, m->getVersion()); + if (GoodFile) { + m->mothurOut("I found " + tempConsFile + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); consfile = tempConsFile; FileTest2.close(); + } + } } } @@ -232,7 +310,7 @@ ChimeraPintailCommand::~ChimeraPintailCommand(){ /* do nothing */ } int ChimeraPintailCommand::execute(){ try{ - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } for (int s = 0; s < fastaFileNames.size(); s++) { @@ -246,32 +324,53 @@ int ChimeraPintailCommand::execute(){ //check for quantile to save the time string tempQuan = ""; if ((!filter) && (maskfile == "")) { - tempQuan = inputDir + getRootName(getSimpleName(templatefile)) + "pintail.quan"; + tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan"; }else if ((!filter) && (maskfile != "")) { - tempQuan = inputDir + getRootName(getSimpleName(templatefile)) + "pintail.masked.quan"; + tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan"; }else if ((filter) && (maskfile != "")) { - tempQuan = inputDir + getRootName(getSimpleName(templatefile)) + "pintail.filtered." + getSimpleName(getRootName(fastaFileNames[s])) + "masked.quan"; + tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan"; }else if ((filter) && (maskfile == "")) { - tempQuan = inputDir + getRootName(getSimpleName(templatefile)) + "pintail.filtered." + getSimpleName(getRootName(fastaFileNames[s])) + "quan"; + tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan"; } ifstream FileTest(tempQuan.c_str()); if(FileTest){ - bool GoodFile = checkReleaseVersion(FileTest, m->getVersion()); + bool GoodFile = m->checkReleaseVersion(FileTest, m->getVersion()); if (GoodFile) { m->mothurOut("I found " + tempQuan + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); quanfile = tempQuan; FileTest.close(); } + }else { + string tryPath = m->getDefaultPath(); + string tempQuan = ""; + if ((!filter) && (maskfile == "")) { + tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan"; + }else if ((!filter) && (maskfile != "")) { + tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan"; + }else if ((filter) && (maskfile != "")) { + tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan"; + }else if ((filter) && (maskfile == "")) { + tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan"; + } + + ifstream FileTest2(tempQuan.c_str()); + if(FileTest2){ + bool GoodFile = m->checkReleaseVersion(FileTest2, m->getVersion()); + if (GoodFile) { + m->mothurOut("I found " + tempQuan + " in your input file directory. I will use it to save time."); m->mothurOutEndLine(); quanfile = tempQuan; FileTest2.close(); + } + } } chimera = new Pintail(fastaFileNames[s], templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir); + if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it string outputFileName, accnosFileName; if (maskfile != "") { - outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".pintail.chimeras"; - accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".pintail.accnos"; + outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.chimeras"; + accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.accnos"; }else { - outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "pintail.chimeras"; - accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "pintail.accnos"; + outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "pintail.chimeras"; + accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "pintail.accnos"; } if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } @@ -284,7 +383,7 @@ int ChimeraPintailCommand::execute(){ templateSeqsLength = chimera->getLength(); #ifdef USE_MPI - int pid, end, numSeqsPerProcessor; + int pid, numSeqsPerProcessor; int tag = 2001; vector MPIPos; @@ -312,11 +411,11 @@ int ChimeraPintailCommand::execute(){ MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI); MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } if (pid == 0) { //you are the root process - MPIPos = setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs + MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs //send file positions to all processes for(int i = 1; i < processors; i++) { @@ -332,7 +431,7 @@ int ChimeraPintailCommand::execute(){ //do your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } }else{ //you are a child process MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); @@ -347,7 +446,7 @@ int ChimeraPintailCommand::execute(){ //do your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } } //close files @@ -356,77 +455,44 @@ int ChimeraPintailCommand::execute(){ MPI_File_close(&outMPIAccnos); MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - + vector positions = m->divideFile(fastaFileNames[s], processors); + + for (int i = 0; i < (positions.size()-1); i++) { + lines.push_back(new linePair(positions[i], positions[(i+1)])); + } + //break up file #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) if(processors == 1){ - ifstream inFASTA; - openInputFile(fastaFileNames[s], inFASTA); - getNumSeqs(inFASTA, numSeqs); - inFASTA.close(); - - lines.push_back(new linePair(0, numSeqs)); - - driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); + + numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); - if (m->control_pressed) { - remove(outputFileName.c_str()); - remove(accnosFileName.c_str()); - for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - delete chimera; - return 0; - } + if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } }else{ - vector positions; processIDS.resize(0); - ifstream inFASTA; - openInputFile(fastaFileNames[s], inFASTA); - - string input; - while(!inFASTA.eof()){ - input = getline(inFASTA); - if (input.length() != 0) { - if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } - } - } - inFASTA.close(); - - numSeqs = positions.size(); - - int numSeqsPerProcessor = numSeqs / processors; - - for (int i = 0; i < processors; i++) { - unsigned long int startPos = positions[ i * numSeqsPerProcessor ]; - if(i == processors - 1){ - numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; - } - lines.push_back(new linePair(startPos, numSeqsPerProcessor)); - } - - createProcesses(outputFileName, fastaFileNames[s], accnosFileName); + numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName); rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str()); rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str()); //append output files for(int i=1;iappendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName); remove((outputFileName + toString(processIDS[i]) + ".temp").c_str()); } //append output files for(int i=1;iappendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName); remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); } if (m->control_pressed) { remove(outputFileName.c_str()); remove(accnosFileName.c_str()); - for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } + for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; @@ -434,22 +500,9 @@ int ChimeraPintailCommand::execute(){ } #else - ifstream inFASTA; - openInputFile(fastaFileNames[s], inFASTA); - getNumSeqs(inFASTA, numSeqs); - inFASTA.close(); - lines.push_back(new linePair(0, numSeqs)); + numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); - driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); - - if (m->control_pressed) { - remove(outputFileName.c_str()); - remove(accnosFileName.c_str()); - for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - delete chimera; - return 0; - } + if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } #endif #endif @@ -457,8 +510,8 @@ int ChimeraPintailCommand::execute(){ delete chimera; for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - outputNames.push_back(outputFileName); - outputNames.push_back(accnosFileName); + outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName); + outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName); m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); @@ -479,24 +532,27 @@ int ChimeraPintailCommand::execute(){ } //********************************************************************************************************************** -int ChimeraPintailCommand::driver(linePair* line, string outputFName, string filename, string accnos){ +int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string filename, string accnos){ try { ofstream out; - openOutputFile(outputFName, out); + m->openOutputFile(outputFName, out); ofstream out2; - openOutputFile(accnos, out2); + m->openOutputFile(accnos, out2); ifstream inFASTA; - openInputFile(filename, inFASTA); + m->openInputFile(filename, inFASTA); - inFASTA.seekg(line->start); - - for(int i=0;inumSeqs;i++){ - + inFASTA.seekg(filePos->start); + + bool done = false; + int count = 0; + + while (!done) { + if (m->control_pressed) { return 1; } - Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA); + Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file @@ -511,20 +567,28 @@ int ChimeraPintailCommand::driver(linePair* line, string outputFName, string fil //print results chimera->print(out, out2); } + count++; } delete candidateSeq; + #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((i+1) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine(); } + if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } } //report progress - if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine(); } + if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } out.close(); out2.close(); inFASTA.close(); - return 0; + return count; } catch(exception& e) { m->errorOut(e, "ChimeraPintailCommand", "driver"); @@ -555,7 +619,7 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi istringstream iss (tempBuf,istringstream::in); delete buf4; - Sequence* candidateSeq = new Sequence(iss); gobble(iss); + Sequence* candidateSeq = new Sequence(iss); m->gobble(iss); if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file @@ -568,7 +632,7 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi if (m->control_pressed) { delete candidateSeq; return 1; } //print results - bool isChimeric = chimera->print(outMPI, outAccMPI); + chimera->print(outMPI, outAccMPI); } } delete candidateSeq; @@ -595,7 +659,7 @@ int ChimeraPintailCommand::createProcesses(string outputFileName, string filenam try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; - // processIDS.resize(0); + int num = 0; //loop through and create all the processes you want while (process != processors) { @@ -605,9 +669,21 @@ int ChimeraPintailCommand::createProcesses(string outputFileName, string filenam 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], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp"); + num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp"); + + //pass numSeqs to parent + ofstream out; + string tempFile = outputFileName + 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); - }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); } + } } //force parent to wait until all the processes are done @@ -616,7 +692,15 @@ int ChimeraPintailCommand::createProcesses(string outputFileName, string filenam wait(&temp); } - return 0; + for (int i = 0; i < processIDS.size(); i++) { + ifstream in; + string tempFile = outputFileName + 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()); + } + + return num; #endif } catch(exception& e) {