X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;fp=chimeraslayercommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=2c435cadb11c1bc413b982676ac58082d4683992;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp deleted file mode 100644 index 2c435ca..0000000 --- a/chimeraslayercommand.cpp +++ /dev/null @@ -1,1884 +0,0 @@ -/* - * 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 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 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 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 myArray = setParameters(); - - OptionParser parser(option); - map parameters = parser.getParameters(); - - ValidParameters validParameter("chimera.slayer"); - map::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 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 > fileToPriority; - map >::iterator itFile; - map 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 thisPriority = itFile->second; -#ifdef USE_MPI - MPIExecute(thisFastaName, outputFileName, accnosFileName, trimFastaFileName, thisPriority); -#else - //break up file - vector 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 >& fileToPriority, map& 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 >::iterator itFile; - vector 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 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 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& priority){ - try { - -#ifdef USE_MPI - int pid, numSeqsPerProcessor; - int tag = 2001; - vector 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 uniqueNames = parser->getAllSeqsMap(); - map::iterator itUnique; - int total = 0; - - if (trimera) { //add in more potential uniqueNames - map newUniqueNames = uniqueNames; - for (map::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 chimerasInFile; - set::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 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::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& fileGroup, map >& 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 groups = parser->getNamesOfGroups(); - - for (int i = 0; i < groups.size(); i++) { - vector thisGroupsSeqs = parser->getSeqs(groups[i]); - map 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 > 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 >& fileToPriority, map& fileGroup){ - try { - int totalSeqs = 0; - - for (map >::iterator itFile = fileToPriority.begin(); itFile != fileToPriority.end(); itFile++) { - - if (m->control_pressed) { return 0; } - - int start = time(NULL); - string thisFastaName = itFile->first; - map 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 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 >& fileToPriority, map& 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 > > breakUp; - - for (int i = 0; i < processors; i++) { - map > thisFileToPriority; - map >::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;iopenInputFile(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 pDataArray; - DWORD dwThreadIdArray[processors-1]; - HANDLE hThreadArray[processors-1]; - - //Create processor worker threads. - for(int i=1; icount; - CloseHandle(hThreadArray[i]); - delete pDataArray[i]; - } -#endif - - //append output files - for(int i=0;iappendFiles((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& 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& MPIPos, string filename, map& 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;icontrol_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& 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;iopenInputFile(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 pDataArray; - DWORD dwThreadIdArray[processors]; - HANDLE hThreadArray[processors]; - - //Create processor worker threads. - for( int i=0; icount; - 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;iappendFiles((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 ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) { - try { - map nameAbund; - - //read through fastafile and store info - map 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 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 ChimeraSlayerCommand::sortFastaFile(vector& thisseqs, map& nameMap, string newFile) { - try { - map nameAbund; - vector nameVector; - - //read through fastafile and store info - map seqs; - - for (int i = 0; i < thisseqs.size(); i++) { - - if (m->control_pressed) { return nameAbund; } - - map::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); - } -} -/**************************************************************************************************/ -