X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=7c35453a8993363512c9121aed83cd664ebcb799;hb=4e4d3cb3315fe25b40383c6f65cd6be23f58903d;hp=8a80d4dc2517309b3778186ed6ac4e5c937a73f1;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp index 8a80d4d..7c35453 100644 --- a/chimeraslayercommand.cpp +++ b/chimeraslayercommand.cpp @@ -9,22 +9,119 @@ #include "chimeraslayercommand.h" #include "chimeraslayer.h" +#include "deconvolutecommand.h" +#include "referencedb.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 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 += "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; + abort = false; calledHelp = false; + ReferenceDB* rdb = ReferenceDB::getInstance(); //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"fasta", "processors", "window", "template","numwanted", "ksize", "match","mismatch", - "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -37,76 +134,233 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { 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 = ""; } - else { - string path; - it = parameters.find("template"); - //user has given a template file - if(it != parameters.end()){ - path = m->hasPath(it->second); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["template"] = inputDir + it->second; } - } - } - - + //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", false); - if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; } - else { + 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++) { - 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]; } + + 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--; + } } - - int ableToOpen; - ifstream in; - ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror"); + 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]); + } + } + } - //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(); - ableToOpen = m->openInputFile(tryPath, in, "noerror"); - fastaFileNames[i] = tryPath; + //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--; } } - 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--; + 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 (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; } + 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; } + //if the user changes the output directory command factory will send this info to us in the output parameter - outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ - outputDir = ""; - outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it - } - - templatefile = validParameter.validFile(parameters, "template", true); - if (templatefile == "not open") { abort = true; } - else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; } - - string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; } + 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); convert(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"; } convert(temp, ksize); @@ -131,18 +385,24 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; } convert(temp, minBS); - temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "100"; } + temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; } convert(temp, minSNP); temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; } convert(temp, parents); - temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "f"; } + temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "t"; } realign = m->isTrue(temp); - search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; } + temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; } + trim = m->isTrue(temp); - temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; } + 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"; } convert(temp, iters); temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; } @@ -150,8 +410,47 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; } convert(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) + if (lastChar != "/") { blastlocation += "/"; } +#else + if (lastChar != "\\") { blastlocation += "\\"; } +#endif + blastlocation = m->getFullPathName(blastlocation); + string formatdbCommand = ""; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + 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) + 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 != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); 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; } } } catch(exception& e) { @@ -159,70 +458,62 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { exit(1); } } -//********************************************************************************************************************** - -void ChimeraSlayerCommand::help(){ - try { - - m->mothurOut("The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n"); - m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n"); - m->mothurOut("The chimera.slayer command parameters are fasta, template, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign, - m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n"); - m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n"); - m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n"); - m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"); - #ifdef USE_MPI - m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n"); - #endif - m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n"); - m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n"); - m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n"); - m->mothurOut("The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n"); - m->mothurOut("The match parameter allows you to reward matched bases in blast search, default is 5. \n"); - m->mothurOut("The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n"); - m->mothurOut("The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n"); - m->mothurOut("The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n"); - m->mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n"); - m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n"); - m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n"); - m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n"); - m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n"); - m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n"); - m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. \n"); - m->mothurOut("The chimera.slayer command should be in the following format: \n"); - m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n"); - m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "ChimeraSlayerCommand", "help"); - exit(1); - } -} - -//*************************************************************************************************************** - -ChimeraSlayerCommand::~ChimeraSlayerCommand(){ /* do nothing */ } - //*************************************************************************************************************** int ChimeraSlayerCommand::execute(){ try{ - - if (abort == true) { return 0; } - + 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); - chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign); - - string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras"; + if (templatefile != "self") { //you want to run slayer with a refernce template + chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation); + }else { + if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; } + string nameFile = ""; + if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one + nameFile = nameFileNames[s]; + }else { + 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=" + fastaFileNames[s]; + m->mothurOut("/******************************************/"); m->mothurOutEndLine(); + m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); + + Command* uniqueCommand = new DeconvoluteCommand(inputString); + uniqueCommand->execute(); + + map > filenames = uniqueCommand->getOutputFiles(); + + delete uniqueCommand; + + m->mothurOut("/******************************************/"); m->mothurOutEndLine(); + + nameFile = filenames["name"][0]; + fastaFileNames[s] = filenames["fasta"][0]; + } + + //sort fastafile by abundance, returns new sorted fastafile name + m->mothurOut("Sorting fastafile according to abundance..."); cout.flush(); + map priority = sortFastaFile(fastaFileNames[s], nameFile); + m->mothurOut("Done."); m->mothurOutEndLine(); + + if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } + + chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation); + } + + 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"; - if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } + if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); @@ -232,7 +523,7 @@ int ChimeraSlayerCommand::execute(){ templateSeqsLength = chimera->getLength(); #ifdef USE_MPI - int pid, end, numSeqsPerProcessor; + int pid, numSeqsPerProcessor; int tag = 2001; vector MPIPos; @@ -243,6 +534,7 @@ int ChimeraSlayerCommand::execute(){ 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; @@ -252,6 +544,9 @@ int ChimeraSlayerCommand::execute(){ char outAccnosFilename[1024]; strcpy(outAccnosFilename, accnosFileName.c_str()); + + char outFastaFilename[1024]; + strcpy(outFastaFilename, trimFastaFileName.c_str()); char inFileName[1024]; strcpy(inFileName, fastaFileNames[s].c_str()); @@ -259,8 +554,9 @@ int ChimeraSlayerCommand::execute(){ 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); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; } if (pid == 0) { //you are the root process m->mothurOutEndLine(); @@ -279,42 +575,65 @@ int ChimeraSlayerCommand::execute(){ MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs - //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); + 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, MPIPos); + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); + + int numNoParents = chimera->getNumNoParents(); + int temp; + for(int i = 1; i < processors; i++) { + MPI_Recv(&temp, 1, MPI_INT, 1, tag, MPI_COMM_WORLD, &status); + numNoParents += temp; + } - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); delete chimera; return 0; } + + if (numSeqs == numNoParents) { 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(); } + + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); delete chimera; return 0; } }else{ //you are a child process - MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); - MPIPos.resize(numSeqs+1); - MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + 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; } + //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, MPIPos); + //do your part + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); + + int numNoParents = chimera->getNumNoParents(); + MPI_Send(&numNoParents, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; } + + } } //close files MPI_File_close(&inMPI); MPI_File_close(&outMPI); - MPI_File_close(&outMPIAccnos); + MPI_File_close(&outMPIAccnos); + if (trim) { MPI_File_close(&outMPIFasta); } MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else @@ -334,43 +653,58 @@ int ChimeraSlayerCommand::execute(){ //break up file #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) if(processors == 1){ - numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); + numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName); + + int numNoParents = chimera->getNumNoParents(); + if (numNoParents == numSeqs) { 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(); } - if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } }else{ processIDS.resize(0); - numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName); + numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName); rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str()); rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str()); + if (trim) { rename((trimFastaFileName + toString(processIDS[0]) + ".temp").c_str(), trimFastaFileName.c_str()); } //append output files for(int i=1;iappendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName); - remove((outputFileName + toString(processIDS[i]) + ".temp").c_str()); + m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp")); } //append output files for(int i=1;iappendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName); - remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); + m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp")); } - if (m->control_pressed) { remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } + if (trim) { + for(int i=1;iappendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName); + m->mothurRemove((trimFastaFileName + toString(processIDS[i]) + ".temp")); + } + } + + if (m->control_pressed) { 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]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } } #else - numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); + numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName); + + int numNoParents = chimera->getNumNoParents(); + if (numNoParents == numSeqs) { 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(); } + - if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } + if (m->control_pressed) { outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } #endif m->appendFiles(outputFileName, tempHeader); - remove(outputFileName.c_str()); + m->mothurRemove(outputFileName); rename(tempHeader.c_str(), outputFileName.c_str()); #endif @@ -379,12 +713,27 @@ int ChimeraSlayerCommand::execute(){ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - outputNames.push_back(outputFileName); - outputNames.push_back(accnosFileName); + 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); } 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(); } @@ -400,7 +749,7 @@ int ChimeraSlayerCommand::execute(){ } //********************************************************************************************************************** -int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos){ +int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos, string fasta){ try { ofstream out; m->openOutputFile(outputFName, out); @@ -408,6 +757,9 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f ofstream out2; m->openOutputFile(accnos, out2); + ofstream out3; + if (trim) { m->openOutputFile(fasta, out3); } + ifstream inFASTA; m->openInputFile(filename, inFASTA); @@ -418,12 +770,12 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f while (!done) { - if (m->control_pressed) { return 1; } + if (m->control_pressed) { 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{ @@ -431,17 +783,68 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f chimera->getChimeras(candidateSeq); if (m->control_pressed) { delete candidateSeq; return 1; } - - //print results - chimera->print(out, out2); + + //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++; + count++; } - delete candidateSeq; - unsigned long int pos = inFASTA.tellg(); - if ((pos == -1) || (pos >= filePos->end)) { break; } + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + unsigned long int 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(); } } @@ -450,6 +853,7 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f out.close(); out2.close(); + if (trim) { out3.close(); } inFASTA.close(); return count; @@ -461,7 +865,7 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f } //********************************************************************************************************************** #ifdef USE_MPI -int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector& MPIPos){ +int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector& MPIPos){ try { MPI_Status status; int pid; @@ -484,6 +888,7 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil 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 @@ -495,9 +900,75 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil chimera->getChimeras(candidateSeq); if (m->control_pressed) { delete candidateSeq; return 1; } - //cout << "about to print" << endl; - //print results - bool isChimeric = chimera->print(outMPI, outAccMPI); + + //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; @@ -520,7 +991,7 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil /**************************************************************************************************/ -int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos) { +int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta) { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; @@ -534,17 +1005,20 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename 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"); + num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp"); //pass numSeqs to parent ofstream out; string tempFile = outputFileName + toString(getpid()) + ".num.temp"; m->openOutputFile(tempFile, out); - out << num << endl; + out << num << '\t' << chimera->getNumNoParents() << endl; out.close(); - exit(0); - }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); 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 @@ -553,14 +1027,17 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename wait(&temp); } + int numNoParents = 0; 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(); remove(tempFile.c_str()); + if (!in.eof()) { int tempNum = 0; int tempNumParents = 0; in >> tempNum >> tempNumParents; num += tempNum; numNoParents += tempNumParents; } + in.close(); m->mothurRemove(tempFile); } + if (num == numNoParents) { 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(); } + return num; #endif } @@ -572,4 +1049,94 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename /**************************************************************************************************/ +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); + } +} + +/**************************************************************************************************/