X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeracheckcommand.cpp;h=31a36f73c6d0339d775dd6a1a4efa8e523c0f14f;hp=de6f438d81f7fcd62e111d97a02e87d63aad1e66;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=b45e6f3d505a212cebad5ca22e2611b1466bca48 diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp index de6f438..31a36f7 100644 --- a/chimeracheckcommand.cpp +++ b/chimeracheckcommand.cpp @@ -8,20 +8,102 @@ */ #include "chimeracheckcommand.h" +#include "referencedb.h" -//*************************************************************************************************************** +//********************************************************************************************************************** +vector ChimeraCheckCommand::setParameters(){ + try { + CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera",false,true,true); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname); + CommandParameter psvg("svg", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psvg); + CommandParameter pincrement("increment", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pincrement); + CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); + CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave); + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCheckCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string ChimeraCheckCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The chimera.check command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n"; + helpString += "This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n"; + helpString += "The chimera.check command parameters are fasta, reference, processors, ksize, increment, svg and name.\n"; + helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required unless you have a valid current fasta file. \n"; + helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"; + helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. \n"; + helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"; +#ifdef USE_MPI + helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n"; +#endif + helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n"; + helpString += "The ksize parameter allows you to input kmersize, default is 7. \n"; + helpString += "The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence, default is False.\n"; + helpString += "The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n"; + helpString += "You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n"; + 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 chimera.check command should be in the following format: \n"; + helpString += "chimera.check(fasta=yourFastaFile, reference=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n"; + helpString += "Example: chimera.check(fasta=AD.fasta, reference=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCheckCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string ChimeraCheckCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "chimera") { pattern = "[filename],chimeracheck.chimeras"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCheckCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +ChimeraCheckCommand::ChimeraCheckCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand"); + exit(1); + } +} +//*************************************************************************************************************** ChimeraCheckCommand::ChimeraCheckCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; + ReferenceDB* rdb = ReferenceDB::getInstance(); //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 Array[] = {"fasta","processors","increment","template","ksize","svg", "name","outputdir","inputdir" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -34,54 +116,95 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + //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 { - it = parameters.find("template"); + it = parameters.find("reference"); //user has given a template file if(it != parameters.end()){ - string path = hasPath(it->second); + string 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 fastafile = validParameter.validFile(parameters, "fasta", false); - if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true; } - else { - splitAtDash(fastafile, fastaFileNames); + if (fastafile == "not found") { + //if there is a current fasta file, use it + string filename = m->getFastaFile(); + if (filename != "") { fastaFileNames.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 fasta parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { + 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]); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; } - } - - int ableToOpen; - ifstream in; - ableToOpen = 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]); - m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); - fastaFileNames[i] = tryPath; + bool ignore = false; + if (fastaFileNames[i] == "current") { + fastaFileNames[i] = m->getFastaFile(); + if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[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 + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; } } - in.close(); - if (ableToOpen == 1) { - m->mothurOut("Unable to open " + fastaFileNames[i] +". It will be disregarded."); m->mothurOutEndLine(); - //erase from file list - fastaFileNames.erase(fastaFileNames.begin()+i); - i--; + if (!ignore) { + + + if (inputDir != "") { + 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]; } + } + + int ableToOpen; + ifstream in; + + 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() + m->getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; + } + } + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(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; + } + } + + in.close(); + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + fastaFileNames[i] +". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; + }else { + m->setFastaFile(fastaFileNames[i]); + } } } @@ -91,47 +214,75 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { //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 = ""; } - - templatefile = validParameter.validFile(parameters, "template", true); - if (templatefile == "not open") { abort = true; } - else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true; } namefile = validParameter.validFile(parameters, "name", false); if (namefile == "not found") { namefile = ""; } else { - splitAtDash(namefile, nameFileNames); + m->splitAtDash(namefile, nameFileNames); //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < nameFileNames.size(); i++) { - if (inputDir != "") { - string path = hasPath(nameFileNames[i]); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; } - } - - int ableToOpen; - ifstream in; - ableToOpen = openInputFile(nameFileNames[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(nameFileNames[i]); - m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); - nameFileNames[i] = tryPath; + bool ignore = false; + if (nameFileNames[i] == "current") { + nameFileNames[i] = m->getNameFile(); + if (nameFileNames[i] != "") { m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true; + //erase from file list + nameFileNames.erase(nameFileNames.begin()+i); + i--; } } - in.close(); - if (ableToOpen == 1) { - m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); - //erase from file list - nameFileNames.erase(nameFileNames.begin()+i); - i--; - } + if (!ignore) { + if (inputDir != "") { + string path = m->hasPath(nameFileNames[i]); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; } + } + + int ableToOpen; + ifstream in; + + ableToOpen = m->openInputFile(nameFileNames[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() + m->getSimpleName(nameFileNames[i]); + m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + nameFileNames[i] = tryPath; + } + } + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]); + m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + nameFileNames[i] = tryPath; + } + } + + in.close(); + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + nameFileNames.erase(nameFileNames.begin()+i); + i--; + }else { + m->setNameFile(nameFileNames[i]); + } + } } //make sure there is at least one valid file left @@ -143,18 +294,41 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { } } - string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; } - convert(temp, processors); + string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + m->mothurConvert(temp, processors); + + 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 + templatefile = validParameter.validFile(parameters, "reference", true); + if (templatefile == "not found") { + //check for saved reference sequences + if (rdb->referenceSeqs.size() != 0) { + templatefile = "saved"; + }else { + m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required."); + m->mothurOutEndLine(); + abort = true; + } + }else if (templatefile == "not open") { abort = true; } + else { if (save) { rdb->setSavedReference(templatefile); } } + temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; } - convert(temp, ksize); + m->mothurConvert(temp, ksize); temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; } - svg = isTrue(temp); + svg = m->isTrue(temp); if (nameFileNames.size() != 0) { svg = true; } temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; } - convert(temp, increment); + m->mothurConvert(temp, increment); } } catch(exception& e) { @@ -162,47 +336,12 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { exit(1); } } -//********************************************************************************************************************** - -void ChimeraCheckCommand::help(){ - try { - - m->mothurOut("The chimera.check command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n"); - m->mothurOut("This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n"); - m->mothurOut("The chimera.check command parameters are fasta, template, processors, ksize, increment, svg and name.\n"); - m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n"); - m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); - m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n"); - m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"); - #ifdef USE_MPI - m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n"); - #endif - m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n"); - m->mothurOut("The ksize parameter allows you to input kmersize, default is 7. \n"); - m->mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence, default is False.\n"); - m->mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n"); - m->mothurOut("You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n"); - m->mothurOut("The chimera.check command should be in the following format: \n"); - m->mothurOut("chimera.check(fasta=yourFastaFile, template=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n"); - m->mothurOut("Example: chimera.check(fasta=AD.fasta, template=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "ChimeraCheckCommand", "help"); - exit(1); - } -} - -//*************************************************************************************************************** - -ChimeraCheckCommand::~ChimeraCheckCommand(){ /* do nothing */ } - //*************************************************************************************************************** int ChimeraCheckCommand::execute(){ try{ - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } for (int i = 0; i < fastaFileNames.size(); i++) { @@ -217,14 +356,17 @@ int ChimeraCheckCommand::execute(){ if (m->control_pressed) { delete chimera; return 0; } - string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras"; - outputNames.push_back(outputFileName); + if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])); + string outputFileName = getOutputFileName("chimera", variables); + outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName); #ifdef USE_MPI - int pid, end, numSeqsPerProcessor; + int pid, numSeqsPerProcessor; int tag = 2001; - vector MPIPos; + vector MPIPos; MPI_Status status; MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are @@ -245,10 +387,10 @@ int ChimeraCheckCommand::execute(){ MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } if (pid == 0) { //you are the root process - MPIPos = setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs + MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs //send file positions to all processes for(int j = 1; j < processors; j++) { @@ -265,12 +407,12 @@ int ChimeraCheckCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } //wait on chidren for(int j = 1; j < processors; j++) { - char buf[4]; - MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); + char buf[5]; + MPI_Recv(buf, 5, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); } }else{ //you are a child process MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); @@ -285,12 +427,12 @@ int ChimeraCheckCommand::execute(){ //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } //tell parent you are done. - char buf[4]; + char buf[5]; strcpy(buf, "done"); - MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); + MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD); } //close files @@ -299,18 +441,20 @@ int ChimeraCheckCommand::execute(){ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - vector positions = divideFile(fastaFileNames[i], processors); - - for (int s = 0; s < (positions.size()-1); s++) { - lines.push_back(new linePair(positions[s], positions[(s+1)])); - } + //break up file - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + vector positions = m->divideFile(fastaFileNames[i], processors); + + for (int s = 0; s < (positions.size()-1); s++) { + lines.push_back(new linePair(positions[s], positions[(s+1)])); + } + if(processors == 1){ numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]); - if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int j = 0; j < lines.size(); j++) { delete lines[j]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; } }else{ processIDS.resize(0); @@ -321,12 +465,12 @@ int ChimeraCheckCommand::execute(){ //append output files for(int j=1;jappendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName); + m->mothurRemove((outputFileName + toString(processIDS[j]) + ".temp")); } if (m->control_pressed) { - for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } + for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); delete chimera; return 0; @@ -334,9 +478,10 @@ int ChimeraCheckCommand::execute(){ } #else + lines.push_back(new linePair(0, 1000)); numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]); - if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; } #endif #endif delete chimera; @@ -365,12 +510,12 @@ int ChimeraCheckCommand::execute(){ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string filename){ try { ofstream out; - openOutputFile(outputFName, out); + m->openOutputFile(outputFName, out); ofstream out2; ifstream inFASTA; - openInputFile(filename, inFASTA); + m->openInputFile(filename, inFASTA); inFASTA.seekg(filePos->start); @@ -381,7 +526,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi 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 //find chimeras @@ -394,14 +539,18 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi } delete candidateSeq; - unsigned long int pos = inFASTA.tellg(); - if ((pos == -1) || (pos >= filePos->end)) { break; } + #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("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } + if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); } } //report progress - if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } + if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); } out.close(); inFASTA.close(); @@ -415,7 +564,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi } //********************************************************************************************************************** #ifdef USE_MPI -int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos){ +int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos){ try { MPI_File outAccMPI; MPI_Status status; @@ -437,7 +586,7 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File 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 //find chimeras @@ -449,10 +598,10 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File delete candidateSeq; //report progress - if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); } + if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; } } //report progress - if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); } + if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; } return 0; } @@ -467,7 +616,7 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) int process = 0; int num = 0; @@ -484,12 +633,16 @@ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) //pass numSeqs to parent ofstream out; string tempFile = outputFileName + toString(getpid()) + ".num.temp"; - openOutputFile(tempFile, out); + 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); + } } //force parent to wait until all the processes are done @@ -501,9 +654,9 @@ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) for (int i = 0; i < processIDS.size(); i++) { ifstream in; string tempFile = outputFileName + toString(processIDS[i]) + ".num.temp"; - openInputFile(tempFile, in); + m->openInputFile(tempFile, in); if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; } - in.close(); remove(tempFile.c_str()); + in.close(); m->mothurRemove(tempFile); } return num;