X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makecontigscommand.cpp;h=4ae25ce0e2623ec9db0dc6568a37df7e64382140;hb=cc19310422f125d6628980bd1148e1e816792382;hp=697521c16abc44dbeee019590f66fb4d03032c64;hpb=15b252e317fde72ce0a5de8776cb88112e0ed2b6;p=mothur.git diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp index 697521c..4ae25ce 100644 --- a/makecontigscommand.cpp +++ b/makecontigscommand.cpp @@ -13,11 +13,20 @@ vector MakeContigsCommand::setParameters(){ try { CommandParameter pfasta("ffastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); CommandParameter prfasta("rfastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(prfasta); - CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign); + CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos); + CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs); + CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs); + CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs); + CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs); + CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs); + + CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "",false,false); parameters.push_back(palign); + CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pallfiles); CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch); CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch); CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen); CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend); + CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "",false,false); parameters.push_back(pthreshold); CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); @@ -36,14 +45,22 @@ string MakeContigsCommand::getHelpString(){ try { string helpString = ""; helpString += "The make.contigs command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.\n"; - helpString += "The make.contigs command parameters are ffastq, rfastq, align, match, mismatch, gapopen, gapextend and processors.\n"; - helpString += "The ffastq and rfastq parameter is required.\n"; - helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n"; + helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n"; + helpString += "The make.contigs command parameters are ffastq, rfastq, oligos, tdiffs, bdiffs, ldiffs, sdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, allfiles and processors.\n"; + helpString += "The ffastq and rfastq parameters are required.\n"; + helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh and needleman. The default is needleman.\n"; + helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n"; + helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n"; + helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n"; + helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n"; + helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n"; helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n"; helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n"; helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n"; helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n"; + helpString += "The threshold parameter allows you to set a quality scores threshold. In the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it. Default=40.\n"; helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"; + helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n"; helpString += "The make.contigs command should be in the following format: \n"; helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n"; helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n"; @@ -54,7 +71,29 @@ string MakeContigsCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string MakeContigsCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "fasta") { outputFileName = "contigs.fasta"; } + else if (type == "qfile") { outputFileName = "contigs.qual"; } + else if (type == "group") { outputFileName = "groups"; } + else if (type == "mismatch") { outputFileName = "contigs.mismatch"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "MakeContigsCommand", "getOutputFileNameTag"); + exit(1); + } +} //********************************************************************************************************************** MakeContigsCommand::MakeContigsCommand(){ try { @@ -63,6 +102,8 @@ MakeContigsCommand::MakeContigsCommand(){ vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["qfile"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["mismatch"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand"); @@ -96,6 +137,8 @@ MakeContigsCommand::MakeContigsCommand(string option) { vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["qfile"] = tempOutNames; + outputTypes["mismatch"] = tempOutNames; + outputTypes["group"] = tempOutNames; //if the user changes the input directory command factory will send this info to us in the output parameter @@ -118,6 +161,14 @@ MakeContigsCommand::MakeContigsCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["rfastq"] = inputDir + it->second; } } + + it = parameters.find("oligos"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["oligos"] = inputDir + it->second; } + } } ffastqfile = validParameter.validFile(parameters, "ffastq", true); @@ -128,6 +179,11 @@ MakeContigsCommand::MakeContigsCommand(string option) { if (rfastqfile == "not open") { rfastqfile = ""; abort = true; } else if (rfastqfile == "not found") { rfastqfile = ""; abort=true; m->mothurOut("The rfastq parameter is required.\n"); } + oligosfile = validParameter.validFile(parameters, "oligos", true); + if (oligosfile == "not found") { oligosfile = ""; } + else if(oligosfile == "not open") { abort = true; } + else { m->setOligosFile(oligosfile); } + //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 = m->hasPath(ffastqfile); } @@ -150,12 +206,36 @@ MakeContigsCommand::MakeContigsCommand(string option) { m->mothurConvert(temp, gapExtend); if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; } + temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "40"; } + m->mothurConvert(temp, threshold); + if ((threshold < 0) || (threshold > 40)) { m->mothurOut("[ERROR]: threshold must be between 0 and 40.\n"); abort=true; } + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); m->mothurConvert(temp, processors); + + temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; } + m->mothurConvert(temp, bdiffs); + + temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; } + m->mothurConvert(temp, pdiffs); + + temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; } + m->mothurConvert(temp, ldiffs); + + temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; } + m->mothurConvert(temp, sdiffs); + + temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); } + m->mothurConvert(temp, tdiffs); + + if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; } + + temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; } + allFiles = m->isTrue(temp); align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; } - if ((align != "needleman") && (align != "blast") && (align != "gotoh") && (align != "noalign")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman, blast, gotoh and noalign. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; } + if ((align != "needleman") && (align != "gotoh")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman or gotoh. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; } } } @@ -173,12 +253,31 @@ int MakeContigsCommand::execute(){ //this function will create a forward and reverse, fasta and qual files for each processor. //files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual int numReads = 0; - m->mothurOut("Reading fastq data..."); cout.flush(); + int start = time(NULL); + longestBase = 1000; + m->mothurOut("Reading fastq data...\n"); vector< vector > files = readFastqFiles(numReads); m->mothurOut("Done.\n"); + + if (m->control_pressed) { return 0; } + + string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("fasta"); + string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("qfile"); + string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("mismatch"); + outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile); + outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile); + outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile); + + m->mothurOut("Making contigs...\n"); + createProcesses(files, outFastaFile, outQualFile, outMisMatchFile); + m->mothurOut("Done.\n"); + + //remove temp fasta and qual files + for (int i = 0; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - + m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n"); string currentFasta = ""; itTypes = outputTypes.find("fasta"); @@ -191,6 +290,12 @@ int MakeContigsCommand::execute(){ if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); } } + + string currentGroup = ""; + itTypes = outputTypes.find("group"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { currentGroup = (itTypes->second)[0]; m->setGroupFile(currentGroup); } + } //output files created by command m->mothurOutEndLine(); @@ -198,7 +303,6 @@ int MakeContigsCommand::execute(){ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine(); - return 0; } catch(exception& e) { @@ -207,6 +311,265 @@ int MakeContigsCommand::execute(){ } } //********************************************************************************************************************** +int MakeContigsCommand::createProcesses(vector< vector > files, string outputFasta, string outputQual, string outputMisMatches) { + try { + int num = 0; + vector processIDS; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + int process = 0; + + //loop through and create all the processes you want + while (process != processors-1) { + int pid = fork(); + + if (pid > 0) { + processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later + process++; + }else if (pid == 0){ + num = driver(files[process], outputFasta + toString(getpid()) + ".temp", outputQual + toString(getpid()) + ".temp", outputMisMatches + toString(getpid()) + ".temp"); + + //pass numSeqs to parent + ofstream out; + string tempFile = outputFasta + 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); + } + } + + //do my part + num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches); + + //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 contigsData 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=0; icount; + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + + #endif + + for (int i = 0; i < processIDS.size(); i++) { + m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta); + m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp")); + + m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual); + m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp")); + + m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches); + m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp")); + } + + return num; + } + catch(exception& e) { + m->errorOut(e, "MakeContigsCommand", "createProcesses"); + exit(1); + } +} +//********************************************************************************************************************** +int MakeContigsCommand::driver(vector files, string outputFasta, string outputQual, string outputMisMatches){ + try { + + Alignment* alignment; + if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); } + else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); } + + int num = 0; + string thisffastafile = files[0]; + string thisfqualfile = files[1]; + string thisrfastafile = files[2]; + string thisrqualfile = files[3]; + + if (m->debug) { m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); } + + ifstream inFFasta, inRFasta, inFQual, inRQual; + m->openInputFile(thisffastafile, inFFasta); + m->openInputFile(thisfqualfile, inFQual); + m->openInputFile(thisrfastafile, inRFasta); + m->openInputFile(thisrqualfile, inRQual); + + ofstream outFasta, outQual, outMisMatch; + m->openOutputFile(outputFasta, outFasta); + m->openOutputFile(outputQual, outQual); + m->openOutputFile(outputMisMatches, outMisMatch); + outMisMatch << "Name\tLength\tMisMatches\n"; + + while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) { + + if (m->control_pressed) { break; } + + //read seqs and quality info + Sequence fSeq(inFFasta); m->gobble(inFFasta); + Sequence rSeq(inRFasta); m->gobble(inRFasta); + QualityScores fQual(inFQual); m->gobble(inFQual); + QualityScores rQual(inRQual); m->gobble(inRQual); + + //flip the reverse reads + rSeq.reverseComplement(); + rQual.flipQScores(); + + //pairwise align + alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned()); + map ABaseMap = alignment->getSeqAAlnBaseMap(); + map BBaseMap = alignment->getSeqBAlnBaseMap(); + fSeq.setAligned(alignment->getSeqAAln()); + rSeq.setAligned(alignment->getSeqBAln()); + int length = fSeq.getAligned().length(); + + //traverse alignments merging into one contiguous seq + string contig = ""; + vector contigScores; + int numMismatches = 0; + string seq1 = fSeq.getAligned(); + string seq2 = rSeq.getAligned(); + vector scores1 = fQual.getQualityScores(); + vector scores2 = rQual.getQualityScores(); + + // if (num < 5) { cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; } + int overlapStart = fSeq.getStartPos(); + int seq2Start = rSeq.getStartPos(); + //bigger of the 2 starting positions is the location of the overlapping start + if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1 + overlapStart = seq2Start; + for (int i = 0; i < overlapStart; i++) { + contig += seq1[i]; + contigScores.push_back(scores1[ABaseMap[i]]); + } + }else { //seq1 starts later so take from 0 to overlapStart from seq2 + for (int i = 0; i < overlapStart; i++) { + contig += seq2[i]; + contigScores.push_back(scores2[BBaseMap[i]]); + } + } + + int seq1End = fSeq.getEndPos(); + int seq2End = rSeq.getEndPos(); + int overlapEnd = seq1End; + if (seq2End < overlapEnd) { overlapEnd = seq2End; } //smallest end position is where overlapping ends + + for (int i = overlapStart; i < overlapEnd; i++) { + if (seq1[i] == seq2[i]) { //match, add base and choose highest score + contig += seq1[i]; + contigScores.push_back(scores1[ABaseMap[i]]); + if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; } + }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base + if (scores2[BBaseMap[i]] < threshold) { } // + else { + contig += seq2[i]; + contigScores.push_back(scores2[BBaseMap[i]]); + } + }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base + if (scores1[ABaseMap[i]] < threshold) { } // + else { + contig += seq1[i]; + contigScores.push_back(scores1[ABaseMap[i]]); + } + }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality + char c = seq1[i]; + contigScores.push_back(scores1[ABaseMap[i]]); + if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; } + contig += c; + numMismatches++; + }else { //should never get here + m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n"); + } + } + + if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2 + for (int i = overlapEnd; i < length; i++) { + contig += seq2[i]; + contigScores.push_back(scores2[BBaseMap[i]]); + } + }else { //seq2 ends before seq1 so take from overlap to length from seq1 + for (int i = overlapEnd; i < length; i++) { + contig += seq1[i]; + contigScores.push_back(scores1[ABaseMap[i]]); + } + + } + //if (num < 5) { cout << overlapStart << '\t' << overlapEnd << endl << seq1 << endl << seq2 << endl<< contig << endl; } + //output + outFasta << ">" << fSeq.getName() << endl << contig << endl; + outQual << ">" << fSeq.getName() << endl; + for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; } + outQual << endl; + outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl; + + num++; + + //report progress + if((num) % 1000 == 0){ m->mothurOut(toString(num)); m->mothurOutEndLine(); } + } + + //report progress + if((num) % 1000 != 0){ m->mothurOut(toString(num)); m->mothurOutEndLine(); } + + inFFasta.close(); + inFQual.close(); + inRFasta.close(); + inRQual.close(); + outFasta.close(); + outQual.close(); + outMisMatch.close(); + delete alignment; + + if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta); m->mothurRemove(outputMisMatches);} + + return num; + } + catch(exception& e) { + m->errorOut(e, "MakeContigsCommand", "driver"); + exit(1); + } +} +//********************************************************************************************************************** vector< vector > MakeContigsCommand::readFastqFiles(int& count){ try { vector< vector > files; @@ -287,7 +650,7 @@ vector< vector > MakeContigsCommand::readFastqFiles(int& count){ //report progress if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } - + //close files, delete ofstreams for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close(); delete (it->second)[i]; } } @@ -308,7 +671,6 @@ vector< vector > MakeContigsCommand::readFastqFiles(int& count){ exit(1); } } - //********************************************************************************************************************** fastqRead MakeContigsCommand::readFastq(ifstream& in){ try { @@ -394,6 +756,262 @@ bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse){ exit(1); } } +//*************************************************************************************************************** +//illumina data requires paired forward and reverse data +//BARCODE atgcatgc atgcatgc groupName +//PRIMER atgcatgc atgcatgc groupName +//PRIMER atgcatgc atgcatgc +bool MakeContigsCommand::getOligos(vector >& fastaFileNames, vector >& qualFileNames){ + try { + ifstream in; + m->openInputFile(oligosfile, in); + + ofstream test; + + string type, foligo, roligo, group; + + int indexPrimer = 0; + int indexBarcode = 0; + set uniquePrimers; + set uniqueBarcodes; + + while(!in.eof()){ + + in >> type; + + if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); } + + if(type[0] == '#'){ + while (!in.eof()) { char c = in.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + m->gobble(in); + } + else{ + m->gobble(in); + //make type case insensitive + for(int i=0;i> foligo; + + if (m->debug) { m->mothurOut("[DEBUG]: reading - " + foligo + ".\n"); } + + for(int i=0;igobble(in); + + in >> roligo; + + for(int i=0;imothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine(); } + else { uniquePrimers.insert(tempPair); } + + if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } } + + primers[indexPrimer]=newPrimer; indexPrimer++; + primerNameVector.push_back(group); + }else if(type == "BARCODE"){ + m->gobble(in); + + in >> roligo; + + for(int i=0;idebug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); } + + //check for repeat barcodes + string tempPair = foligo+roligo; + if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse + " is in your oligos file already, disregarding."); m->mothurOutEndLine(); } + else { uniqueBarcodes.insert(tempPair); } + + barcodes[indexBarcode]=newPair; indexBarcode++; + barcodeNameVector.push_back(group); + }else if(type == "LINKER"){ + linker.push_back(foligo); + }else if(type == "SPACER"){ + spacer.push_back(foligo); + } + else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are primer, barcode, linker and spacer. Ignoring " + foligo + "."); m->mothurOutEndLine(); } + } + m->gobble(in); + } + in.close(); + + if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; } + + //add in potential combos + if(barcodeNameVector.size() == 0){ + oligosPair temp("", ""); + barcodes[0] = temp; + barcodeNameVector.push_back(""); + } + + if(primerNameVector.size() == 0){ + oligosPair temp("", ""); + primers[0] = temp; + primerNameVector.push_back(""); + } + + fastaFileNames.resize(barcodeNameVector.size()); + for(int i=0;i uniqueNames; //used to cleanup outputFileNames + for(map::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){ + for(map::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){ + + string primerName = primerNameVector[itPrimer->first]; + string barcodeName = barcodeNameVector[itBar->first]; + + string comboGroupName = ""; + string fastaFileName = ""; + string qualFileName = ""; + string nameFileName = ""; + string countFileName = ""; + + if(primerName == ""){ + comboGroupName = barcodeNameVector[itBar->first]; + } + else{ + if(barcodeName == ""){ + comboGroupName = primerNameVector[itPrimer->first]; + } + else{ + comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first]; + } + } + + + ofstream temp; + fastaFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + comboGroupName + ".fasta"; + if (uniqueNames.count(fastaFileName) == 0) { + outputNames.push_back(fastaFileName); + outputTypes["fasta"].push_back(fastaFileName); + uniqueNames.insert(fastaFileName); + } + + fastaFileNames[itBar->first][itPrimer->first] = fastaFileName; + m->openOutputFile(fastaFileName, temp); temp.close(); + + + qualFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + comboGroupName + ".qual"; + if (uniqueNames.count(qualFileName) == 0) { + outputNames.push_back(qualFileName); + outputTypes["qfile"].push_back(qualFileName); + } + + qualFileNames[itBar->first][itPrimer->first] = qualFileName; + m->openOutputFile(qualFileName, temp); temp.close(); + } + } + } + + bool allBlank = true; + for (int i = 0; i < barcodeNameVector.size(); i++) { + if (barcodeNameVector[i] != "") { + allBlank = false; + break; + } + } + for (int i = 0; i < primerNameVector.size(); i++) { + if (primerNameVector[i] != "") { + allBlank = false; + break; + } + } + + if (allBlank) { + m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine(); + allFiles = false; + return false; + } + + return true; + + } + catch(exception& e) { + m->errorOut(e, "MakeContigsCommand", "getOligos"); + exit(1); + } +} +//********************************************************************/ +string MakeContigsCommand::reverseOligo(string oligo){ + try { + string reverse = ""; + + for(int i=oligo.length()-1;i>=0;i--){ + + if(oligo[i] == 'A') { reverse += 'T'; } + else if(oligo[i] == 'T'){ reverse += 'A'; } + else if(oligo[i] == 'U'){ reverse += 'A'; } + + else if(oligo[i] == 'G'){ reverse += 'C'; } + else if(oligo[i] == 'C'){ reverse += 'G'; } + + else if(oligo[i] == 'R'){ reverse += 'Y'; } + else if(oligo[i] == 'Y'){ reverse += 'R'; } + + else if(oligo[i] == 'M'){ reverse += 'K'; } + else if(oligo[i] == 'K'){ reverse += 'M'; } + + else if(oligo[i] == 'W'){ reverse += 'W'; } + else if(oligo[i] == 'S'){ reverse += 'S'; } + + else if(oligo[i] == 'B'){ reverse += 'V'; } + else if(oligo[i] == 'V'){ reverse += 'B'; } + + else if(oligo[i] == 'D'){ reverse += 'H'; } + else if(oligo[i] == 'H'){ reverse += 'D'; } + + else { reverse += 'N'; } + } + + + return reverse; + } + catch(exception& e) { + m->errorOut(e, "MakeContigsCommand", "reverseOligo"); + exit(1); + } +} //**********************************************************************************************************************