+/*
+ * chimeraslayercommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 3/31/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "chimeraslayercommand.h"
+#include "bellerophon.h"
+#include "pintail.h"
+#include "ccode.h"
+#include "chimeracheckrdp.h"
+#include "chimeraslayer.h"
+
+
+//***************************************************************************************************************
+
+ChimeraSlayerCommand::ChimeraSlayerCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta", "processors", "window", "template","numwanted", "ksize", "match","mismatch",
+ "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ 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; }
+ }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("template");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = 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; }
+ }
+ }
+
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.slayer command."); 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
+ }
+
+ 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.slayer command."); m->mothurOutEndLine(); abort = true; }
+
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
+ convert(temp, processors);
+
+ temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
+ convert(temp, ksize);
+
+ temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "50"; }
+ convert(temp, window);
+
+ temp = validParameter.validFile(parameters, "match", false); if (temp == "not found") { temp = "5"; }
+ convert(temp, match);
+
+ temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found") { temp = "-4"; }
+ convert(temp, mismatch);
+
+ temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.007"; }
+ convert(temp, divR);
+
+ temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "90"; }
+ convert(temp, minSimilarity);
+
+ temp = validParameter.validFile(parameters, "mincov", false); if (temp == "not found") { temp = "70"; }
+ convert(temp, minCoverage);
+
+ temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; }
+ convert(temp, minBS);
+
+ temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; }
+ convert(temp, minSNP);
+
+ temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
+ convert(temp, parents);
+
+ temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "f"; }
+ realign = isTrue(temp);
+
+ search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; }
+
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
+ convert(temp, iters);
+
+ temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; }
+ convert(temp, increment);
+
+ temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; }
+ convert(temp, numwanted);
+
+ if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void ChimeraSlayerCommand::help(){
+ try {
+
+ m->mothurOut("The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
+ m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n");
+ m->mothurOut("The chimera.slayer command parameters are fasta, template, filter, mask, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
+ m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \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 mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n");
+ m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
+ m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
+ m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
+ m->mothurOut("The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n");
+ m->mothurOut("The match parameter allows you to reward matched bases in blast search, default is 5. \n");
+ m->mothurOut("The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n");
+ m->mothurOut("The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n");
+ m->mothurOut("The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n");
+ m->mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n");
+ m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n");
+ m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
+ m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
+ m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
+ m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n");
+ //m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. Found to make results worse. \n");
+ m->mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
+ m->mothurOut("The chimera.slayer command should be in the following format: \n");
+ m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n");
+ m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \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, "ChimeraSlayerCommand", "help");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+ChimeraSlayerCommand::~ChimeraSlayerCommand(){ /* do nothing */ }
+
+//***************************************************************************************************************
+
+int ChimeraSlayerCommand::execute(){
+ try{
+
+ if (abort == true) { return 0; }
+
+ int start = time(NULL);
+
+ chimera = new ChimeraSlayer(fastafile, templatefile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
+
+ string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "slayer.chimeras";
+ string accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + "slayer.accnos";
+ bool hasAccnos = true;
+
+ if (m->control_pressed) { delete chimera; return 0; }
+
+ if (chimera->getUnaligned()) {
+ m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
+ delete chimera;
+ return 0;
+ }
+ templateSeqsLength = chimera->getLength();
+
+ #ifdef USE_MPI
+ int pid, end, numSeqsPerProcessor;
+ int tag = 2001;
+ vector<long> MPIPos;
+ MPIWroteAccnos = false;
+
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ MPI_File inMPI;
+ MPI_File outMPI;
+ MPI_File outMPIAccnos;
+
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+ int inMode=MPI_MODE_RDONLY;
+
+ char outFilename[outputFileName.length()];
+ strcpy(outFilename, outputFileName.c_str());
+
+ char outAccnosFilename[accnosFileName.length()];
+ strcpy(outAccnosFilename, accnosFileName.c_str());
+
+ char inFileName[fastafile.length()];
+ strcpy(inFileName, fastafile.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);
+ 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); delete chimera; return 0; }
+
+
+ if (pid == 0) { //you are the root process
+ m->mothurOutEndLine();
+ m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
+ m->mothurOutEndLine();
+
+ string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
+
+ //print header
+ int length = outTemp.length();
+ char buf2[length];
+ strcpy(buf2, outTemp.c_str());
+ MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
+
+ MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
+
+ //send file positions to all processes
+ MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
+ MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numSeqs / processors;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+ int startIndex = pid * numSeqsPerProcessor;
+
+ //align 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()); delete chimera; return 0; }
+
+ for (int i = 1; i < processors; i++) {
+ bool tempResult;
+ MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
+ if (tempResult != 0) { MPIWroteAccnos = true; }
+ }
+ }else{ //you are a child process
+ MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+ MPIPos.resize(numSeqs+1);
+ MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numSeqs / processors;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+ int startIndex = pid * numSeqsPerProcessor;
+
+ //align 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); delete chimera; return 0; }
+
+ MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
+ }
+
+ //close files
+ MPI_File_close(&inMPI);
+ MPI_File_close(&outMPI);
+ MPI_File_close(&outMPIAccnos);
+
+ //delete accnos file if blank
+ if (pid == 0) {
+ if (!MPIWroteAccnos) {
+ //MPI_Info info;
+ //MPI_File_delete(outAccnosFilename, info);
+ hasAccnos = false;
+ remove(accnosFileName.c_str());
+ }
+ }
+
+ #else
+ ofstream outHeader;
+ string tempHeader = outputDir + getRootName(getSimpleName(fastafile)) + "slayer.chimeras.tempHeader";
+ openOutputFile(tempHeader, outHeader);
+
+ chimera->printHeader(outHeader);
+ outHeader.close();
+
+ //break up file
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(fastafile, inFASTA);
+ numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numSeqs));
+
+ driver(lines[0], outputFileName, fastafile, accnosFileName);
+
+ if (m->control_pressed) {
+ remove(outputFileName.c_str());
+ remove(tempHeader.c_str());
+ remove(accnosFileName.c_str());
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ delete chimera;
+ return 0;
+ }
+
+ //delete accnos file if its blank
+ if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
+
+ }else{
+ vector<int> positions;
+ processIDS.resize(0);
+
+ ifstream inFASTA;
+ openInputFile(fastafile, inFASTA);
+
+ string input;
+ while(!inFASTA.eof()){
+ input = getline(inFASTA);
+ if (input.length() != 0) {
+ if(input[0] == '>'){ 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++) {
+ long int startPos = positions[ i * numSeqsPerProcessor ];
+ if(i == processors - 1){
+ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+
+
+ createProcesses(outputFileName, fastafile, accnosFileName);
+
+ rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
+
+ //append output files
+ for(int i=1;i<processors;i++){
+ appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
+ remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
+ }
+
+ vector<string> nonBlankAccnosFiles;
+ //delete blank accnos files generated with multiple processes
+ for(int i=0;i<processors;i++){
+ if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
+ nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
+ }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); }
+ }
+
+ //append accnos files
+ if (nonBlankAccnosFiles.size() != 0) {
+ rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
+
+ for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+ appendFiles(nonBlankAccnosFiles[h], accnosFileName);
+ remove(nonBlankAccnosFiles[h].c_str());
+ }
+ }else{ hasAccnos = false; }
+
+ if (m->control_pressed) {
+ remove(outputFileName.c_str());
+ remove(accnosFileName.c_str());
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ delete chimera;
+ return 0;
+ }
+
+ }
+
+ #else
+ ifstream inFASTA;
+ openInputFile(candidateFileNames[s], inFASTA);
+ numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+ lines.push_back(new linePair(0, numSeqs));
+
+ driver(lines[0], outputFileName, fastafile, accnosFileName);
+
+ if (m->control_pressed) {
+ remove(outputFileName.c_str());
+ remove(tempHeader.c_str());
+ remove(accnosFileName.c_str());
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ delete chimera;
+ return 0;
+ }
+
+ //delete accnos file if its blank
+ if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
+ #endif
+
+ appendFiles(tempHeader, outputFileName);
+
+ remove(outputFileName.c_str());
+ rename(tempHeader.c_str(), outputFileName.c_str());
+
+ #endif
+ delete chimera;
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ if (hasAccnos) { m->mothurOut(accnosFileName); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+
+ m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int ChimeraSlayerCommand::driver(linePair* line, string outputFName, string filename, string accnos){
+ try {
+ ofstream out;
+ openOutputFile(outputFName, out);
+
+ ofstream out2;
+ openOutputFile(accnos, out2);
+
+ ifstream inFASTA;
+ openInputFile(filename, inFASTA);
+
+ inFASTA.seekg(line->start);
+
+ for(int i=0;i<line->numSeqs;i++){
+
+ if (m->control_pressed) { return 1; }
+
+ Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+
+ if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
+
+ if (candidateSeq->getAligned().length() != templateSeqsLength) {
+ m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
+ }else{
+ //find chimeras
+ chimera->getChimeras(candidateSeq);
+
+ if (m->control_pressed) { delete candidateSeq; return 1; }
+
+ //print results
+ chimera->print(out, out2);
+ }
+ }
+ delete candidateSeq;
+
+ //report progress
+ if((i+1) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine(); }
+ }
+ //report progress
+ if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine(); }
+
+ out.close();
+ out2.close();
+ inFASTA.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+#ifdef USE_MPI
+int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
+ try {
+
+ 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 1; }
+
+ //read next sequence
+ int length = MPIPos[start+i+1] - MPIPos[start+i];
+
+ char buf4[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);
+
+ Sequence* candidateSeq = new Sequence(iss); gobble(iss);
+
+ if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
+
+ if (candidateSeq->getAligned().length() != templateSeqsLength) {
+ m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
+ }else{
+ //find chimeras
+ chimera->getChimeras(candidateSeq);
+
+ if (m->control_pressed) { delete candidateSeq; return 1; }
+
+ //print results
+ bool isChimeric = chimera->print(outMPI, outAccMPI);
+ if (isChimeric) { MPIWroteAccnos = true; }
+ }
+ }
+ 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, "ChimeraSlayerCommand", "driverMPI");
+ exit(1);
+ }
+}
+#endif
+
+/**************************************************************************************************/
+
+int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 0;
+ // processIDS.resize(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){
+ driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
+ 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
+ for (int i=0;i<processors;i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ return 0;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+