+++ /dev/null
-/*
- * chimeracheckcommand.cpp
- * Mothur
- *
- * Created by westcott on 3/31/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "chimeracheckcommand.h"
-#include "referencedb.h"
-
-//**********************************************************************************************************************
-vector<string> ChimeraCheckCommand::setParameters(){
- try {
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); 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); 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<string> 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);
- }
-}
-//**********************************************************************************************************************
-ChimeraCheckCommand::ChimeraCheckCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["chimera"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
- exit(1);
- }
-}
-//***************************************************************************************************************
-ChimeraCheckCommand::ChimeraCheckCommand(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("chimera.check");
- 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; }
- }
-
- vector<string> 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("reference");
- //user has given a template file
- if(it != parameters.end()){
- string 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; }
- }
- }
-
- //check for required parameters
- fastafile = validParameter.validFile(parameters, "fasta", false);
- 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++) {
-
- 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--;
- }
- }
-
- 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]);
- }
- }
- }
-
- //make sure there is at least one valid file left
- if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); 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 = ""; }
-
- namefile = validParameter.validFile(parameters, "name", false);
- if (namefile == "not found") { namefile = ""; }
- else {
- 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++) {
-
- 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--;
- }
- }
-
- 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
- if (nameFileNames.size() != 0) {
- if (nameFileNames.size() != fastaFileNames.size()) {
- m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine();
- abort = true;
- }
- }
- }
-
- 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"; }
- m->mothurConvert(temp, ksize);
-
- temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; }
- svg = m->isTrue(temp);
- if (nameFileNames.size() != 0) { svg = true; }
-
- temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; }
- m->mothurConvert(temp, increment);
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-int ChimeraCheckCommand::execute(){
- try{
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- for (int i = 0; i < fastaFileNames.size(); i++) {
-
- m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
-
- int start = time(NULL);
-
- string thisNameFile = "";
- if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; }
-
- chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir);
-
- if (m->control_pressed) { delete chimera; return 0; }
-
- if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras";
- outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
-
- #ifdef USE_MPI
-
- int pid, numSeqsPerProcessor;
- int tag = 2001;
- vector<unsigned long long> MPIPos;
-
- 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 outMPI;
-
- int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
- int inMode=MPI_MODE_RDONLY;
-
- char outFilename[1024];
- strcpy(outFilename, outputFileName.c_str());
-
- char inFileName[1024];
- strcpy(inFileName, fastaFileNames[i].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, 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++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; }
-
- if (pid == 0) { //you are the root process
- MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
-
- //send file positions to all processes
- for(int j = 1; j < processors; j++) {
- MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
- MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, tag, MPI_COMM_WORLD);
- }
-
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
-
-
- //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++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; }
-
- //wait on chidren
- for(int j = 1; j < processors; j++) {
- 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);
- MPIPos.resize(numSeqs+1);
- MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
-
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
-
- //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++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; }
-
- //tell parent you are done.
- char buf[5];
- strcpy(buf, "done");
- MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
- }
-
- //close files
- MPI_File_close(&inMPI);
- MPI_File_close(&outMPI);
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- #else
-
-
-
- //break up file
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- vector<unsigned long long> 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++) { 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);
-
- numSeqs = createProcesses(outputFileName, fastaFileNames[i]);
-
- rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
-
- //append output files
- for(int j=1;j<processors;j++){
- m->appendFiles((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++) { m->mothurRemove(outputNames[j]); } outputTypes.clear();
- for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear();
- delete chimera;
- return 0;
- }
- }
-
- #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++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); delete chimera; return 0; }
- #endif
- #endif
- delete chimera;
- for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear();
-
- m->mothurOutEndLine(); m->mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); m->mothurOutEndLine();
- m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
-
- }
-
- 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, "ChimeraCheckCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string filename){
- try {
- ofstream out;
- m->openOutputFile(outputFName, out);
-
- ofstream out2;
-
- ifstream inFASTA;
- m->openInputFile(filename, inFASTA);
-
- inFASTA.seekg(filePos->start);
-
- bool done = false;
- int count = 0;
-
- while (!done) {
-
- if (m->control_pressed) { return 1; }
-
- 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
- chimera->getChimeras(candidateSeq);
-
- if (m->control_pressed) { delete candidateSeq; return 1; }
-
- //print results
- chimera->print(out, out2);
- }
- 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("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
- }
- //report progress
- if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
-
- out.close();
- inFASTA.close();
-
- return count;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraCheckCommand", "driver");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-#ifdef USE_MPI
-int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos){
- try {
- MPI_File outAccMPI;
- MPI_Status status;
- int pid;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- for(int i=0;i<num;i++){
-
- if (m->control_pressed) { return 0; }
-
- //read next sequence
- int length = MPIPos[start+i+1] - MPIPos[start+i];
-
- char* buf4 = new char[length];
- MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
-
- string tempBuf = buf4;
- if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
- istringstream iss (tempBuf,istringstream::in);
- delete buf4;
-
- 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
- chimera->getChimeras(candidateSeq);
-
- //print results
- chimera->print(outMPI, outAccMPI);
- }
- delete candidateSeq;
-
- //report progress
- if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); }
- }
- //report progress
- if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraCheckCommand", "driverMPI");
- exit(1);
- }
-}
-#endif
-
-/**************************************************************************************************/
-
-int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
- try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- int process = 0;
- int num = 0;
-
- //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], outputFileName + toString(getpid()) + ".temp", filename);
-
- //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);
- }
- }
-
- //force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- 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(); m->mothurRemove(tempFile);
- }
-
- return num;
-#endif
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraCheckCommand", "createProcesses");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-
projects / mothur.git / blobdiff