+++ /dev/null
-/*
- * chimeraslayercommand.cpp
- * Mothur
- *
- * Created by westcott on 3/31/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "chimeraslayercommand.h"
-#include "deconvolutecommand.h"
-#include "referencedb.h"
-#include "sequenceparser.h"
-
-//**********************************************************************************************************************
-vector<string> ChimeraSlayerCommand::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 pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pwindow("window", "Number", "", "50", "", "", "",false,false); parameters.push_back(pwindow);
- CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
- CommandParameter pmatch("match", "Number", "", "5.0", "", "", "",false,false); parameters.push_back(pmatch);
- CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "",false,false); parameters.push_back(pmismatch);
- CommandParameter pminsim("minsim", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminsim);
- CommandParameter pmincov("mincov", "Number", "", "70", "", "", "",false,false); parameters.push_back(pmincov);
- CommandParameter pminsnp("minsnp", "Number", "", "10", "", "", "",false,false); parameters.push_back(pminsnp);
- CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs);
- CommandParameter psearch("search", "Multiple", "kmer-blast", "blast", "", "", "",false,false); parameters.push_back(psearch);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter prealign("realign", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(prealign);
- CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim);
- CommandParameter psplit("split", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psplit);
- CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "",false,false); parameters.push_back(pnumwanted);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "",false,false); parameters.push_back(pdivergence);
- CommandParameter pparents("parents", "Number", "", "3", "", "", "",false,false); parameters.push_back(pparents);
- CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement);
- CommandParameter pblastlocation("blastlocation", "String", "", "", "", "", "",false,false); parameters.push_back(pblastlocation);
- 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, "ChimeraSlayerCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string ChimeraSlayerCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The chimera.slayer command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
- helpString += "This command was modeled after the chimeraSlayer written by the Broad Institute.\n";
- helpString += "The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment, numwanted, blastlocation and realign.\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 += "The name parameter allows you to provide a name file, if you are using reference=self. \n";
- helpString += "The group parameter allows you to provide a group file. The group file can be used with a namesfile and reference=self. When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
- helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
- helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \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 trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest piece, default=F. \n";
- helpString += "The split parameter allows you to check both pieces of non-chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n";
- helpString += "The window parameter allows you to specify the window size for searching for chimeras, default=50. \n";
- helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n";
- helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n";
- helpString += "The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n";
- helpString += "The match parameter allows you to reward matched bases in blast search, default is 5. \n";
- helpString += "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";
- helpString += "The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n";
- helpString += "The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n";
- helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=1000.\n";
- helpString += "The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n";
- helpString += "The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n";
- helpString += "The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n";
- helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n";
- helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are blast, and kmer, default blast. \n";
- helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true. \n";
- helpString += "The blastlocation parameter allows you to specify the location of your blast executable. By default mothur will look in ./blast/bin relative to mothur's executable. \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.slayer command should be in the following format: \n";
- helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n";
- helpString += "Example: chimera.slayer(fasta=AD.align, reference=core_set_aligned.imputed.fasta, search=kmer) \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, "ChimeraSlayerCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-ChimeraSlayerCommand::ChimeraSlayerCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["chimera"] = tempOutNames;
- outputTypes["accnos"] = tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
- exit(1);
- }
-}
-//***************************************************************************************************************
-ChimeraSlayerCommand::ChimeraSlayerCommand(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.slayer");
- 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;
- outputTypes["accnos"] = tempOutNames;
- outputTypes["fasta"] = 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 = ""; }
-
- //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 (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("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
- }
-
-
- //check for required parameters
- bool hasName = true;
- namefile = validParameter.validFile(parameters, "name", false);
- if (namefile == "not found") { namefile = ""; hasName = false; }
- 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 (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) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; }
- }
-
- if (hasName && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of namefiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
-
- bool hasGroup = true;
- groupfile = validParameter.validFile(parameters, "group", false);
- if (groupfile == "not found") { groupfile = ""; hasGroup = false; }
- else {
- m->splitAtDash(groupfile, groupFileNames);
-
- //go through files and make sure they are good, if not, then disregard them
- for (int i = 0; i < groupFileNames.size(); i++) {
-
- bool ignore = false;
- if (groupFileNames[i] == "current") {
- groupFileNames[i] = m->getGroupFile();
- if (groupFileNames[i] != "") { m->mothurOut("Using " + groupFileNames[i] + " as input file for the group 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
- groupFileNames.erase(groupFileNames.begin()+i);
- i--;
- }
- }
-
- if (!ignore) {
-
- if (inputDir != "") {
- string path = m->hasPath(groupFileNames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { groupFileNames[i] = inputDir + groupFileNames[i]; }
- }
-
- int ableToOpen;
- ifstream in;
-
- ableToOpen = m->openInputFile(groupFileNames[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(groupFileNames[i]);
- m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- groupFileNames[i] = tryPath;
- }
- }
-
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(groupFileNames[i]);
- m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- groupFileNames[i] = tryPath;
- }
- }
-
- in.close();
-
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + groupFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- groupFileNames.erase(groupFileNames.begin()+i);
- i--;
- }else {
- m->setGroupFile(groupFileNames[i]);
- }
- }
- }
-
- //make sure there is at least one valid file left
- if (groupFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid group files."); m->mothurOutEndLine(); abort = true; }
- }
-
- if (hasGroup && (groupFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of groupfiles does not match the number of fastafiles, please correct."); 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 = ""; }
-
- 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();
- }
-
- string path;
- it = parameters.find("reference");
- //user has given a template file
- if(it != parameters.end()){
- if (it->second == "self") {
- templatefile = "self";
- if (save) {
- m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
- m->mothurOutEndLine();
- save = false;
- }
- }
- else {
- 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; }
-
- templatefile = validParameter.validFile(parameters, "reference", true);
- if (templatefile == "not open") { abort = true; }
- else 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 (save) { rdb->setSavedReference(templatefile); } }
- }
- }else if (hasName) { templatefile = "self";
- if (save) {
- m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
- m->mothurOutEndLine();
- save = false;
- }
- }
- else {
- 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();
- templatefile = ""; abort = true;
- }
- }
-
-
-
- temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
- m->mothurConvert(temp, ksize);
-
- temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "50"; }
- m->mothurConvert(temp, window);
-
- temp = validParameter.validFile(parameters, "match", false); if (temp == "not found") { temp = "5"; }
- m->mothurConvert(temp, match);
-
- temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found") { temp = "-4"; }
- m->mothurConvert(temp, mismatch);
-
- temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.007"; }
- m->mothurConvert(temp, divR);
-
- temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "90"; }
- m->mothurConvert(temp, minSimilarity);
-
- temp = validParameter.validFile(parameters, "mincov", false); if (temp == "not found") { temp = "70"; }
- m->mothurConvert(temp, minCoverage);
-
- temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; }
- m->mothurConvert(temp, minBS);
-
- temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; }
- m->mothurConvert(temp, minSNP);
-
- temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
- m->mothurConvert(temp, parents);
-
- temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "t"; }
- realign = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; }
- trim = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "split", false); if (temp == "not found") { temp = "f"; }
- trimera = m->isTrue(temp);
-
- search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "blast"; }
-
- temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- m->mothurConvert(temp, iters);
-
- temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; }
- m->mothurConvert(temp, increment);
-
- temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; }
- m->mothurConvert(temp, numwanted);
-
- blastlocation = validParameter.validFile(parameters, "blastlocation", false);
- if (blastlocation == "not found") { blastlocation = ""; }
- else {
- //add / to name if needed
- string lastChar = blastlocation.substr(blastlocation.length()-1);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- if (lastChar != "/") { blastlocation += "/"; }
-#else
- if (lastChar != "\\") { blastlocation += "\\"; }
-#endif
- blastlocation = m->getFullPathName(blastlocation);
- string formatdbCommand = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- formatdbCommand = blastlocation + "formatdb";
-#else
- formatdbCommand = blastlocation + "formatdb.exe";
-#endif
-
- //test to make sure formatdb exists
- ifstream in;
- formatdbCommand = m->getFullPathName(formatdbCommand);
- int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
- if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
-
- string blastCommand = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- blastCommand = blastlocation + "megablast";
-#else
- blastCommand = blastlocation + "megablast.exe";
-#endif
- //test to make sure formatdb exists
- ifstream in2;
- blastCommand = m->getFullPathName(blastCommand);
- ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
- if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
- }
-
- if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; }
-
- if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
- if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
-
- //until we resolve the issue 10-18-11
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-#else
- //processors=1;
-#endif
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-int ChimeraSlayerCommand::execute(){
- try{
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- for (int s = 0; s < fastaFileNames.size(); s++) {
-
- m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
-
- int start = time(NULL);
- if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.accnos";
- string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.fasta";
-
- //clears files
- ofstream out, out1, out2;
- m->openOutputFile(outputFileName, out); out.close();
- m->openOutputFile(accnosFileName, out1); out1.close();
- if (trim) { m->openOutputFile(trimFastaFileName, out2); out2.close(); }
- outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
- outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
- if (trim) { outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); }
-
- //maps a filename to priority map.
- //if no groupfile this is fastafileNames[s] -> prioirity
- //if groupfile then this is each groups seqs -> priority
- map<string, map<string, int> > fileToPriority;
- map<string, map<string, int> >::iterator itFile;
- map<string, string> fileGroup;
- fileToPriority[fastaFileNames[s]] = priority; //default
- fileGroup[fastaFileNames[s]] = "noGroup";
- SequenceParser* parser = NULL;
- int totalChimeras = 0;
- lines.clear();
-
- if (templatefile == "self") { setUpForSelfReference(parser, fileGroup, fileToPriority, s); }
-
- if (m->control_pressed) { if (parser != NULL) { delete parser; } for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
-
- if (fileToPriority.size() == 1) { //you running without a groupfile
- itFile = fileToPriority.begin();
- string thisFastaName = itFile->first;
- map<string, int> thisPriority = itFile->second;
-#ifdef USE_MPI
- MPIExecute(thisFastaName, outputFileName, accnosFileName, trimFastaFileName, thisPriority);
-#else
- //break up file
- vector<unsigned long long> positions;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- positions = m->divideFile(thisFastaName, processors);
- for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
-#else
- if (processors == 1) { lines.push_back(linePair(0, 1000)); }
- else {
- positions = m->setFilePosFasta(thisFastaName, numSeqs);
- if (positions.size() < processors) { processors = positions.size(); }
-
- //figure out how many sequences you have to process
- int numSeqsPerProcessor = numSeqs / processors;
- for (int i = 0; i < processors; i++) {
- int startIndex = i * numSeqsPerProcessor;
- if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; }
- lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
- }
- }
-#endif
- if(processors == 1){ numSeqs = driver(lines[0], outputFileName, thisFastaName, accnosFileName, trimFastaFileName, thisPriority); }
- else{ numSeqs = createProcesses(outputFileName, thisFastaName, accnosFileName, trimFastaFileName, thisPriority); }
-
- if (m->control_pressed) { if (parser != NULL) { delete parser; } outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
-#endif
- }else { //you have provided a groupfile
-#ifdef USE_MPI
- MPIExecuteGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup);
-#else
- if (processors == 1) { numSeqs = driverGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup); }
- else { numSeqs = createProcessesGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup); } //destroys fileToPriority
-#endif
-
-#ifdef USE_MPI
- int pid;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
-#endif
-
- totalChimeras = deconvoluteResults(parser, outputFileName, accnosFileName, trimFastaFileName);
-#ifdef USE_MPI
- }
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
-#endif
- }
-
- if (parser != NULL) { delete parser; }
-
- m->mothurOutEndLine(); m->mothurOut(toString(totalChimeras) + " chimera found."); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
- }
-
- //set accnos file as new current accnosfile
- string current = "";
- itTypes = outputTypes.find("accnos");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
- }
-
- if (trim) {
- itTypes = outputTypes.find("fasta");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
- }
- }
-
- 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, "ChimeraSlayerCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int ChimeraSlayerCommand::MPIExecuteGroups(string outputFileName, string accnosFileName, string trimFastaFileName, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup){
- try {
-#ifdef USE_MPI
- int pid;
- int tag = 2001;
-
- MPI_Status status;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
- //put filenames in a vector, then pass each process a starting and ending point in the vector
- //all processes already have the fileToPriority and fileGroup, they just need to know which files to process
- map<string, map<string, int> >::iterator itFile;
- vector<string> filenames;
- for(itFile = fileToPriority.begin(); itFile != fileToPriority.end(); itFile++) { filenames.push_back(itFile->first); }
-
- int numGroupsPerProcessor = filenames.size() / processors;
- int startIndex = pid * numGroupsPerProcessor;
- int endIndex = (pid+1) * numGroupsPerProcessor;
- if(pid == (processors - 1)){ endIndex = filenames.size(); }
-
- vector<unsigned long long> MPIPos;
-
- MPI_File outMPI;
- MPI_File outMPIAccnos;
- MPI_File outMPIFasta;
-
- int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
- int inMode=MPI_MODE_RDONLY;
-
- char outFilename[1024];
- strcpy(outFilename, outputFileName.c_str());
-
- char outAccnosFilename[1024];
- strcpy(outAccnosFilename, accnosFileName.c_str());
-
- char outFastaFilename[1024];
- strcpy(outFastaFilename, trimFastaFileName.c_str());
-
- 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 (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
-
- if (m->control_pressed) { MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); return 0; }
-
- //print headers
- 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 = new char[length];
- memcpy(buf2, outTemp.c_str(), length);
-
- MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
- }
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
-
- for (int i = startIndex; i < endIndex; i++) {
-
- int start = time(NULL);
- int num = 0;
- string thisFastaName = filenames[i];
- map<string, int> thisPriority = fileToPriority[thisFastaName];
-
- char inFileName[1024];
- strcpy(inFileName, thisFastaName.c_str());
- MPI_File inMPI;
- MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
-
- MPIPos = m->setFilePosFasta(thisFastaName, num); //fills MPIPos, returns numSeqs
-
- cout << endl << "Checking sequences from group: " << fileGroup[thisFastaName] << "." << endl;
-
- driverMPI(0, num, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos, thisFastaName, thisPriority, true);
- numSeqs += num;
-
- MPI_File_close(&inMPI);
- m->mothurRemove(thisFastaName);
-
- cout << endl << "It took " << toString(time(NULL) - start) << " secs to check " + toString(num) + " sequences from group " << fileGroup[thisFastaName] << "." << endl;
- }
-
- if (pid == 0) {
- for(int i = 1; i < processors; i++) {
- int temp = 0;
- MPI_Recv(&temp, 1, MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
- numSeqs += temp;
- }
- }else{ MPI_Send(&numSeqs, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD); }
-
- MPI_File_close(&outMPI);
- MPI_File_close(&outMPIAccnos);
- if (trim) { MPI_File_close(&outMPIFasta); }
-
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
-#endif
- return 0;
-
- }catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "MPIExecuteGroups");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int ChimeraSlayerCommand::MPIExecute(string inputFile, string outputFileName, string accnosFileName, string trimFastaFileName, map<string, int>& priority){
- try {
-
-#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;
- MPI_File outMPIAccnos;
- MPI_File outMPIFasta;
-
- int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
- int inMode=MPI_MODE_RDONLY;
-
- char outFilename[1024];
- strcpy(outFilename, outputFileName.c_str());
-
- char outAccnosFilename[1024];
- strcpy(outAccnosFilename, accnosFileName.c_str());
-
- char outFastaFilename[1024];
- strcpy(outFastaFilename, trimFastaFileName.c_str());
-
- char inFileName[1024];
- strcpy(inFileName, inputFile.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 (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
-
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); 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 = new char[length];
- memcpy(buf2, outTemp.c_str(), length);
-
- MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
-
- MPIPos = m->setFilePosFasta(inputFile, numSeqs); //fills MPIPos, returns numSeqs
-
- if (templatefile != "self") { //if template=self we can only use 1 processor
- //send file positions to all processes
- for(int i = 1; i < processors; i++) {
- MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
- MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, 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; }
-
- if (templatefile == "self") { //if template=self we can only use 1 processor
- startIndex = 0;
- numSeqsPerProcessor = numSeqs;
- }
-
- //do your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos, inputFile, priority, false);
-
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); return 0; }
-
- }else{ //you are a child process
- if (templatefile != "self") { //if template=self we can only use 1 processor
- 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; }
-
- //do your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos, inputFile, priority, false);
-
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); return 0; }
-
- }
- }
-
- //close files
- MPI_File_close(&inMPI);
- MPI_File_close(&outMPI);
- MPI_File_close(&outMPIAccnos);
- if (trim) { MPI_File_close(&outMPIFasta); }
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-
-
-#endif
- return numSeqs;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "MPIExecute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int ChimeraSlayerCommand::deconvoluteResults(SequenceParser* parser, string outputFileName, string accnosFileName, string trimFileName){
- try {
- map<string, string> uniqueNames = parser->getAllSeqsMap();
- map<string, string>::iterator itUnique;
- int total = 0;
-
- if (trimera) { //add in more potential uniqueNames
- map<string, string> newUniqueNames = uniqueNames;
- for (map<string, string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) {
- newUniqueNames[(it->first)+"_LEFT"] = (it->first)+"_LEFT";
- newUniqueNames[(it->first)+"_RIGHT"] = (it->first)+"_RIGHT";
- }
- uniqueNames = newUniqueNames;
- newUniqueNames.clear();
- }
-
- //edit accnos file
- ifstream in2;
- m->openInputFile(accnosFileName, in2, "no error");
-
- ofstream out2;
- m->openOutputFile(accnosFileName+".temp", out2);
-
- string name; name = "";
- set<string> chimerasInFile;
- set<string>::iterator itChimeras;
-
- while (!in2.eof()) {
- if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
-
- in2 >> name; m->gobble(in2);
-
- //find unique name
- itUnique = uniqueNames.find(name);
-
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- itChimeras = chimerasInFile.find((itUnique->second));
-
- if (itChimeras == chimerasInFile.end()) {
- out2 << itUnique->second << endl;
- chimerasInFile.insert((itUnique->second));
- total++;
- }
- }
- }
- in2.close();
- out2.close();
-
- m->mothurRemove(accnosFileName);
- rename((accnosFileName+".temp").c_str(), accnosFileName.c_str());
-
-
- //edit chimera file
- ifstream in;
- m->openInputFile(outputFileName, in);
-
- ofstream out;
- m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- string rest, parent1, parent2, line;
- set<string> namesInFile; //this is so if a sequence is found to be chimera in several samples we dont write it to the results file more than once
- set<string>::iterator itNames;
-
- //assumptions - in file each read will always look like...
- /*
- F11Fcsw_92754 no
- F11Fcsw_63104 F11Fcsw_33372 F11Fcsw_37007 0.89441 80.4469 0.2 1.03727 93.2961 52.2 no 0-241 243-369
- */
-
- //get header line
- if (!in.eof()) {
- line = m->getline(in); m->gobble(in);
- out << line << endl;
- }
-
- //for the chimera file, we want to make sure if any group finds a sequence to be chimeric then all groups do,
- //so if this is a report that did not find it to be chimeric, but it appears in the accnos file,
- //then ignore this report and continue until we find the report that found it to be chimeric
-
- while (!in.eof()) {
-
- if (m->control_pressed) { in.close(); out.close(); m->mothurRemove((outputFileName+".temp")); return 0; }
-
- in >> name; m->gobble(in);
- in >> parent1; m->gobble(in);
-
- if (name == "Name") { //name = "Name" because we append the header line each time we add results from the groups
- line = m->getline(in); m->gobble(in);
- }else {
- if (parent1 == "no") {
- //find unique name
- itUnique = uniqueNames.find(name);
-
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- //is this sequence really not chimeric??
- itChimeras = chimerasInFile.find(itUnique->second);
-
- if (itChimeras == chimerasInFile.end()) {
- //is this sequence not already in the file
- itNames = namesInFile.find((itUnique->second));
-
- if (itNames == namesInFile.end()) { out << itUnique->second << '\t' << "no" << endl; namesInFile.insert(itUnique->second); }
- }
- }
- }else { //read the rest of the line
- double DivQLAQRB,PerIDQLAQRB,BootStrapA,DivQLBQRA,PerIDQLBQRA,BootStrapB;
- string flag, range1, range2;
- bool print = false;
- in >> parent2 >> DivQLAQRB >> PerIDQLAQRB >> BootStrapA >> DivQLBQRA >> PerIDQLBQRA >> BootStrapB >> flag >> range1 >> range2; m->gobble(in);
-
- //find unique name
- itUnique = uniqueNames.find(name);
-
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- name = itUnique->second;
- //is this name already in the file
- itNames = namesInFile.find((name));
-
- if (itNames == namesInFile.end()) { //no not in file
- if (flag == "no") { //are you really a no??
- //is this sequence really not chimeric??
- itChimeras = chimerasInFile.find(name);
-
- //then you really are a no so print, otherwise skip
- if (itChimeras == chimerasInFile.end()) { print = true; }
-
- }else{ print = true; }
- }
- }
-
- if (print) {
- out << name << '\t';
-
- namesInFile.insert(name);
-
- //output parent1's name
- itUnique = uniqueNames.find(parent1);
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent1 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else { out << itUnique->second << '\t'; }
-
- //output parent2's name
- itUnique = uniqueNames.find(parent2);
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else { out << itUnique->second << '\t'; }
-
- out << DivQLAQRB << '\t' << PerIDQLAQRB << '\t' << BootStrapA << '\t' << DivQLBQRA << '\t' << PerIDQLBQRA << '\t' << BootStrapB << '\t' << flag << '\t' << range1 << '\t' << range2 << endl;
- }
- }
- }
- }
- in.close();
- out.close();
-
- m->mothurRemove(outputFileName);
- rename((outputFileName+".temp").c_str(), outputFileName.c_str());
-
- //edit fasta file
- if (trim) {
- ifstream in3;
- m->openInputFile(trimFileName, in3);
-
- ofstream out3;
- m->openOutputFile(trimFileName+".temp", out3);
-
- namesInFile.clear();
-
- while (!in3.eof()) {
- if (m->control_pressed) { in3.close(); out3.close(); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); m->mothurRemove((trimFileName+".temp")); return 0; }
-
- Sequence seq(in3); m->gobble(in3);
-
- if (seq.getName() != "") {
- //find unique name
- itUnique = uniqueNames.find(seq.getName());
-
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ seq.getName() + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- itNames = namesInFile.find((itUnique->second));
-
- if (itNames == namesInFile.end()) {
- seq.printSequence(out3);
- }
- }
- }
- }
- in3.close();
- out3.close();
-
- m->mothurRemove(trimFileName);
- rename((trimFileName+".temp").c_str(), trimFileName.c_str());
- }
-
- return total;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "deconvoluteResults");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int ChimeraSlayerCommand::setUpForSelfReference(SequenceParser*& parser, map<string, string>& fileGroup, map<string, map<string, int> >& fileToPriority, int s){
- try {
- fileGroup.clear();
- fileToPriority.clear();
-
- string nameFile = "";
- if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
- nameFile = nameFileNames[s];
- }else { nameFile = getNamesFile(fastaFileNames[s]); }
-
- //you provided a groupfile
- string groupFile = "";
- if (groupFileNames.size() != 0) { groupFile = groupFileNames[s]; }
-
- if (groupFile == "") {
- if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
-
- //sort fastafile by abundance, returns new sorted fastafile name
- m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
- priority = sortFastaFile(fastaFileNames[s], nameFile);
- m->mothurOut("Done."); m->mothurOutEndLine();
-
- fileToPriority[fastaFileNames[s]] = priority;
- fileGroup[fastaFileNames[s]] = "noGroup";
- }else {
- //Parse sequences by group
- parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
- vector<string> groups = parser->getNamesOfGroups();
-
- for (int i = 0; i < groups.size(); i++) {
- vector<Sequence> thisGroupsSeqs = parser->getSeqs(groups[i]);
- map<string, string> thisGroupsMap = parser->getNameMap(groups[i]);
- string newFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + groups[i] + "-sortedTemp.fasta";
- priority = sortFastaFile(thisGroupsSeqs, thisGroupsMap, newFastaFile);
- fileToPriority[newFastaFile] = priority;
- fileGroup[newFastaFile] = groups[i];
- }
- }
-
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "setUpForSelfReference");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-string ChimeraSlayerCommand::getNamesFile(string& inputFile){
- try {
- string nameFile = "";
-
- m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
-
- //use unique.seqs to create new name and fastafile
- string inputString = "fasta=" + inputFile;
- m->mothurOut("/******************************************/"); m->mothurOutEndLine();
- m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
- m->mothurCalling = true;
-
- Command* uniqueCommand = new DeconvoluteCommand(inputString);
- uniqueCommand->execute();
-
- map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
-
- delete uniqueCommand;
- m->mothurCalling = false;
- m->mothurOut("/******************************************/"); m->mothurOutEndLine();
-
- nameFile = filenames["name"][0];
- inputFile = filenames["fasta"][0];
-
- return nameFile;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "getNamesFile");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int ChimeraSlayerCommand::driverGroups(string outputFName, string accnos, string fasta, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup){
- try {
- int totalSeqs = 0;
-
- for (map<string, map<string, int> >::iterator itFile = fileToPriority.begin(); itFile != fileToPriority.end(); itFile++) {
-
- if (m->control_pressed) { return 0; }
-
- int start = time(NULL);
- string thisFastaName = itFile->first;
- map<string, int> thisPriority = itFile->second;
- string thisoutputFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.chimera";
- string thisaccnosFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.accnos";
- string thistrimFastaFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.fasta";
-
- m->mothurOutEndLine(); m->mothurOut("Checking sequences from group: " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine();
-
- lines.clear();
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- int proc = 1;
- vector<unsigned long long> positions = m->divideFile(thisFastaName, proc);
- lines.push_back(linePair(positions[0], positions[1]));
-#else
- lines.push_back(linePair(0, 1000));
-#endif
- int numSeqs = driver(lines[0], thisoutputFileName, thisFastaName, thisaccnosFileName, thistrimFastaFileName, thisPriority);
-
- //append files
- m->appendFiles(thisoutputFileName, outputFName); m->mothurRemove(thisoutputFileName);
- m->appendFiles(thisaccnosFileName, accnos); m->mothurRemove(thisaccnosFileName);
- if (trim) { m->appendFiles(thistrimFastaFileName, fasta); m->mothurRemove(thistrimFastaFileName); }
- m->mothurRemove(thisFastaName);
-
- totalSeqs += numSeqs;
-
- m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine();
- }
-
- return totalSeqs;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "driverGroups");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accnos, string fasta, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup) {
- try {
- int process = 1;
- int num = 0;
- processIDS.clear();
-
- if (fileToPriority.size() < processors) { processors = fileToPriority.size(); }
-
- int groupsPerProcessor = fileToPriority.size() / processors;
- int remainder = fileToPriority.size() % processors;
-
- vector< map<string, map<string, int> > > breakUp;
-
- for (int i = 0; i < processors; i++) {
- map<string, map<string, int> > thisFileToPriority;
- map<string, map<string, int> >::iterator itFile;
- int count = 0;
- int enough = groupsPerProcessor;
- if (i == 0) { enough = groupsPerProcessor + remainder; }
-
- for (itFile = fileToPriority.begin(); itFile != fileToPriority.end();) {
- thisFileToPriority[itFile->first] = itFile->second;
- fileToPriority.erase(itFile++);
- count++;
- if (count == enough) { break; }
- }
- breakUp.push_back(thisFileToPriority);
- }
-
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- //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 = driverGroups(outputFName + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", breakUp[process], fileGroup);
-
- //pass numSeqs to parent
- ofstream out;
- string tempFile = outputFName + 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);
- }
- }
-
- num = driverGroups(outputFName, accnos, fasta, breakUp[0], fileGroup);
-
- //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 = outputFName + toString(processIDS[i]) + ".num.temp";
- m->openInputFile(tempFile, in);
- if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
- in.close(); m->mothurRemove(tempFile);
- }
-#else
-
- //////////////////////////////////////////////////////////////////////////////////////////////////////
- //Windows version shared memory, so be careful when passing variables through the slayerData struct.
- //Above fork() will clone, so memory is separate, but that's not the case with windows,
- //////////////////////////////////////////////////////////////////////////////////////////////////////
-
- vector<slayerData*> pDataArray;
- DWORD dwThreadIdArray[processors-1];
- HANDLE hThreadArray[processors-1];
-
- //Create processor worker threads.
- for(int i=1; i<processors; i++ ){
- string extension = toString(i) + ".temp";
- slayerData* tempslayer = new slayerData((outputFName + extension), (fasta + extension), (accnos + extension), templatefile, search, blastlocation, trimera, trim, realign, m, breakUp[i], fileGroup, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);
- pDataArray.push_back(tempslayer);
- processIDS.push_back(i);
-
- //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
- //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
- hThreadArray[i-1] = CreateThread(NULL, 0, MySlayerGroupThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
- }
-
- num = driverGroups(outputFName, accnos, fasta, breakUp[0], fileGroup);
-
- //Wait until all threads have terminated.
- WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
-
- //Close all thread handles and free memory allocations.
- for(int i=0; i < pDataArray.size(); i++){
- num += pDataArray[i]->count;
- CloseHandle(hThreadArray[i]);
- delete pDataArray[i];
- }
-#endif
-
- //append output files
- for(int i=0;i<processIDS.size();i++){
- m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
- m->mothurRemove((outputFName + toString(processIDS[i]) + ".temp"));
-
- m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
- m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
-
- if (trim) {
- m->appendFiles((fasta + toString(processIDS[i]) + ".temp"), fasta);
- m->mothurRemove((fasta + toString(processIDS[i]) + ".temp"));
- }
- }
-
-
- return num;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "createProcessesGroups");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int ChimeraSlayerCommand::driver(linePair filePos, string outputFName, string filename, string accnos, string fasta, map<string, int>& priority){
- try {
-
- Chimera* chimera;
- if (templatefile != "self") { //you want to run slayer with a reference template
- chimera = new ChimeraSlayer(filename, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
- }else {
- chimera = new ChimeraSlayer(filename, templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
- }
-
- if (m->control_pressed) { delete chimera; return 0; }
-
- if (chimera->getUnaligned()) { delete chimera; m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
- templateSeqsLength = chimera->getLength();
-
- ofstream out;
- m->openOutputFile(outputFName, out);
-
- ofstream out2;
- m->openOutputFile(accnos, out2);
-
- ofstream out3;
- if (trim) { m->openOutputFile(fasta, out3); }
-
- ifstream inFASTA;
- m->openInputFile(filename, inFASTA);
-
- inFASTA.seekg(filePos.start);
-
- if (filePos.start == 0) { chimera->printHeader(out); }
-
- bool done = false;
- int count = 0;
-
- while (!done) {
-
- if (m->control_pressed) { delete chimera; out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1; }
-
- Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
- string candidateAligned = candidateSeq->getAligned();
-
- 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 chimera; delete candidateSeq; return 1; }
-
- //if you are not chimeric, then check each half
- data_results wholeResults = chimera->getResults();
-
- //determine if we need to split
- bool isChimeric = false;
-
- if (wholeResults.flag == "yes") {
- string chimeraFlag = "no";
- if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
- ||
- (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
-
-
- if (chimeraFlag == "yes") {
- if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
- }
- }
-
- if ((!isChimeric) && trimera) {
-
- //split sequence in half by bases
- string leftQuery, rightQuery;
- Sequence tempSeq(candidateSeq->getName(), candidateAligned);
- divideInHalf(tempSeq, leftQuery, rightQuery);
-
- //run chimeraSlayer on each piece
- Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
- Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
-
- //find chimeras
- chimera->getChimeras(left);
- data_results leftResults = chimera->getResults();
-
- chimera->getChimeras(right);
- data_results rightResults = chimera->getResults();
-
- //if either piece is chimeric then report
- Sequence trimmed = chimera->print(out, out2, leftResults, rightResults);
- if (trim) { trimmed.printSequence(out3); }
-
- delete left; delete right;
-
- }else { //already chimeric
- //print results
- Sequence trimmed = chimera->print(out, out2);
- if (trim) { trimmed.printSequence(out3); }
- }
-
-
- }
- count++;
- }
-
- #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
-
- delete candidateSeq;
- //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(); }
-
- int numNoParents = chimera->getNumNoParents();
- if (numNoParents == count) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
-
- out.close();
- out2.close();
- if (trim) { out3.close(); }
- inFASTA.close();
- delete chimera;
-
- return count;
-
-
- }
- 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, MPI_File& outFastaMPI, vector<unsigned long long>& MPIPos, string filename, map<string, int>& priority, bool byGroup){
- try {
- MPI_Status status;
- int pid;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- Chimera* chimera;
- if (templatefile != "self") { //you want to run slayer with a reference template
- chimera = new ChimeraSlayer(filename, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
- }else {
- chimera = new ChimeraSlayer(filename, templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand(), byGroup);
- }
-
- if (m->control_pressed) { delete chimera; return 0; }
-
- if (chimera->getUnaligned()) { delete chimera; m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
- templateSeqsLength = chimera->getLength();
-
- for(int i=0;i<num;i++){
-
- if (m->control_pressed) { delete chimera; return 1; }
-
- //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);
- string candidateAligned = candidateSeq->getAligned();
-
- 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 chimera; delete candidateSeq; return 1; }
-
- //if you are not chimeric, then check each half
- data_results wholeResults = chimera->getResults();
-
- //determine if we need to split
- bool isChimeric = false;
-
- if (wholeResults.flag == "yes") {
- string chimeraFlag = "no";
- if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
- ||
- (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
-
-
- if (chimeraFlag == "yes") {
- if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
- }
- }
-
- if ((!isChimeric) && trimera) {
- //split sequence in half by bases
- string leftQuery, rightQuery;
- Sequence tempSeq(candidateSeq->getName(), candidateAligned);
- divideInHalf(tempSeq, leftQuery, rightQuery);
-
- //run chimeraSlayer on each piece
- Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
- Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
-
- //find chimeras
- chimera->getChimeras(left);
- data_results leftResults = chimera->getResults();
-
- chimera->getChimeras(right);
- data_results rightResults = chimera->getResults();
-
- //if either piece is chimeric then report
- Sequence trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
- if (trim) {
- string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
-
- //write to accnos file
- int length = outputString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outputString.c_str(), length);
-
- MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
- }
-
- delete left; delete right;
-
- }else {
- //print results
- Sequence trimmed = chimera->print(outMPI, outAccMPI);
-
- if (trim) {
- string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
-
- //write to accnos file
- int length = outputString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outputString.c_str(), length);
-
- MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
- }
- }
-
- }
- }
- 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"); }
-
- int numNoParents = chimera->getNumNoParents();
- if (numNoParents == num) { cout << "[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors." << endl; }
-
- delete chimera;
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
- exit(1);
- }
-}
-#endif
-
-/**************************************************************************************************/
-
-int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta, map<string, int>& thisPriority) {
- try {
- int process = 0;
- int num = 0;
- processIDS.clear();
-
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- //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, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", thisPriority);
-
- //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);
- }
-#else
-
- //////////////////////////////////////////////////////////////////////////////////////////////////////
- //Windows version shared memory, so be careful when passing variables through the slayerData struct.
- //Above fork() will clone, so memory is separate, but that's not the case with windows,
- //////////////////////////////////////////////////////////////////////////////////////////////////////
-
- vector<slayerData*> pDataArray;
- DWORD dwThreadIdArray[processors];
- HANDLE hThreadArray[processors];
-
- //Create processor worker threads.
- for( int i=0; i<processors; i++ ){
- string extension = toString(i) + ".temp";
- slayerData* tempslayer = new slayerData((outputFileName + extension), (fasta + extension), (accnos + extension), filename, templatefile, search, blastlocation, trimera, trim, realign, m, lines[i].start, lines[i].end, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);
- pDataArray.push_back(tempslayer);
- processIDS.push_back(i);
-
- //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
- //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
- hThreadArray[i] = CreateThread(NULL, 0, MySlayerThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
- }
-
- //Wait until all threads have terminated.
- WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
-
- //Close all thread handles and free memory allocations.
- for(int i=0; i < pDataArray.size(); i++){
- num += pDataArray[i]->count;
- CloseHandle(hThreadArray[i]);
- delete pDataArray[i];
- }
-#endif
-
- rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
- rename((accnos + toString(processIDS[0]) + ".temp").c_str(), accnos.c_str());
- if (trim) { rename((fasta + toString(processIDS[0]) + ".temp").c_str(), fasta.c_str()); }
-
- //append output files
- for(int i=1;i<processIDS.size();i++){
- m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
- m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
-
- m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
- m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
-
- if (trim) {
- m->appendFiles((fasta + toString(processIDS[i]) + ".temp"), fasta);
- m->mothurRemove((fasta + toString(processIDS[i]) + ".temp"));
- }
- }
-
-
- return num;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-int ChimeraSlayerCommand::divideInHalf(Sequence querySeq, string& leftQuery, string& rightQuery) {
- try {
-
- string queryUnAligned = querySeq.getUnaligned();
- int numBases = int(queryUnAligned.length() * 0.5);
-
- string queryAligned = querySeq.getAligned();
- leftQuery = querySeq.getAligned();
- rightQuery = querySeq.getAligned();
-
- int baseCount = 0;
- int leftSpot = 0;
- for (int i = 0; i < queryAligned.length(); i++) {
- //if you are a base
- if (isalpha(queryAligned[i])) {
- baseCount++;
- }
-
- //if you have half
- if (baseCount >= numBases) { leftSpot = i; break; } //first half
- }
-
- //blank out right side
- for (int i = leftSpot; i < leftQuery.length(); i++) { leftQuery[i] = '.'; }
-
- //blank out left side
- for (int i = 0; i < leftSpot; i++) { rightQuery[i] = '.'; }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "divideInHalf");
- exit(1);
- }
-}
-/**************************************************************************************************/
-map<string, int> ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) {
- try {
- map<string, int> nameAbund;
-
- //read through fastafile and store info
- map<string, string> seqs;
- ifstream in;
- m->openInputFile(fastaFile, in);
-
- while (!in.eof()) {
-
- if (m->control_pressed) { in.close(); return nameAbund; }
-
- Sequence seq(in); m->gobble(in);
- seqs[seq.getName()] = seq.getAligned();
- }
-
- in.close();
-
- //read namefile
- vector<seqPriorityNode> nameMapCount;
- int error = m->readNames(nameFile, nameMapCount, seqs);
-
- if (m->control_pressed) { return nameAbund; }
-
- if (error == 1) { m->control_pressed = true; return nameAbund; }
- if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return nameAbund; }
-
- sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
-
- string newFasta = fastaFile + ".temp";
- ofstream out;
- m->openOutputFile(newFasta, out);
-
- //print new file in order of
- for (int i = 0; i < nameMapCount.size(); i++) {
- out << ">" << nameMapCount[i].name << endl << nameMapCount[i].seq << endl;
- nameAbund[nameMapCount[i].name] = nameMapCount[i].numIdentical;
- }
- out.close();
-
- rename(newFasta.c_str(), fastaFile.c_str());
-
- return nameAbund;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
- exit(1);
- }
-}
-/**************************************************************************************************/
-map<string, int> ChimeraSlayerCommand::sortFastaFile(vector<Sequence>& thisseqs, map<string, string>& nameMap, string newFile) {
- try {
- map<string, int> nameAbund;
- vector<seqPriorityNode> nameVector;
-
- //read through fastafile and store info
- map<string, string> seqs;
-
- for (int i = 0; i < thisseqs.size(); i++) {
-
- if (m->control_pressed) { return nameAbund; }
-
- map<string, string>::iterator itNameMap = nameMap.find(thisseqs[i].getName());
-
- if (itNameMap == nameMap.end()){
- m->control_pressed = true;
- m->mothurOut("[ERROR]: " + thisseqs[i].getName() + " is in your fastafile, but is not in your namesfile, please correct."); m->mothurOutEndLine();
- }else {
- int num = m->getNumNames(itNameMap->second);
-
- seqPriorityNode temp(num, thisseqs[i].getAligned(), thisseqs[i].getName());
- nameVector.push_back(temp);
- }
- }
-
- //sort by num represented
- sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
-
- if (m->control_pressed) { return nameAbund; }
-
- if (thisseqs.size() != nameVector.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return nameAbund; }
-
- ofstream out;
- m->openOutputFile(newFile, out);
-
- //print new file in order of
- for (int i = 0; i < nameVector.size(); i++) {
- out << ">" << nameVector[i].name << endl << nameVector[i].seq << endl;
- nameAbund[nameVector[i].name] = nameVector[i].numIdentical;
- }
- out.close();
-
- return nameAbund;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
projects / mothur.git / blobdiff