X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsefastaqcommand.cpp;h=7202efdce3bc179d9d1236edd2fc31ae841abcd4;hp=74e3e2bc9f0bdedc88f90e7f923eafdb511470d6;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hpb=e9845ee4c8db2e044e87d721cc2d94f8d609e03d diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp index 74e3e2b..7202efd 100644 --- a/parsefastaqcommand.cpp +++ b/parsefastaqcommand.cpp @@ -14,6 +14,14 @@ vector ParseFastaQCommand::setParameters(){ try { CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pfastq); + CommandParameter poligos("oligos", "InputTypes", "", "", "oligosGroup", "none", "none","",false,false); parameters.push_back(poligos); + CommandParameter pgroup("group", "InputTypes", "", "", "oligosGroup", "none", "none","",false,false); parameters.push_back(pgroup); + CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient); + 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 pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta); CommandParameter pqual("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqual); CommandParameter ppacbio("pacbio", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppacbio); @@ -35,8 +43,16 @@ string ParseFastaQCommand::getHelpString(){ try { string helpString = ""; helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n"; - helpString += "The fastq.info command parameters are fastq, fasta, qfile and format; fastq is required.\n"; + helpString += "The fastq.info command parameters are fastq, fasta, qfile, oligos, group and format; fastq is required.\n"; helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n"; + helpString += "The oligos parameter allows you to provide an oligos file to split your fastq file into separate fastq files by barcode and primers. \n"; + helpString += "The group parameter allows you to provide a group file to split your fastq file into separate fastq files by group. \n"; + helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the reads. 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 checkorient parameter will check look for the reverse compliment of the barcode or primer in the sequence. If found the sequence is flipped. The default is false.\n"; helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=sanger.\n"; helpString += "The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.\n"; helpString += "The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.\n"; @@ -56,7 +72,8 @@ string ParseFastaQCommand::getOutputPattern(string type) { string pattern = ""; if (type == "fasta") { pattern = "[filename],fasta"; } - else if (type == "qfile") { pattern = "[filename],qual"; } + else if (type == "qfile") { pattern = "[filename],qual"; } + else if (type == "fastq") { pattern = "[filename],[group],fastq"; } else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } return pattern; @@ -74,6 +91,7 @@ ParseFastaQCommand::ParseFastaQCommand(){ vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["qfile"] = tempOutNames; + outputTypes["fastq"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand"); @@ -83,7 +101,8 @@ ParseFastaQCommand::ParseFastaQCommand(){ //********************************************************************************************************************** ParseFastaQCommand::ParseFastaQCommand(string option){ try { - abort = false; calledHelp = false; + abort = false; calledHelp = false; + split = 1; if(option == "help") { help(); abort = true; calledHelp = true; } else if(option == "citation") { citation(); abort = true; calledHelp = true;} @@ -106,6 +125,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){ vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["qfile"] = tempOutNames; + outputTypes["fastq"] = tempOutNames; //if the user changes the input directory command factory will send this info to us in the output parameter string inputDir = validParameter.validFile(parameters, "inputdir", false); @@ -119,12 +139,40 @@ ParseFastaQCommand::ParseFastaQCommand(string option){ //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["fastq"] = 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; } + } + + it = parameters.find("group"); + //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["group"] = inputDir + it->second; } + } } //check for required parameters fastaQFile = validParameter.validFile(parameters, "fastq", true); if (fastaQFile == "not found") { m->mothurOut("fastq is a required parameter for the fastq.info command."); m->mothurOutEndLine(); abort = true; } - else if (fastaQFile == "not open") { fastaQFile = ""; abort = true; } + else if (fastaQFile == "not open") { fastaQFile = ""; abort = true; } + + oligosfile = validParameter.validFile(parameters, "oligos", true); + if (oligosfile == "not found") { oligosfile = ""; } + else if (oligosfile == "not open") { oligosfile = ""; abort = true; } + else { m->setOligosFile(oligosfile); split = 2; } + + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not found") { groupfile = ""; } + else if (groupfile == "not open") { groupfile = ""; abort = true; } + else { m->setGroupFile(groupfile); split = 2; } + + if ((groupfile != "") && (oligosfile != "")) { m->mothurOut("You must enter ONLY ONE of the following: oligos or group."); 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 = m->hasPath(fastaQFile); } @@ -139,6 +187,23 @@ ParseFastaQCommand::ParseFastaQCommand(string option){ temp = validParameter.validFile(parameters, "pacbio", false); if(temp == "not found"){ temp = "F"; } pacbio = m->isTrue(temp); + 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; } + format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "sanger"; } @@ -148,6 +213,9 @@ ParseFastaQCommand::ParseFastaQCommand(string option){ } if ((!fasta) && (!qual)) { m->mothurOut("[ERROR]: no outputs selected. Aborting."); m->mothurOutEndLine(); abort=true; } + + temp = validParameter.validFile(parameters, "checkorient", false); if (temp == "not found") { temp = "F"; } + reorient = m->isTrue(temp); } } @@ -171,6 +239,21 @@ int ParseFastaQCommand::execute(){ if (fasta) { m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile); } if (qual) { m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile); outputTypes["qfile"].push_back(qualFile); } + + TrimOligos* trimOligos = NULL; TrimOligos* rtrimOligos = NULL; + pairedOligos = false; numBarcodes = 0; numPrimers= 0; numLinkers= 0; numSpacers = 0; numRPrimers = 0; + if (oligosfile != "") { + readOligos(oligosfile); + //find group read belongs to + if (pairedOligos) { trimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos.getPairedPrimers(), oligos.getPairedBarcodes()); numBarcodes = oligos.getPairedBarcodes().size(); numPrimers = oligos.getPairedPrimers().size(); } + else { trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, oligos.getPrimers(), oligos.getBarcodes(), oligos.getReversePrimers(), oligos.getLinkers(), oligos.getSpacers()); numPrimers = oligos.getPrimers().size(); numBarcodes = oligos.getBarcodes().size(); } + + if (reorient) { + rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos.getReorientedPairedPrimers(), oligos.getReorientedPairedBarcodes()); numBarcodes = oligos.getReorientedPairedBarcodes().size(); + } + + } + else if (groupfile != "") { readGroup(groupfile); } ifstream in; m->openInputFile(fastaQFile, in); @@ -181,65 +264,99 @@ int ParseFastaQCommand::execute(){ convertTable.push_back(temp); } + + int count = 0; while (!in.eof()) { if (m->control_pressed) { break; } - - //read sequence name - string name = m->getline(in); m->gobble(in); - if (name == "") { m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; break; } - else if (name[0] != '@') { m->mothurOut("[ERROR]: reading " + name + " expected a name with @ as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; } - else { - name = name.substr(1); - for (int i = 0; i < name.length(); i++) { if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; } } - } - - //read sequence - string sequence = m->getline(in); m->gobble(in); - if (sequence == "") { m->mothurOut("[ERROR]: missing sequence for " + name); m->mothurOutEndLine(); m->control_pressed = true; break; } - - //read sequence name - string name2 = m->getline(in); m->gobble(in); - if (name2 == "") { m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; break; } - else if (name2[0] != '+') { m->mothurOut("[ERROR]: reading " + name2 + " expected a name with + as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; } - else { - name2 = name2.substr(1); - for (int i = 0; i < name2.length(); i++) { if (name2[i] == ':') { name2[i] = '_'; m->changedSeqNames = true; } } - } - - //read quality scores - string quality = m->getline(in); m->gobble(in); - if (quality == "") { m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; } - - //sanity check sequence length and number of quality scores match - if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } } - if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; } - - vector qualScores; - if (qual) { - qualScores = convertQual(quality); - outQual << ">" << name << endl; - for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; } - outQual << endl; - } - if (m->control_pressed) { break; } + bool ignore; + fastqRead2 thisRead = readFastq(in, ignore); - if (pacbio) { - if (!qual) { qualScores = convertQual(quality); } //get scores if we didn't already - for (int i = 0; i < qualScores.size(); i++) { - if (qualScores[i] == 0){ sequence[i] = 'N'; } + if (!ignore) { + vector qualScores; + if (qual) { + qualScores = convertQual(thisRead.quality); + outQual << ">" << thisRead.seq.getName() << endl; + for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; } + outQual << endl; } - } - - //print sequence info to files - if (fasta) { outFasta << ">" << name << endl << sequence << endl; } - + + if (m->control_pressed) { break; } + + if (pacbio) { + if (!qual) { qualScores = convertQual(thisRead.quality); } //convert if not done + string sequence = thisRead.seq.getAligned(); + for (int i = 0; i < qualScores.size(); i++) { + if (qualScores[i] == 0){ sequence[i] = 'N'; } + } + thisRead.seq.setAligned(sequence); + } + + //print sequence info to files + if (fasta) { thisRead.seq.printSequence(outFasta); } + + if (split > 1) { + int barcodeIndex, primerIndex, trashCodeLength; + if (oligosfile != "") { trashCodeLength = findGroup(thisRead, barcodeIndex, primerIndex, trimOligos, rtrimOligos, numBarcodes, numPrimers); } + else if (groupfile != "") { trashCodeLength = findGroup(thisRead, barcodeIndex, primerIndex, "groupMode"); } + else { m->mothurOut("[ERROR]: uh oh, we shouldn't be here...\n"); } + + if(trashCodeLength == 0){ + ofstream out; + m->openOutputFileAppend(fastqFileNames[barcodeIndex][primerIndex], out); + out << thisRead.wholeRead; + out.close(); + }else{ + ofstream out; + m->openOutputFileAppend(noMatchFile, out); + out << thisRead.wholeRead; + out.close(); + } + } + //report progress + if((count+1) % 10000 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); } + count++; + } } in.close(); if (fasta) { outFasta.close(); } if (qual) { outQual.close(); } + + //report progress + if (!m->control_pressed) { if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } } + + if (split > 1) { + + if (groupfile != "") { delete groupMap; } + else if (oligosfile != "") { delete trimOligos; if (reorient) { delete rtrimOligos; } } + + map::iterator it; + set namesToRemove; + for(int i=0;iisBlank(fastqFileNames[i][j])){ + m->mothurRemove(fastqFileNames[i][j]); + namesToRemove.insert(fastqFileNames[i][j]); + } + } + } + } + } + + //remove names for outputFileNames, just cleans up the output + for(int i = 0; i < outputNames.size(); i++) { + if (namesToRemove.count(outputNames[i]) != 0) { + outputNames.erase(outputNames.begin()+i); + i--; + } + } + if(m->isBlank(noMatchFile)){ m->mothurRemove(noMatchFile); } + else { outputNames.push_back(noMatchFile); outputTypes["fastq"].push_back(noMatchFile); } + } if (m->control_pressed) { outputTypes.clear(); outputNames.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; } @@ -267,6 +384,55 @@ int ParseFastaQCommand::execute(){ exit(1); } } +//********************************************************************************************************************** +fastqRead2 ParseFastaQCommand::readFastq(ifstream& in, bool& ignore){ + try { + ignore = false; + string wholeRead = ""; + + //read sequence name + string line = m->getline(in); m->gobble(in); if (split > 1) { wholeRead += line + "\n"; } + vector pieces = m->splitWhiteSpace(line); + string name = ""; if (pieces.size() != 0) { name = pieces[0]; } + if (name == "") { m->mothurOut("[WARNING]: Blank fasta name, ignoring read."); m->mothurOutEndLine(); ignore=true; } + else if (name[0] != '@') { m->mothurOut("[WARNING]: reading " + name + " expected a name with @ as a leading character, ignoring read."); m->mothurOutEndLine(); ignore=true; } + else { name = name.substr(1); } + + //read sequence + string sequence = m->getline(in); m->gobble(in); if (split > 1) { wholeRead += sequence + "\n"; } + if (sequence == "") { m->mothurOut("[WARNING]: missing sequence for " + name + ", ignoring."); ignore=true; } + + //read sequence name + line = m->getline(in); m->gobble(in); if (split > 1) { wholeRead += line + "\n"; } + pieces = m->splitWhiteSpace(line); + string name2 = ""; if (pieces.size() != 0) { name2 = pieces[0]; } + if (name2 == "") { m->mothurOut("[WARNING]: expected a name with + as a leading character, ignoring."); ignore=true; } + else if (name2[0] != '+') { m->mothurOut("[WARNING]: reading " + name2 + " expected a name with + as a leading character, ignoring."); ignore=true; } + else { name2 = name2.substr(1); if (name2 == "") { name2 = name; } } + + + //read quality scores + string quality = m->getline(in); m->gobble(in); if (split > 1) { wholeRead += quality + "\n"; } + if (quality == "") { m->mothurOut("[WARNING]: missing quality for " + name2 + ", ignoring."); ignore=true; } + + //sanity check sequence length and number of quality scores match + if (name2 != "") { if (name != name2) { m->mothurOut("[WARNING]: names do not match. read " + name + " for fasta and " + name2 + " for quality, ignoring."); ignore=true; } } + if (quality.length() != sequence.length()) { m->mothurOut("[WARNING]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores, ignoring read."); ignore=true; } + + m->checkName(name); + Sequence seq(name, sequence); + fastqRead2 read(seq, quality, wholeRead); + + if (m->debug) { m->mothurOut("[DEBUG]: " + read.seq.getName() + " " + read.seq.getAligned() + " " + quality + "\n"); } + + return read; + } + catch(exception& e) { + m->errorOut(e, "ParseFastaQCommand", "readFastq"); + exit(1); + } +} + //********************************************************************************************************************** vector ParseFastaQCommand::convertQual(string qual) { try { @@ -302,6 +468,306 @@ vector ParseFastaQCommand::convertQual(string qual) { } } //********************************************************************************************************************** +int ParseFastaQCommand::findGroup(fastqRead2 thisRead, int& barcode, int& primer, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos, int numBarcodes, int numPrimers) { + try { + int success = 1; + string trashCode = ""; + int currentSeqsDiffs = 0; + + Sequence currSeq(thisRead.seq.getName(), thisRead.seq.getAligned()); + QualityScores currQual; currQual.setScores(convertQual(thisRead.quality)); + + //for reorient + Sequence savedSeq(currSeq.getName(), currSeq.getAligned()); + QualityScores savedQual(currQual.getName(), currQual.getScores()); + + if(numLinkers != 0){ + success = trimOligos->stripLinker(currSeq, currQual); + if(success > ldiffs) { trashCode += 'k'; } + else{ currentSeqsDiffs += success; } + + } + + if(numBarcodes != 0){ + success = trimOligos->stripBarcode(currSeq, currQual, barcode); + if(success > bdiffs) { trashCode += 'b'; } + else{ currentSeqsDiffs += success; } + } + + if(numSpacers != 0){ + success = trimOligos->stripSpacer(currSeq, currQual); + if(success > sdiffs) { trashCode += 's'; } + else{ currentSeqsDiffs += success; } + + } + + if(numPrimers != 0){ + success = trimOligos->stripForward(currSeq, currQual, primer, true); + if(success > pdiffs) { trashCode += 'f'; } + else{ currentSeqsDiffs += success; } + } + + if (currentSeqsDiffs > tdiffs) { trashCode += 't'; } + + if(numRPrimers != 0){ + success = trimOligos->stripReverse(currSeq, currQual); + if(!success) { trashCode += 'r'; } + } + + if (reorient && (trashCode != "")) { //if you failed and want to check the reverse + int thisSuccess = 0; + string thisTrashCode = ""; + int thisCurrentSeqsDiffs = 0; + + int thisBarcodeIndex = 0; + int thisPrimerIndex = 0; + //cout << currSeq.getName() << '\t' << savedSeq.getUnaligned() << endl; + if(numBarcodes != 0){ + thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex); + if(thisSuccess > bdiffs) { thisTrashCode += "b"; } + else{ thisCurrentSeqsDiffs += thisSuccess; } + } + //cout << currSeq.getName() << '\t' << savedSeq.getUnaligned() << endl; + if(numPrimers != 0){ + thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, true); + if(thisSuccess > pdiffs) { thisTrashCode += "f"; } + else{ thisCurrentSeqsDiffs += thisSuccess; } + } + + if (thisCurrentSeqsDiffs > tdiffs) { thisTrashCode += 't'; } + + if (thisTrashCode == "") { + trashCode = thisTrashCode; + success = thisSuccess; + currentSeqsDiffs = thisCurrentSeqsDiffs; + barcode = thisBarcodeIndex; + primer = thisPrimerIndex; + savedSeq.reverseComplement(); + currSeq.setAligned(savedSeq.getAligned()); + savedQual.flipQScores(); + currQual.setScores(savedQual.getScores()); + }else { trashCode += "(" + thisTrashCode + ")"; } + } + + if (trashCode.length() == 0) { //is this sequence in the ignore group + string thisGroup = oligos.getGroupName(barcode, primer); + + int pos = thisGroup.find("ignore"); + if (pos != string::npos) { trashCode += "i"; } + } + + + return trashCode.length(); + } + catch(exception& e) { + m->errorOut(e, "ParseFastaQCommand", "findGroup"); + exit(1); + } +} +//********************************************************************************************************************** +int ParseFastaQCommand::findGroup(fastqRead2 thisRead, int& barcode, int& primer, string groupMode) { + try { + string trashCode = ""; + primer = 0; + + string group = groupMap->getGroup(thisRead.seq.getName()); + if (group == "not found") { trashCode += "g"; } //scrap for group + + return trashCode.length(); + } + catch(exception& e) { + m->errorOut(e, "ParseFastaQCommand", "findGroup"); + exit(1); + } +} +//*************************************************************************************************************** + +bool ParseFastaQCommand::readOligos(string oligoFile){ + try { + bool allBlank = false; + oligos.read(oligosfile); + + if (m->control_pressed) { return false; } //error in reading oligos + + if (oligos.hasPairedBarcodes()) { + pairedOligos = true; + numPrimers = oligos.getPairedPrimers().size(); + numBarcodes = oligos.getPairedBarcodes().size(); + }else { + pairedOligos = false; + numPrimers = oligos.getPrimers().size(); + numBarcodes = oligos.getBarcodes().size(); + } + + numLinkers = oligos.getLinkers().size(); + numSpacers = oligos.getSpacers().size(); + numRPrimers = oligos.getReversePrimers().size(); + + vector groupNames = oligos.getGroupNames(); + if (groupNames.size() == 0) { allBlank = true; } + + + fastqFileNames.resize(oligos.getBarcodeNames().size()); + for(int i=0;i uniqueNames; //used to cleanup outputFileNames + if (pairedOligos) { + map barcodes = oligos.getPairedBarcodes(); + map primers = oligos.getPairedPrimers(); + for(map::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){ + for(map::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){ + + string primerName = oligos.getPrimerName(itPrimer->first); + string barcodeName = oligos.getBarcodeName(itBar->first); + + if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing + else if ((primerName == "") && (barcodeName == "")) { } //do nothing + else { + string comboGroupName = ""; + string fastaFileName = ""; + string qualFileName = ""; + string nameFileName = ""; + string countFileName = ""; + + if(primerName == ""){ + comboGroupName = barcodeName; + }else{ + if(barcodeName == ""){ + comboGroupName = primerName; + } + else{ + comboGroupName = barcodeName + "." + primerName; + } + } + + ofstream temp; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile)); + variables["[group]"] = comboGroupName; + string fastqFileName = getOutputFileName("fastq", variables); + if (uniqueNames.count(fastqFileName) == 0) { + outputNames.push_back(fastqFileName); + outputTypes["fastq"].push_back(fastqFileName); + uniqueNames.insert(fastqFileName); + } + + fastqFileNames[itBar->first][itPrimer->first] = fastqFileName; + m->openOutputFile(fastqFileName, temp); temp.close(); + } + } + } + }else { + map barcodes = oligos.getBarcodes() ; + map primers = oligos.getPrimers(); + for(map::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){ + for(map::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){ + + string primerName = oligos.getPrimerName(itPrimer->second); + string barcodeName = oligos.getBarcodeName(itBar->second); + + if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing + else if ((primerName == "") && (barcodeName == "")) { } //do nothing + else { + string comboGroupName = ""; + string fastaFileName = ""; + string qualFileName = ""; + string nameFileName = ""; + string countFileName = ""; + + if(primerName == ""){ + comboGroupName = barcodeName; + }else{ + if(barcodeName == ""){ + comboGroupName = primerName; + } + else{ + comboGroupName = barcodeName + "." + primerName; + } + } + + ofstream temp; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile)); + variables["[group]"] = comboGroupName; + string fastqFileName = getOutputFileName("fastq", variables); + if (uniqueNames.count(fastqFileName) == 0) { + outputNames.push_back(fastqFileName); + outputTypes["fastq"].push_back(fastqFileName); + uniqueNames.insert(fastqFileName); + } + + fastqFileNames[itBar->second][itPrimer->second] = fastqFileName; + m->openOutputFile(fastqFileName, temp); temp.close(); + } + } + } + } + + if (allBlank) { + m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine(); + return false; + } + + ofstream temp; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile)); + variables["[group]"] = "scrap"; + noMatchFile = getOutputFileName("fastq", variables); + m->openOutputFile(noMatchFile, temp); temp.close(); + + return true; + + } + catch(exception& e) { + m->errorOut(e, "ParseFastaQCommand", "getOligos"); + exit(1); + } +} +//*************************************************************************************************************** +bool ParseFastaQCommand::readGroup(string groupfile){ + try { + fastqFileNames.clear(); + + groupMap = new GroupMap(); + groupMap->readMap(groupfile); + + //like barcodeNameVector - no primer names + vector groups = groupMap->getNamesOfGroups(); + + fastqFileNames.resize(groups.size()); + for (int i = 0; i < fastqFileNames.size(); i++) { + for (int j = 0; j < 1; j++) { + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile)); + variables["[group]"] = groups[i]; + string thisFilename = getOutputFileName("fastq",variables); + outputNames.push_back(thisFilename); + outputTypes["fastq"].push_back(thisFilename); + + ofstream temp; + m->openOutputFileBinary(thisFilename, temp); temp.close(); + fastqFileNames[i].push_back(thisFilename); + } + } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile)); + variables["[group]"] = "scrap"; + noMatchFile = getOutputFileName("fastq",variables); + m->mothurRemove(noMatchFile); + + return true; + + } + catch(exception& e) { + m->errorOut(e, "ParseFastaQCommand", "readGroup"); + exit(1); + } +} +//**********************************************************************************************************************