From: westcott Date: Wed, 21 Sep 2011 18:23:15 +0000 (+0000) Subject: finished added bygroup processing of chimeras in chimera.slayer and chimera.uchime... X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=8c8acb6218f58f662466e4111ab8aa4da0caf93c finished added bygroup processing of chimeras in chimera.slayer and chimera.uchime. Added mean to summary.seqs --- diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp index 0958630..629eca9 100644 --- a/chimeraslayercommand.cpp +++ b/chimeraslayercommand.cpp @@ -10,6 +10,7 @@ #include "chimeraslayercommand.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); @@ -58,6 +60,7 @@ string ChimeraSlayerCommand::getHelpString(){ helpString += "The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment, numwanted, blastlocation and realign.\n"; helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n"; helpString += "The name parameter allows you to provide a name file, if you are using reference=self. \n"; + helpString += "The group parameter allows you to provide a group file. The group file can be used with a namesfile and reference=self. When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n"; helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n"; helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n"; helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"; @@ -298,6 +301,83 @@ 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 = ""; } @@ -450,6 +530,8 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { 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; } + } } catch(exception& e) { @@ -469,38 +551,59 @@ int ChimeraSlayerCommand::execute(){ int start = time(NULL); - if (templatefile == "self") { + //you provided a groupfile + string groupFile = ""; + if (groupFileNames.size() != 0) { groupFile = groupFileNames[s]; } + + //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; + map priority; + fileToPriority[fastaFileNames[s]] = priority; //default + fileGroup[fastaFileNames[s]] = "noGroup"; + SequenceParser* parser = NULL; + int totalSeqs = 0; + int totalChimeras = 0; + + if ((templatefile == "self") && (groupFile == "")) { + fileGroup.clear(); + fileToPriority.clear(); 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]; - } + }else { nameFile = getNamesFile(fastaFileNames[s]); } //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; if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } + }else if ((templatefile == "self") && (groupFile != "")) { + 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]); } + + //Parse sequences by group + parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile); + vector groups = parser->getNamesOfGroups(); + + for (int i = 0; i < groups.size(); i++) { + vector thisGroupsSeqs = parser->getSeqs(groups[i]); + map thisGroupsMap = parser->getNameMap(groups[i]); + string newFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + groups[i] + "-sortedTemp.fasta"; + priority = sortFastaFile(thisGroupsSeqs, thisGroupsMap, newFastaFile); + fileToPriority[newFastaFile] = priority; + fileGroup[newFastaFile] = groups[i]; + } } if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it @@ -508,225 +611,93 @@ int ChimeraSlayerCommand::execute(){ string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.accnos"; string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.fasta"; - //create chimera here if you are mac or linux because fork will copy for you. Create in create processes instead if you are windows. - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI - if (templatefile != "self") { //you want to run slayer with a reference template - chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand()); - }else { - chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand()); - } + //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); } - 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(); - delete chimera; - return 0; - } - templateSeqsLength = chimera->getLength(); - #else - if (processors == 1) { - if (templatefile != "self") { //you want to run slayer with a reference template - chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand()); - }else { - chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand()); - } + for (itFile = fileToPriority.begin(); itFile != fileToPriority.end(); itFile++) { - if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } + string thisFastaName = itFile->first; + map thisPriority = itFile->second; - if (chimera->getUnaligned()) { - m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); - delete chimera; - return 0; - } - templateSeqsLength = chimera->getLength(); - } - #endif - - #ifdef USE_MPI - int pid, numSeqsPerProcessor; - int tag = 2001; - vector MPIPos; + //this is true when you have parsed by groups + if (fileToPriority.size() > 1) { m->mothurOutEndLine(); m->mothurOut("Checking sequences from group: " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine(); } - 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; + 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"; - int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; - int inMode=MPI_MODE_RDONLY; + //create chimera here if you are mac or linux because fork will copy for you. Create in create processes instead if you are windows. + if (processors == 1) { templateSeqsLength = setupChimera(thisFastaName, thisPriority); } + else { + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI + templateSeqsLength = setupChimera(thisFastaName, thisPriority); + #endif + } - char outFilename[1024]; - strcpy(outFilename, outputFileName.c_str()); + if (m->control_pressed) { if (parser != NULL) { delete parser; } for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } - 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()); - - 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++) { m->mothurRemove(outputNames[j]); } delete chimera; return 0; } - - if (pid == 0) { //you are the root process - m->mothurOutEndLine(); - m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results."); - m->mothurOutEndLine(); - - string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n"; - - //print header - int length = outTemp.length(); - char* buf2 = new char[length]; - memcpy(buf2, outTemp.c_str(), length); - - MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status); - delete buf2; - - MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs + #ifdef USE_MPI + MPIExecute(thisFastaName, thisoutputFileName, thisaccnosFileName, thistrimFastaFileName); + if (m->control_pressed) { outputTypes.clear(); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } + #else + //break up file + vector positions; + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + positions = m->divideFile(thisFastaName, processors); + for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); } + #else + if (processors == 1) { lines.push_back(new linePair(0, 1000)); } + else { + positions = m->setFilePosFasta(thisFastaName, 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 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(new linePair(positions[startIndex], 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; } - - if (templatefile == "self") { //if template=self we can only use 1 processor - startIndex = 0; - numSeqsPerProcessor = numSeqs; - } - - //do your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); + #endif + + if(processors == 1){ + numSeqs = driver(lines[0], thisoutputFileName, thisFastaName, thisaccnosFileName, thistrimFastaFileName); 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 (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 - 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; } + 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(); } - //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) { 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; } - - } - } + }else{ numSeqs = createProcesses(thisoutputFileName, thisFastaName, thisaccnosFileName, thistrimFastaFileName); } - //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 + 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]); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; } - #else - //break up file - vector positions; -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - positions = m->divideFile(fastaFileNames[s], processors); - for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); } -#else - if (processors == 1) { - lines.push_back(new linePair(0, 1000)); - }else { - positions = m->setFilePosFasta(fastaFileNames[s], numSeqs); - - //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(new linePair(positions[startIndex], numSeqsPerProcessor)); - } - } -#endif - - if(processors == 1){ - 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(); } + #endif - 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; } + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI + delete chimera; + #endif - }else{ - processIDS.resize(0); + for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - 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); - m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp")); - - m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName); - m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp")); - - if (trim) { - m->appendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName); - m->mothurRemove((trimFastaFileName + toString(processIDS[i]) + ".temp")); - } - } + //append files + m->appendFiles(thisoutputFileName, outputFileName); m->mothurRemove(thisoutputFileName); + totalChimeras = m->appendFiles(thisaccnosFileName, accnosFileName); m->mothurRemove(thisaccnosFileName); + if (trim) { m->appendFiles(thistrimFastaFileName, trimFastaFileName); m->mothurRemove(thistrimFastaFileName); } - 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; } + totalSeqs += numSeqs; } - - #endif + if (fileToPriority.size() > 1) { totalChimeras = deconvoluteResults(parser, outputFileName, accnosFileName, trimFastaFileName); } - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI - delete chimera; - #endif - - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - - 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); } + if (parser != NULL) { delete parser; } - m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); + m->mothurOutEndLine(); m->mothurOut(toString(totalChimeras) + " chimera found."); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(totalSeqs) + " sequences."); m->mothurOutEndLine(); } //set accnos file as new current accnosfile @@ -757,6 +728,376 @@ int ChimeraSlayerCommand::execute(){ } } //********************************************************************************************************************** +int ChimeraSlayerCommand::MPIExecute(string inputFile, string outputFileName, string accnosFileName, string trimFastaFileName){ + 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); delete chimera; return 0; } + + if (pid == 0) { //you are the root process + m->mothurOutEndLine(); + m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results."); + m->mothurOutEndLine(); + + string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n"; + + //print header + int length = outTemp.length(); + char* buf2 = new char[length]; + memcpy(buf2, outTemp.c_str(), length); + + MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status); + delete buf2; + + MPIPos = m->setFilePosFasta(inputFile, numSeqs); //fills MPIPos, returns numSeqs + + if (templatefile != "self") { //if template=self we can only use 1 processor + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } + } + //figure out how many sequences you have to align + numSeqsPerProcessor = numSeqs / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } + + if (templatefile == "self") { //if template=self we can only use 1 processor + startIndex = 0; + numSeqsPerProcessor = numSeqs; + } + + //do your part + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); + + 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 (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) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); delete chimera; return 0; } + + }else{ //you are a child process + if (templatefile != "self") { //if template=self we can only use 1 processor + MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + MPIPos.resize(numSeqs+1); + MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + + //figure out how many sequences you have to align + numSeqsPerProcessor = numSeqs / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } + + //do your part + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos); + + 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); if (trim) { MPI_File_close(&outMPIFasta); } MPI_File_close(&outMPIAccnos); delete chimera; return 0; } + + } + } + + //close files + MPI_File_close(&inMPI); + MPI_File_close(&outMPI); + MPI_File_close(&outMPIAccnos); + if (trim) { MPI_File_close(&outMPIFasta); } + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case + + +#endif + return 0; + } + 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; + + //edit accnos file + ifstream in2; + m->openInputFile(accnosFileName, in2, "no error"); + + ofstream out2; + m->openOutputFile(accnosFileName+".temp", out2); + + string name; name = ""; + set chimerasInFile; + set::iterator itChimeras; + + while (!in2.eof()) { + if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; } + + in2 >> name; m->gobble(in2); + + //find unique name + itUnique = uniqueNames.find(name); + + if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; } + else { + itChimeras = chimerasInFile.find((itUnique->second)); + + if (itChimeras == chimerasInFile.end()) { + out2 << itUnique->second << endl; + chimerasInFile.insert((itUnique->second)); + total++; + } + } + } + in2.close(); + out2.close(); + + m->mothurRemove(accnosFileName); + rename((accnosFileName+".temp").c_str(), accnosFileName.c_str()); + + + //edit chimera file + ifstream in; + m->openInputFile(outputFileName, in); + + ofstream out; + m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); + + string rest, parent1, parent2, line; + set namesInFile; //this is so if a sequence is found to be chimera in several samples we dont write it to the results file more than once + set::iterator itNames; + + //assumptions - in file each read will always look like... + /* + F11Fcsw_92754 no + F11Fcsw_63104 F11Fcsw_33372 F11Fcsw_37007 0.89441 80.4469 0.2 1.03727 93.2961 52.2 no 0-241 243-369 + */ + + //get header line + if (!in.eof()) { + line = m->getline(in); m->gobble(in); + out << line << endl; + } + + //for the chimera file, we want to make sure if any group finds a sequence to be chimeric then all groups do, + //so if this is a report that did not find it to be chimeric, but it appears in the accnos file, + //then ignore this report and continue until we find the report that found it to be chimeric + + while (!in.eof()) { + + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove((outputFileName+".temp")); return 0; } + + in >> name; m->gobble(in); + in >> parent1; m->gobble(in); + + if (name == "Name") { //name = "Name" because we append the header line each time we add results from the groups + line = m->getline(in); m->gobble(in); + }else { + if (parent1 == "no") { + //find unique name + itUnique = uniqueNames.find(name); + + if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; } + else { + //is this sequence really not chimeric?? + itChimeras = chimerasInFile.find(itUnique->second); + + if (itChimeras == chimerasInFile.end()) { + itNames = namesInFile.find((itUnique->second)); + + if (itNames == namesInFile.end()) {cout << itUnique->second << endl; out << itUnique->second << '\t' << "no" << endl; namesInFile.insert(itUnique->second); } + } + } + }else { //read the rest of the line + double DivQLAQRB,PerIDQLAQRB,BootStrapA,DivQLBQRA,PerIDQLBQRA,BootStrapB; + string flag, range1, range2; + bool print = false; + in >> parent2 >> DivQLAQRB >> PerIDQLAQRB >> BootStrapA >> DivQLBQRA >> PerIDQLBQRA >> BootStrapB >> flag >> range1 >> range2; m->gobble(in); + + //find unique name + itUnique = uniqueNames.find(name); + + if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; } + else { + name = itUnique->second; + //is this name already in the file + itNames = namesInFile.find((name)); + + if (itNames == namesInFile.end()) { //no not in file + if (flag == "no") { //are you really a no?? + //is this sequence really not chimeric?? + itChimeras = chimerasInFile.find(name); + + //then you really are a no so print, otherwise skip + if (itChimeras == chimerasInFile.end()) { print = true; } + }else{ print = true; } + } + } + + if (print) { + out << name << '\t'; + cout << name<< endl; + namesInFile.insert(name); + + //output parent1's name + itUnique = uniqueNames.find(parent1); + if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent1 + "."); m->mothurOutEndLine(); m->control_pressed = true; } + else { out << itUnique->second << '\t'; } + + //output parent2's name + itUnique = uniqueNames.find(parent2); + if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; } + else { out << itUnique->second << '\t'; } + + out << DivQLAQRB << '\t' << PerIDQLAQRB << '\t' << BootStrapA << '\t' << DivQLBQRA << '\t' << PerIDQLBQRA << '\t' << BootStrapB << '\t' << flag << '\t' << range1 << '\t' << range2 << endl; + } + } + } + } + in.close(); + out.close(); + + m->mothurRemove(outputFileName); + rename((outputFileName+".temp").c_str(), outputFileName.c_str()); + + //edit fasta file + if (trim) { + ifstream in3; + m->openInputFile(trimFileName, in3); + + ofstream out3; + m->openOutputFile(trimFileName+".temp", out3); + + namesInFile.clear(); + + while (!in3.eof()) { + if (m->control_pressed) { in3.close(); out3.close(); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); m->mothurRemove((trimFileName+".temp")); return 0; } + + Sequence seq(in3); m->gobble(in3); + + if (seq.getName() != "") { + //find unique name + itUnique = uniqueNames.find(seq.getName()); + + if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ seq.getName() + "."); m->mothurOutEndLine(); m->control_pressed = true; } + else { + itNames = namesInFile.find((itUnique->second)); + + if (itNames == namesInFile.end()) { + seq.printSequence(out3); + } + } + } + } + in3.close(); + out3.close(); + + m->mothurRemove(trimFileName); + rename((trimFileName+".temp").c_str(), trimFileName.c_str()); + } + + return total; + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayerCommand", "deconvoluteResults"); + exit(1); + } +} +//********************************************************************************************************************** +int ChimeraSlayerCommand::setupChimera(string inputFile, map& priority){ + try { + if (templatefile != "self") { //you want to run slayer with a reference template + chimera = new ChimeraSlayer(inputFile, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand()); + }else { + chimera = new ChimeraSlayer(inputFile, 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; } + + return (chimera->getLength()); + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayerCommand", "setupChimera"); + 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::driver(linePair* filePos, string outputFName, string filename, string accnos, string fasta){ try { @@ -1007,6 +1348,7 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename int process = 0; int num = 0; int numNoParents = 0; + processIDS.clear(); #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) //loop through and create all the processes you want @@ -1081,6 +1423,26 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename } #endif 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(); } + + rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str()); + rename((accnos + toString(processIDS[0]) + ".temp").c_str(), accnos.c_str()); + if (trim) { rename((fasta + toString(processIDS[0]) + ".temp").c_str(), fasta.c_str()); } + + //append output files + for(int i=1;iappendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName); + m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp")); + + m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos); + m->mothurRemove((accnos + toString(processIDS[i]) + ".temp")); + + if (trim) { + m->appendFiles((fasta + toString(processIDS[i]) + ".temp"), fasta); + m->mothurRemove((fasta + toString(processIDS[i]) + ".temp")); + } + } + + return num; } catch(exception& e) { @@ -1179,6 +1541,56 @@ 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); + } +} /**************************************************************************************************/ diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h index b37d4c0..9a37a5b 100644 --- a/chimeraslayercommand.h +++ b/chimeraslayercommand.h @@ -14,6 +14,7 @@ #include "command.hpp" #include "chimera.h" #include "chimeraslayer.h" +#include "sequenceparser.h" /***********************************************************/ @@ -43,19 +44,25 @@ private: vector processIDS; //processid vector lines; - map priority; int driver(linePair*, string, string, string, string); int createProcesses(string, string, string, string); int divideInHalf(Sequence, string&, string&); map sortFastaFile(string, string); + map sortFastaFile(vector&, map&, string newFile); + string getNamesFile(string&); + int setupChimera(string, map&); + int MPIExecute(string, string, string, string); + int deconvoluteResults(SequenceParser*, string, string, string); + + #ifdef USE_MPI int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector&); #endif bool abort, realign, trim, trimera, save; - string fastafile, templatefile, outputDir, search, namefile, blastlocation; + string fastafile, groupfile, templatefile, outputDir, search, namefile, blastlocation; int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength; float divR; Chimera* chimera; @@ -63,6 +70,7 @@ private: vector outputNames; vector fastaFileNames; vector nameFileNames; + vector groupFileNames; }; diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp index 73e7ace..c035b01 100644 --- a/chimerauchimecommand.cpp +++ b/chimerauchimecommand.cpp @@ -591,6 +591,47 @@ int ChimeraUchimeCommand::deconvoluteResults(SequenceParser& parser, string outp map::iterator itUnique; int total = 0; + //edit accnos file + ifstream in2; + m->openInputFile(accnosFileName, in2); + + ofstream out2; + m->openOutputFile(accnosFileName+".temp", out2); + + string name; + 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; + set chimerasInFile; + set::iterator itChimeras; + + + while (!in2.eof()) { + if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; } + + in2 >> name; m->gobble(in2); + + //find unique name + itUnique = uniqueNames.find(name); + + if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; } + else { + itChimeras = chimerasInFile.find((itUnique->second)); + + if (itChimeras == chimerasInFile.end()) { + out2 << itUnique->second << endl; + chimerasInFile.insert((itUnique->second)); + total++; + } + } + } + in2.close(); + out2.close(); + + m->mothurRemove(accnosFileName); + rename((accnosFileName+".temp").c_str(), accnosFileName.c_str()); + + + //edit chimera file ifstream in; m->openInputFile(outputFileName, in); @@ -599,12 +640,11 @@ int ChimeraUchimeCommand::deconvoluteResults(SequenceParser& parser, string outp m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); float temp1; - string name, rest, parent1, parent2; - 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; - + string parent1, parent2, temp2, temp3, temp4, temp5, temp6, temp7, temp8, temp9, temp10, temp11, temp12, temp13, flag; + name = ""; + namesInFile.clear(); //assumptions - in file each read will always look like - if uchime source is updated, revisit this code. - /* + /* 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 0.000000 F11Fcsw_33372/ab=18/ * * * * * * * * * * * * * * N 0.018300 F11Fcsw_14980/ab=16/ F11Fcsw_1915/ab=35/ F11Fcsw_6032/ab=42/ 79.9 78.7 78.2 78.7 79.2 3 0 5 11 10 20 1.46 N */ @@ -613,11 +653,13 @@ int ChimeraUchimeCommand::deconvoluteResults(SequenceParser& parser, string outp if (m->control_pressed) { in.close(); out.close(); m->mothurRemove((outputFileName+".temp")); return 0; } + bool print = false; in >> temp1; m->gobble(in); in >> name; m->gobble(in); in >> parent1; m->gobble(in); in >> parent2; m->gobble(in); - rest = m->getline(in); m->gobble(in); + in >> temp2 >> temp3 >> temp4 >> temp5 >> temp6 >> temp7 >> temp8 >> temp9 >> temp10 >> temp11 >> temp12 >> temp13 >> flag; + m->gobble(in); //parse name - name will look like U68590/ab=1/ string restOfName = ""; @@ -632,46 +674,54 @@ int ChimeraUchimeCommand::deconvoluteResults(SequenceParser& parser, string outp if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; } else { - itNames = namesInFile.find((itUnique->second)); + name = itUnique->second; + //is this name already in the file + itNames = namesInFile.find((name)); - if (itNames == namesInFile.end()) { - out << temp1 << '\t' << itUnique->second << restOfName << '\t'; - namesInFile.insert((itUnique->second)); - - //parse parent1 names - if (parent1 != "*") { - restOfName = ""; - pos = parent1.find_first_of('/'); - if (pos != string::npos) { - restOfName = parent1.substr(pos); - parent1 = parent1.substr(0, pos); - } + if (itNames == namesInFile.end()) { //no not in file + if (flag == "N") { //are you really a no?? + //is this sequence really not chimeric?? + itChimeras = chimerasInFile.find(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 << restOfName << '\t'; - } - }else { out << parent1 << '\t'; } + //then you really are a no so print, otherwise skip + if (itChimeras == chimerasInFile.end()) { print = true; } + }else{ print = true; } + } + } + + if (print) { + out << temp1 << '\t' << name << restOfName << '\t'; + namesInFile.insert(name); + + //parse parent1 names + if (parent1 != "*") { + restOfName = ""; + pos = parent1.find_first_of('/'); + if (pos != string::npos) { + restOfName = parent1.substr(pos); + parent1 = parent1.substr(0, pos); + } - //parse parent2 names - if (parent2 != "*") { - restOfName = ""; - pos = parent2.find_first_of('/'); - if (pos != string::npos) { - restOfName = parent2.substr(pos); - parent2 = parent2.substr(0, pos); - } - - itUnique = uniqueNames.find(parent2); - if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentB "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; } - else { - out << itUnique->second << restOfName << '\t'; - } - }else { out << parent2 << '\t'; } + 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 << restOfName << '\t'; } + }else { out << parent1 << '\t'; } + + //parse parent2 names + if (parent2 != "*") { + restOfName = ""; + pos = parent2.find_first_of('/'); + if (pos != string::npos) { + restOfName = parent2.substr(pos); + parent2 = parent2.substr(0, pos); + } - out << rest << endl; - } + itUnique = uniqueNames.find(parent2); + if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentB "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; } + else { out << itUnique->second << restOfName << '\t'; } + }else { out << parent2 << '\t'; } + + out << temp2 << '\t' << temp3 << '\t' << temp4 << '\t' << temp5 << '\t' << temp6 << '\t' << temp7 << '\t' << temp8 << '\t' << temp9 << '\t' << temp10 << '\t' << temp11 << '\t' << temp12 << temp13 << '\t' << flag << endl; } } in.close(); @@ -680,41 +730,7 @@ int ChimeraUchimeCommand::deconvoluteResults(SequenceParser& parser, string outp m->mothurRemove(outputFileName); rename((outputFileName+".temp").c_str(), outputFileName.c_str()); - //edit accnos file - ifstream in2; - m->openInputFile(accnosFileName, in2); - - ofstream out2; - m->openOutputFile(accnosFileName+".temp", out2); - - name = ""; - namesInFile.clear(); - - while (!in2.eof()) { - if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; } - - in2 >> name; m->gobble(in2); - - //find unique name - itUnique = uniqueNames.find(name); - - if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; } - else { - itNames = namesInFile.find((itUnique->second)); - - if (itNames == namesInFile.end()) { - out2 << itUnique->second << endl; - namesInFile.insert((itUnique->second)); - total++; - } - } - } - in2.close(); - out2.close(); - - m->mothurRemove(accnosFileName); - rename((accnosFileName+".temp").c_str(), accnosFileName.c_str()); - + //edit anls file //assumptions - in file each read will always look like - if uchime source is updated, revisit this code. /* diff --git a/mothurout.cpp b/mothurout.cpp index c80bff2..45d1176 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -958,7 +958,7 @@ int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){ } /**************************************************************************************************/ -void MothurOut::appendFiles(string temp, string filename) { +int MothurOut::appendFiles(string temp, string filename) { try{ ofstream output; ifstream input; @@ -968,15 +968,18 @@ void MothurOut::appendFiles(string temp, string filename) { int ableToOpen = openInputFile(temp, input, "no error"); //int ableToOpen = openInputFile(temp, input); + int numLines = 0; if (ableToOpen == 0) { //you opened it while(char c = input.get()){ if(input.eof()) { break; } - else { output << c; } + else { output << c; if (c == '\n') {numLines++;} } } input.close(); } output.close(); + + return numLines; } catch(exception& e) { errorOut(e, "MothurOut", "appendFiles"); diff --git a/mothurout.h b/mothurout.h index 013aa54..3019386 100644 --- a/mothurout.h +++ b/mothurout.h @@ -62,7 +62,7 @@ class MothurOut { vector setFilePosEachLine(string, int&); vector setFilePosFasta(string, int&); string sortFile(string, string); - void appendFiles(string, string); + int appendFiles(string, string); int renameFile(string, string); //oldname, newname string getFullPathName(string); string hasPath(string); diff --git a/qualityscores.cpp b/qualityscores.cpp index 5b64b13..566b44c 100644 --- a/qualityscores.cpp +++ b/qualityscores.cpp @@ -327,7 +327,7 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int return 1; } catch(exception& e) { - m->errorOut(e, "QualityScores", "flipQScores"); + m->errorOut(e, "QualityScores", "stripQualWindowAverage"); exit(1); } diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp index be75e4f..eeba041 100644 --- a/seqsummarycommand.cpp +++ b/seqsummarycommand.cpp @@ -317,6 +317,19 @@ int SeqSummaryCommand::execute(){ sort(ambigBases.begin(), ambigBases.end()); sort(longHomoPolymer.begin(), longHomoPolymer.end()); int size = startPosition.size(); + + //find means + float meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer; + meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0; + for (int i = 0; i < size; i++) { + meanStartPosition += startPosition[i]; + meanEndPosition += endPosition[i]; + meanSeqLength += seqLength[i]; + meanAmbigBases += ambigBases[i]; + meanLongHomoPolymer += longHomoPolymer[i]; + } + //this is an int divide so the remainder is lost + meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size; int ptile0_25 = int(size * 0.025); int ptile25 = int(size * 0.250); @@ -340,6 +353,8 @@ int SeqSummaryCommand::execute(){ m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75]) + "\t" + toString(ptile75+1)); m->mothurOutEndLine(); m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5]) + "\t" + toString(ptile97_5+1)); m->mothurOutEndLine(); m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine(); + m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine(); + if (namefile == "") { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); } else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }