--- /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