X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=8647e7510088014e48153f33a81fec8fd62ee64e;hb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;hp=97edf1130be292c1495811a4a9c52acc77cde04b;hpb=1cf188b912d6da8f2cd03dd71cecef664a699c1a;p=mothur.git diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp index 97edf11..8647e75 100644 --- a/chimeraslayercommand.cpp +++ b/chimeraslayercommand.cpp @@ -8,8 +8,9 @@ */ #include "chimeraslayercommand.h" -#include "chimeraslayer.h" #include "deconvolutecommand.h" +#include "referencedb.h" +#include "sequenceparser.h" //********************************************************************************************************************** vector ChimeraSlayerCommand::setParameters(){ @@ -17,6 +18,7 @@ vector ChimeraSlayerCommand::setParameters(){ 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); @@ -25,7 +27,7 @@ vector ChimeraSlayerCommand::setParameters(){ 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-distance", "distance", "", "", "",false,false); parameters.push_back(psearch); + 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); @@ -35,9 +37,11 @@ vector ChimeraSlayerCommand::setParameters(){ 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; @@ -53,9 +57,10 @@ string ChimeraSlayerCommand::getHelpString(){ 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, and realign.\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 template=self. \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"; @@ -77,8 +82,10 @@ string ChimeraSlayerCommand::getHelpString(){ 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 distance, blast, and kmer, default distance. \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"; @@ -109,9 +116,11 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(){ 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(); @@ -204,6 +213,8 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { //erase from file list fastaFileNames.erase(fastaFileNames.begin()+i); i--; + }else { + m->setFastaFile(fastaFileNames[i]); } } } @@ -278,6 +289,8 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { //erase from file list nameFileNames.erase(nameFileNames.begin()+i); i--; + }else { + m->setNameFile(nameFileNames[i]); } } } @@ -288,15 +301,109 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { 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 (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. @@ -304,43 +411,64 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { templatefile = validParameter.validFile(parameters, "reference", true); if (templatefile == "not open") { abort = true; } - else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); 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; + } + } + - string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } - m->setProcessors(temp); - convert(temp, processors); temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; } - convert(temp, ksize); + m->mothurConvert(temp, ksize); temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "50"; } - convert(temp, window); + m->mothurConvert(temp, window); temp = validParameter.validFile(parameters, "match", false); if (temp == "not found") { temp = "5"; } - convert(temp, match); + m->mothurConvert(temp, match); temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found") { temp = "-4"; } - convert(temp, mismatch); + m->mothurConvert(temp, mismatch); temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.007"; } - convert(temp, divR); + m->mothurConvert(temp, divR); temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "90"; } - convert(temp, minSimilarity); + m->mothurConvert(temp, minSimilarity); temp = validParameter.validFile(parameters, "mincov", false); if (temp == "not found") { temp = "70"; } - convert(temp, minCoverage); + m->mothurConvert(temp, minCoverage); temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; } - convert(temp, minBS); + m->mothurConvert(temp, minBS); temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; } - convert(temp, minSNP); + m->mothurConvert(temp, minSNP); temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; } - convert(temp, parents); + m->mothurConvert(temp, parents); temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "t"; } realign = m->isTrue(temp); @@ -351,18 +479,64 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { 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 = "distance"; } + 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); + m->mothurConvert(temp, iters); temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; } - convert(temp, increment); + m->mothurConvert(temp, increment); temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; } - convert(temp, numwanted); + 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; } - if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); 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) { @@ -375,274 +549,827 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { 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"; - 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); - }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(); + //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(); } - nameFile = filenames["name"][0]; - fastaFileNames[s] = filenames["fasta"][0]; + //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); } - //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) { 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 - if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } + 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(); - chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign); + 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; } - - 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"; + }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); - if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } + MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status); + delete buf2; - if (chimera->getUnaligned()) { - m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); - delete chimera; - return 0; + 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; } - templateSeqsLength = chimera->getLength(); - #ifdef USE_MPI - int pid, numSeqsPerProcessor; - int tag = 2001; - vector MPIPos; + //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); - 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; + //figure out how many sequences you have to align + numSeqsPerProcessor = numSeqs / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } - int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; - int inMode=MPI_MODE_RDONLY; + //do your part + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos, inputFile, priority, false); - char outFilename[1024]; - strcpy(outFilename, outputFileName.c_str()); + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); return 0; } - char outAccnosFilename[1024]; - strcpy(outAccnosFilename, accnosFileName.c_str()); + } + } + + //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; } - char outFastaFilename[1024]; - strcpy(outFastaFilename, trimFastaFileName.c_str()); - - char inFileName[1024]; - strcpy(inFileName, fastaFileNames[s].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) { 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++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + in2 >> name; m->gobble(in2); - if (pid == 0) { //you are the root process - m->mothurOutEndLine(); - m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results."); - m->mothurOutEndLine(); + //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(); - 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; + 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); - MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs + 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 (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); + 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); } } } - //figure out how many sequences you have to align - numSeqsPerProcessor = numSeqs / processors; - int startIndex = pid * numSeqsPerProcessor; - if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } + }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); - if (templatefile == "self") { //if template=self we can only use 1 processor - startIndex = 0; - numSeqsPerProcessor = numSeqs; - } + //find unique name + itUnique = uniqueNames.find(name); - //do your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); + 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 (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++) { remove(outputNames[j].c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); delete chimera; return 0; } + if (print) { + out << name << '\t'; + + namesInFile.insert(name); - }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); - - 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++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } - + //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; } - } - - //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 - - #else - ofstream outHeader; - string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader"; - m->openOutputFile(tempHeader, outHeader); + } + } + } + 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); - chimera->printHeader(outHeader); - outHeader.close(); + ofstream out3; + m->openOutputFile(trimFileName+".temp", out3); - vector positions = m->divideFile(fastaFileNames[s], processors); + 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; } - for (int i = 0; i < (positions.size()-1); i++) { - lines.push_back(new linePair(positions[i], positions[(i+1)])); - } - - //break up file - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - if(processors == 1){ - numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName); - - if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } 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; } - - }else{ - processIDS.resize(0); - - numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName); + Sequence seq(in3); m->gobble(in3); - 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()); - } - - //append output files - for(int i=1;iappendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName); - remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); - } + if (seq.getName() != "") { + //find unique name + itUnique = uniqueNames.find(seq.getName()); - if (trim) { - for(int i=1;iappendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName); - remove((trimFastaFileName + toString(processIDS[i]) + ".temp").c_str()); + 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); } } - - if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } 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; } } - - #else - numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName); - - if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } 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; } - - #endif + } + 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(); - m->appendFiles(outputFileName, tempHeader); + 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]; + } + } - remove(outputFileName.c_str()); - rename(tempHeader.c_str(), outputFileName.c_str()); + + 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(); + + Command* uniqueCommand = new DeconvoluteCommand(inputString); + uniqueCommand->execute(); + + map > filenames = uniqueCommand->getOutputFiles(); + + delete uniqueCommand; + + 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++) { - #endif - delete chimera; + 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"; - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); + m->mothurOutEndLine(); m->mothurOut("Checking sequences from group: " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine(); - 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); } + 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); - m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); + //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(); } - //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); } - } + 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 (trim) { - itTypes = outputTypes.find("fasta"); - if (itTypes != outputTypes.end()) { - if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } + 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); } } - 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(); + num = driverGroups(outputFName, accnos, fasta, breakUp[0], fileGroup); - return 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-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", "execute"); + m->errorOut(e, "ChimeraSlayerCommand", "createProcessesGroups"); exit(1); } } //********************************************************************************************************************** -int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos, string fasta){ +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); @@ -655,27 +1382,28 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f ifstream inFASTA; m->openInputFile(filename, inFASTA); - inFASTA.seekg(filePos->start); + inFASTA.seekg(filePos.start); + + if (filePos.start == 0) { chimera->printHeader(out); } bool done = false; int count = 0; while (!done) { - if (m->control_pressed) { out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1; } + 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 candidateSeq; return 1; } + if (m->control_pressed) { delete chimera; delete candidateSeq; return 1; } //if you are not chimeric, then check each half data_results wholeResults = chimera->getResults(); @@ -714,15 +1442,15 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f 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 trimmed; } + 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); delete trimmed; } + Sequence trimmed = chimera->print(out, out2); + if (trim) { trimmed.printSequence(out3); } } @@ -730,10 +1458,9 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f count++; } - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - unsigned long int pos = inFASTA.tellg(); - //cout << candidateSeq->getName() << '\t' << pos << endl; - if ((pos == -1) || (pos >= filePos->end)) { break; } + #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 @@ -745,12 +1472,18 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f //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"); @@ -759,15 +1492,27 @@ 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, MPI_File& outFastaMPI, vector& MPIPos){ - try { +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) { return 1; } + if (m->control_pressed) { delete chimera; return 1; } //read next sequence int length = MPIPos[start+i+1] - MPIPos[start+i]; @@ -793,7 +1538,7 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil //find chimeras chimera->getChimeras(candidateSeq); - if (m->control_pressed) { delete candidateSeq; return 1; } + if (m->control_pressed) { delete chimera; delete candidateSeq; return 1; } //if you are not chimeric, then check each half data_results wholeResults = chimera->getResults(); @@ -831,10 +1576,9 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil data_results rightResults = chimera->getResults(); //if either piece is chimeric then report - Sequence* trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults); + Sequence trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults); if (trim) { - string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n"; - delete trimmed; + string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n"; //write to accnos file int length = outputString.length(); @@ -849,11 +1593,10 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil }else { //print results - Sequence* trimmed = chimera->print(outMPI, outAccMPI); + Sequence trimmed = chimera->print(outMPI, outAccMPI); if (trim) { - string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n"; - delete trimmed; + string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n"; //write to accnos file int length = outputString.length(); @@ -875,7 +1618,10 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil //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) { @@ -887,12 +1633,13 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil /**************************************************************************************************/ -int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta) { +int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta, map& thisPriority) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) 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(); @@ -901,7 +1648,7 @@ 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", fasta + toString(getpid()) + ".temp"); + num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", thisPriority); //pass numSeqs to parent ofstream out; @@ -909,7 +1656,6 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename m->openOutputFile(tempFile, out); out << num << endl; out.close(); - exit(0); }else { m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); @@ -928,12 +1674,63 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename 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; 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; -#endif } catch(exception& e) { m->errorOut(e, "ChimeraSlayerCommand", "createProcesses"); @@ -1031,6 +1828,56 @@ map ChimeraSlayerCommand::sortFastaFile(string fastaFile, string na 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); + } +} /**************************************************************************************************/