*/
#include "chimeraseqscommand.h"
-#include "bellerophon.h"
-#include "pintail.h"
-#include "ccode.h"
-#include "chimeracheckrdp.h"
-#include "chimeraslayer.h"
-
//***************************************************************************************************************
-ChimeraSeqsCommand::ChimeraSeqsCommand(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", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask",
- "numwanted", "ksize", "svg", "name", "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; }
- }
-
- it = parameters.find("conservation");
- //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["conservation"] = inputDir + it->second; }
- }
-
- it = parameters.find("quantile");
- //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["quantile"] = inputDir + it->second; }
- }
-
- it = parameters.find("name");
- //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["name"] = 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.seqs 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 = ""; }
-
- consfile = validParameter.validFile(parameters, "conservation", true);
- if (consfile == "not open") { abort = true; }
- else if (consfile == "not found") { consfile = ""; }
-
- quanfile = validParameter.validFile(parameters, "quantile", true);
- if (quanfile == "not open") { abort = true; }
- else if (quanfile == "not found") { quanfile = ""; }
-
- namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
- else if (namefile == "not found") { namefile = ""; }
-
- maskfile = validParameter.validFile(parameters, "mask", false);
- if (maskfile == "not found") { maskfile = ""; }
- else if (maskfile != "default") {
- if (inputDir != "") {
- string path = hasPath(maskfile);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { maskfile = inputDir + maskfile; }
- }
-
- ifstream in;
- int ableToOpen = openInputFile(maskfile, in);
- if (ableToOpen == 1) { abort = true; }
- in.close();
- }
-
- method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "pintail"; }
-
- string temp;
- temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
- filter = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; }
- correction = isTrue(temp);
-
- 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, "svg", false); if (temp == "not found") { temp = "F"; }
- svg = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "window", false);
- if ((temp == "not found") && (method == "chimeraslayer")) { temp = "50"; }
- else if (temp == "not found") { temp = "0"; }
- 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") && (method == "chimeraslayer")) { temp = "100"; }
- else if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
-
- temp = validParameter.validFile(parameters, "increment", false);
- if ((temp == "not found") && (method == "chimeracheck")) { temp = "10"; }
- else if ((temp == "not found") && (method == "chimeraslayer")) { temp = "5"; }
- else if (temp == "not found") { temp = "25"; }
- convert(temp, increment);
-
- temp = validParameter.validFile(parameters, "numwanted", false);
- if ((temp == "not found") && (method == "chimeraslayer")) { temp = "15"; }
- else if (temp == "not found") { temp = "20"; }
- convert(temp, numwanted);
-
- if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; }
-
- if (((method != "bellerophon")) && (templatefile == "")) { m->mothurOut("You must provide a template file with the pintail, ccode, chimeraslayer or chimeracheck methods."); m->mothurOutEndLine(); abort = true; }
-
-
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand");
- exit(1);
- }
-}
+ChimeraSeqsCommand::ChimeraSeqsCommand(string option) {}
//**********************************************************************************************************************
-void ChimeraSeqsCommand::help(){
- try {
-
- //"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name"
- //m->mothurOut("chimera.seqs ASSUMES that your sequences are ALIGNED and if using a template that the template file sequences are the same length as the fasta file sequences.\n\n");
- m->mothurOut("The chimera.seqs command reads a fastafile and creates list of potentially chimeric sequences.\n");
- m->mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask, method, window, increment, template, conservation, quantile, numwanted, ksize, svg, name, iters, search, realign.\n");
- m->mothurOut("The fasta parameter is always required and template is required if using pintail, ccode or chimeracheck.\n");
- m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n");
- m->mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs.\n");
- m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
- m->mothurOut("The method parameter allows you to specify the method for finding chimeric sequences. The default is pintail. Options include bellerophon, ccode and chimeracheck \n");
- 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. \n");
- m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences.\n");
- m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences. \n");
- m->mothurOut("The conservation parameter allows you to enter a frequency file containing the highest bases frequency at each place in the alignment.\n");
- m->mothurOut("The quantile parameter allows you to enter a file containing quantiles for a template files sequences.\n");
- m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n");
- m->mothurOut("The ksize parameter allows you to input kmersize. \n");
- m->mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence.\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("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method.\n");
- m->mothurOut("The minsim parameter allows you .... \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. -used only by chimeraslayer. \n");
- m->mothurOut("The realign parameter allows you to realign the query to the potential paretns. Choices are true or false, default false. -used only by chimeraslayer. \n");
- m->mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
- m->mothurOut("Details for each method: \n");
- m->mothurOut("\tpintail: \n");
- m->mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=300, increment=25, conservation=not required, but will improve speed, quantile=not required, but will greatly improve speed. \n");
- m->mothurOut("\t\tIf you have run chimera.seqs using pintail a .quan and .freq file will be created for your template, if you have not provided them for use in future command executions.\n");
- m->mothurOut("\tbellerophon: \n");
- m->mothurOut("\t\tparameters: fasta=required, filter=F, processors=1, window=1/4 length of seq, increment=25, correction=T. \n");
- m->mothurOut("\tccode: \n");
- m->mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=10% of length, numwanted=20\n");
- m->mothurOut("\tchimeracheck: \n");
- m->mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, ksize=7, svg=F, name=none\n\n");
- m->mothurOut("\tchimeraslayer: \n");
- m->mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, mask=no mask, numwanted=10, match=5, mismatch=-4, divergence=1.0, minsim=90, parents=5, iters=1000, window=100. \n\n");
- m->mothurOut("The chimera.seqs command should be in the following format: \n");
- m->mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
- m->mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, method=bellerophon, window=200) \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, "ChimeraSeqsCommand", "help");
- exit(1);
- }
-}
+void ChimeraSeqsCommand::help(){}
//***************************************************************************************************************
//***************************************************************************************************************
int ChimeraSeqsCommand::execute(){
- try{
-
- if (abort == true) { return 0; }
-
- int start = time(NULL);
-
- if (method == "bellerophon") { chimera = new Bellerophon(fastafile, outputDir); }
- else if (method == "pintail") { chimera = new Pintail(fastafile, outputDir); }
- else if (method == "ccode") { chimera = new Ccode(fastafile, outputDir); }
- else if (method == "chimeracheck") { chimera = new ChimeraCheckRDP(fastafile, outputDir); }
- else if (method == "chimeraslayer") { chimera = new ChimeraSlayer(search, realign, fastafile); }
- else { m->mothurOut("Not a valid method."); m->mothurOutEndLine(); return 0; }
-
- //set user options
- if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); }
-
- chimera->setCons(consfile);
- chimera->setQuantiles(quanfile);
- chimera->setMask(maskfile);
- chimera->setFilter(filter);
- chimera->setCorrection(correction);
- chimera->setProcessors(processors);
- chimera->setWindow(window);
- chimera->setIncrement(increment);
- chimera->setNumWanted(numwanted);
- chimera->setKmerSize(ksize);
- chimera->setSVG(svg);
- chimera->setName(namefile);
- chimera->setMatch(match);
- chimera->setMisMatch(mismatch);
- chimera->setDivR(divR);
- chimera->setParents(parents);
- chimera->setMinSim(minSimilarity);
- chimera->setMinCoverage(minCoverage);
- chimera->setMinBS(minBS);
- chimera->setMinSNP(minSNP);
- chimera->setIters(iters);
-
-
- string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + method + maskfile + ".chimeras";
- string accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + method + maskfile + ".accnos";
- bool hasAccnos = true;
-
- if (method == "bellerophon") {//run bellerophon separately since you need to read entire fastafile to run it
- chimera->getChimeras();
-
- if (m->control_pressed) { delete chimera; return 0; }
-
- ofstream out;
- openOutputFile(outputFileName, out);
-
- ofstream out2;
- openOutputFile(accnosFileName, out2);
-
- chimera->print(out, out2);
- out.close();
- out2.close();
-
- if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); delete chimera; return 0; }
-
- //delete accnos file if its blank
- if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
- if (hasAccnos) { m->mothurOut(accnosFileName); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
-
- delete chimera;
- return 0;
- }
-
- //reads template
- chimera->setTemplateFile(templatefile);
-
- if (m->control_pressed) { delete chimera; return 0; }
-
- if (method != "chimeracheck") {
- if (chimera->getUnaligned()) {
- m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
- delete chimera;
- return 0;
- }
- }
-
- //some methods need to do prep work before processing the chimeras
- chimera->doPrep();
-
- if (m->control_pressed) { delete chimera; return 0; }
-
- templateSeqsLength = chimera->getLength();
-
- ofstream outHeader;
- string tempHeader = outputDir + getRootName(getSimpleName(fastafile)) + method + maskfile + ".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++){
- appendOutputFiles((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++) {
- appendOutputFiles(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
-
- //m->mothurOut("Output File Names: ");
- //if ((filter) && (method == "bellerophon")) { m->mothurOut(
- //if (outputDir == "") { fastafile = getRootName(fastafile) + "filter.fasta"; }
- // else { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; }
-
- appendOutputFiles(tempHeader, outputFileName);
- remove(outputFileName.c_str());
- rename(tempHeader.c_str(), outputFileName.c_str());
+ m->mothurOut("The chimera.seqs command has been broken up into 5 separate commands.\n");
+ m->mothurOut("The chimera.bellerophon, chimera.ccode, chimera.check, chimera.pintail and chimera.slayer commands.\n");
- delete chimera;
-
- if (method == "chimeracheck") { remove(accnosFileName.c_str()); 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("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, "ChimeraSeqsCommand", "execute");
- exit(1);
- }
-}//**********************************************************************************************************************
-
-int ChimeraSeqsCommand::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) && (method != "chimeracheck")) { //chimeracheck does not require seqs to be aligned
- 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, "ChimeraSeqsCommand", "driver");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-int ChimeraSeqsCommand::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, "ChimeraSeqsCommand", "createProcesses");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-void ChimeraSeqsCommand::appendOutputFiles(string temp, string filename) {
- try{
-
- ofstream output;
- ifstream input;
-
- openOutputFileAppend(temp, output);
- openInputFile(filename, input, "noerror");
-
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
- }
-
- input.close();
- output.close();
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSeqsCommand", "appendOuputFiles");
- exit(1);
- }
+ return 0;
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff