X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimseqscommand.cpp;h=060733036297fb2bd023a2783774218e2f513e80;hp=5a5d445cb8624386e90d4c714c1f460f1be0d509;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hpb=b740fb182372143e152143c6cc5b9ac8591f09b7 diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp index 5a5d445..0607330 100644 --- a/trimseqscommand.cpp +++ b/trimseqscommand.cpp @@ -12,6 +12,7 @@ #include "trimoligos.h" + //********************************************************************************************************************** vector TrimSeqsCommand::setParameters(){ try { @@ -24,7 +25,7 @@ vector TrimSeqsCommand::setParameters(){ CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient); CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxambig); CommandParameter pmaxhomop("maxhomop", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxhomop); - CommandParameter pminlength("minlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pminlength); + CommandParameter pminlength("minlength", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pminlength); CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxlength); CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs); CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs); @@ -34,6 +35,7 @@ vector TrimSeqsCommand::setParameters(){ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles); CommandParameter pkeepforward("keepforward", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkeepforward); + CommandParameter plogtransform("logtransform", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plogtransform); CommandParameter pqtrim("qtrim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pqtrim); CommandParameter pqthreshold("qthreshold", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pqthreshold); CommandParameter pqaverage("qaverage", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pqaverage); @@ -61,10 +63,10 @@ string TrimSeqsCommand::getHelpString(){ string helpString = ""; helpString += "The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.\n"; helpString += "The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.\n"; - helpString += "The trim.seqs command parameters are fasta, name, count, flip, checkorient, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n"; + helpString += "The trim.seqs command parameters are fasta, name, count, flip, checkorient, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast, logtransform and allfiles.\n"; helpString += "The fasta parameter is required.\n"; helpString += "The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n"; - helpString += "The checkorient parameter will check the reverse compliment of the sequence if the barcodes and primers cannot be found in the forward. The default is false.\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 oligos parameter allows you to provide an oligos file.\n"; helpString += "The name parameter allows you to provide a names file with your fasta file.\n"; helpString += "The count parameter allows you to provide a count file with your fasta file.\n"; @@ -84,6 +86,7 @@ string TrimSeqsCommand::getHelpString(){ helpString += "The qwindowaverage parameter allows you to set a minimum average quality score allowed over a window. \n"; helpString += "The rollaverage parameter allows you to set a minimum rolling average quality score allowed over a window. \n"; helpString += "The qstepsize parameter allows you to set a number of bases to move the window over. Default=1.\n"; + helpString += "The logtransform parameter allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform. Default=F.\n"; helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n"; helpString += "The keepforward parameter allows you to indicate whether you want the forward primer removed or not. The default is F, meaning remove the forward primer.\n"; helpString += "The qtrim parameter will trim sequence from the point that they fall below the qthreshold and put it in the .trim file if set to true. The default is T.\n"; @@ -256,7 +259,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option) { temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "0"; } m->mothurConvert(temp, maxHomoP); - temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; } + temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "1"; } m->mothurConvert(temp, minLength); temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; } @@ -329,6 +332,9 @@ TrimSeqsCommand::TrimSeqsCommand(string option) { temp = validParameter.validFile(parameters, "keepforward", false); if (temp == "not found") { temp = "F"; } keepforward = m->isTrue(temp); + temp = validParameter.validFile(parameters, "logtransform", false); if (temp == "not found") { temp = "F"; } + logtransform = m->isTrue(temp); + temp = validParameter.validFile(parameters, "checkorient", false); if (temp == "not found") { temp = "F"; } reorient = m->isTrue(temp); @@ -380,6 +386,7 @@ int TrimSeqsCommand::execute(){ vector > fastaFileNames; vector > qualFileNames; vector > nameFileNames; + map uniqueFastaNames;// so we don't add the same groupfile multiple times map variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile)); @@ -422,7 +429,7 @@ int TrimSeqsCommand::execute(){ if (countfile != "") { CountTable ct; - ct.readTable(countfile); + ct.readTable(countfile, true, false); nameCount = ct.getNameMap(); outputNames.push_back(trimCountFile); outputNames.push_back(scrapCountFile); @@ -435,7 +442,7 @@ int TrimSeqsCommand::execute(){ string outputGroupFileName; if(oligoFile != ""){ - createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames); + createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames, uniqueFastaNames); if ((createGroup) && (countfile == "")){ map myvariables; myvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile)); @@ -444,8 +451,6 @@ int TrimSeqsCommand::execute(){ } } - if (!pairedOligos) { if (reorient) { m->mothurOut("[WARNING]: You cannot use reorient without paired barcodes or primers, skipping."); m->mothurOutEndLine(); reorient = false; } } - if (m->control_pressed) { return 0; } //fills lines and qlines @@ -461,7 +466,6 @@ int TrimSeqsCommand::execute(){ if (m->control_pressed) { return 0; } if(allFiles){ - map uniqueFastaNames;// so we don't add the same groupfile multiple times map::iterator it; set namesToRemove; for(int i=0;imothurRemove(nameFileNames[i][j]); namesToRemove.insert(nameFileNames[i][j]); } - }else{ - it = uniqueFastaNames.find(fastaFileNames[i][j]); - if (it == uniqueFastaNames.end()) { - uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i]; - } + uniqueFastaNames.erase(fastaFileNames[i][j]); //remove from list for group file print } } } @@ -540,7 +540,7 @@ int TrimSeqsCommand::execute(){ if (countfile != "") { //create countfile with group info included CountTable* ct = new CountTable(); - ct->readTable(trimCountFile); + ct->readTable(trimCountFile, true, false); map justTrimmedNames = ct->getNameMap(); delete ct; @@ -676,26 +676,13 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string int count = 0; bool moreSeqs = 1; - int numBarcodes = barcodes.size(); TrimOligos* trimOligos = NULL; - if (pairedOligos) { trimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, pairedPrimers, pairedBarcodes); numBarcodes = pairedBarcodes.size(); } - else { trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer); } + if (pairedOligos) { trimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos.getPairedPrimers(), oligos.getPairedBarcodes()); } + else { trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, oligos.getPrimers(), oligos.getBarcodes(), oligos.getReversePrimers(), oligos.getLinkers(), oligos.getSpacers()); } TrimOligos* rtrimOligos = NULL; if (reorient) { - //create reoriented primer and barcode pairs - map rpairedPrimers, rpairedBarcodes; - for (map::iterator it = pairedPrimers.begin(); it != pairedPrimers.end(); it++) { - oligosPair tempPair(reverseOligo((it->second).reverse), (reverseOligo((it->second).forward))); //reversePrimer, rc ForwardPrimer - rpairedPrimers[it->first] = tempPair; - //cout << reverseOligo((it->second).reverse) << '\t' << (reverseOligo((it->second).forward)) << '\t' << primerNameVector[it->first] << endl; - } - for (map::iterator it = pairedBarcodes.begin(); it != pairedBarcodes.end(); it++) { - oligosPair tempPair(reverseOligo((it->second).reverse), (reverseOligo((it->second).forward))); //reverseBarcode, rc ForwardBarcode - rpairedBarcodes[it->first] = tempPair; - //cout << reverseOligo((it->second).reverse) << '\t' << (reverseOligo((it->second).forward)) << '\t' << barcodeNameVector[it->first] << endl; - } - rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes); numBarcodes = rpairedBarcodes.size(); + rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos.getReorientedPairedPrimers(), oligos.getReorientedPairedBarcodes()); numBarcodes = oligos.getReorientedPairedBarcodes().size(); } while (moreSeqs) { @@ -715,7 +702,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string int currentSeqsDiffs = 0; Sequence currSeq(inFASTA); m->gobble(inFASTA); - //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl; + //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl; Sequence savedSeq(currSeq.getName(), currSeq.getAligned()); QualityScores currQual; QualityScores savedQual; @@ -745,7 +732,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string } else{ currentSeqsDiffs += success; } } - + //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl; if(numSpacers != 0){ success = trimOligos->stripSpacer(currSeq, currQual); if(success > sdiffs) { trashCode += 's'; } @@ -775,13 +762,13 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string 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(numFPrimers != 0){ thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, keepforward); if(thisSuccess > pdiffs) { thisTrashCode += "f"; } @@ -819,9 +806,9 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string int origLength = currSeq.getNumBases(); if(qThreshold != 0) { success = currQual.stripQualThreshold(currSeq, qThreshold); } - else if(qAverage != 0) { success = currQual.cullQualAverage(currSeq, qAverage); } - else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage); } - else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage); } + else if(qAverage != 0) { success = currQual.cullQualAverage(currSeq, qAverage, logtransform); } + else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage, logtransform); } + else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage, logtransform); } else { success = 1; } //you don't want to trim, if it fails above then scrap it @@ -854,20 +841,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string if(trashCode.length() == 0){ string thisGroup = ""; - if (createGroup) { - if(numBarcodes != 0){ - thisGroup = barcodeNameVector[barcodeIndex]; - if (numFPrimers != 0) { - if (primerNameVector[primerIndex] != "") { - if(thisGroup != "") { - thisGroup += "." + primerNameVector[primerIndex]; - }else { - thisGroup = primerNameVector[primerIndex]; - } - } - } - } - } + if (createGroup) { thisGroup = oligos.getGroupName(barcodeIndex, primerIndex); } int pos = thisGroup.find("ignore"); if (pos == string::npos) { @@ -1013,7 +987,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) //loop through and create all the processes you want while (process != processors) { - int pid = fork(); + pid_t 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 @@ -1030,15 +1004,15 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName for(int i=0;imothurGetpid(process) + ".temp"; m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close(); if(qFileName != ""){ - tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp"; + tempPrimerQualFileNames[i][j] += m->mothurGetpid(process) + ".temp"; m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close(); } if(nameFile != ""){ - tempNameFileNames[i][j] += toString(getpid()) + ".temp"; + tempNameFileNames[i][j] += m->mothurGetpid(process) + ".temp"; m->openOutputFile(tempNameFileNames[i][j], temp); temp.close(); } } @@ -1048,27 +1022,27 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName driverCreateTrim(filename, qFileName, - (trimFASTAFileName + toString(getpid()) + ".temp"), - (scrapFASTAFileName + toString(getpid()) + ".temp"), - (trimQualFileName + toString(getpid()) + ".temp"), - (scrapQualFileName + toString(getpid()) + ".temp"), - (trimNameFileName + toString(getpid()) + ".temp"), - (scrapNameFileName + toString(getpid()) + ".temp"), - (trimCountFileName + toString(getpid()) + ".temp"), - (scrapCountFileName + toString(getpid()) + ".temp"), - (groupFile + toString(getpid()) + ".temp"), + (trimFASTAFileName + m->mothurGetpid(process) + ".temp"), + (scrapFASTAFileName + m->mothurGetpid(process) + ".temp"), + (trimQualFileName + m->mothurGetpid(process) + ".temp"), + (scrapQualFileName + m->mothurGetpid(process) + ".temp"), + (trimNameFileName + m->mothurGetpid(process) + ".temp"), + (scrapNameFileName + m->mothurGetpid(process) + ".temp"), + (trimCountFileName + m->mothurGetpid(process) + ".temp"), + (scrapCountFileName + m->mothurGetpid(process) + ".temp"), + (groupFile + m->mothurGetpid(process) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames, tempNameFileNames, lines[process], qLines[process]); - if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + toString(getpid()) + '\n'); } + if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + m->mothurGetpid(process) + '\n'); } //pass groupCounts to parent if(createGroup){ ofstream out; - string tempFile = filename + toString(getpid()) + ".num.temp"; + string tempFile = filename + m->mothurGetpid(process) + ".num.temp"; m->openOutputFile(tempFile, out); out << groupCounts.size() << endl; @@ -1172,9 +1146,9 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName tempPrimerQualFileNames, tempNameFileNames, lines[h].start, lines[h].end, qLines[h].start, qLines[h].end, m, - pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer, pairedBarcodes, pairedPrimers, pairedOligos, - primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast, - qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage, + pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, oligoFile, + createGroup, allFiles, keepforward, keepFirst, removeLast, + qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage, logtransform, minLength, maxAmbig, maxHomoP, maxLength, flip, reorient, nameMap, nameCount); pDataArray.push_back(tempTrim); @@ -1391,9 +1365,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) { string sname = ""; nameStream >> sname; sname = sname.substr(1); - for (int i = 0; i < sname.length(); i++) { - if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; } - } + m->checkName(sname); map::iterator it = firstSeqNames.find(sname); @@ -1486,9 +1458,201 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) { //*************************************************************************************************************** -bool TrimSeqsCommand::getOligos(vector >& fastaFileNames, vector >& qualFileNames, vector >& nameFileNames){ +bool TrimSeqsCommand::getOligos(vector >& fastaFileNames, vector >& qualFileNames, vector >& nameFileNames, map& fastaFile2Group){ try { - ifstream inOligos; + + bool allBlank = false; + oligos.read(oligoFile); + + if (m->control_pressed) { return false; } //error in reading oligos + + if (oligos.hasPairedBarcodes()) { + pairedOligos = true; + numFPrimers = oligos.getPairedPrimers().size(); + numBarcodes = oligos.getPairedBarcodes().size(); + }else { + pairedOligos = false; + numFPrimers = 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) { allFiles = 0; allBlank = true; } + + + fastaFileNames.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(fastaFile)); + variables["[tag]"] = comboGroupName; + fastaFileName = getOutputFileName("fasta", variables); + if (uniqueNames.count(fastaFileName) == 0) { + outputNames.push_back(fastaFileName); + outputTypes["fasta"].push_back(fastaFileName); + uniqueNames.insert(fastaFileName); + fastaFile2Group[fastaFileName] = comboGroupName; + } + + fastaFileNames[itBar->first][itPrimer->first] = fastaFileName; + m->openOutputFile(fastaFileName, temp); temp.close(); + + if(qFileName != ""){ + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qFileName)); + qualFileName = getOutputFileName("qfile", variables); + 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(); + } + + if(nameFile != ""){ + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFile)); + nameFileName = getOutputFileName("name", variables); + if (uniqueNames.count(nameFileName) == 0) { + outputNames.push_back(nameFileName); + outputTypes["name"].push_back(nameFileName); + } + + nameFileNames[itBar->first][itPrimer->first] = nameFileName; + m->openOutputFile(nameFileName, 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(fastaFile)); + variables["[tag]"] = comboGroupName; + fastaFileName = getOutputFileName("fasta", variables); + if (uniqueNames.count(fastaFileName) == 0) { + outputNames.push_back(fastaFileName); + outputTypes["fasta"].push_back(fastaFileName); + uniqueNames.insert(fastaFileName); + fastaFile2Group[fastaFileName] = comboGroupName; + } + + fastaFileNames[itBar->second][itPrimer->second] = fastaFileName; + m->openOutputFile(fastaFileName, temp); temp.close(); + + if(qFileName != ""){ + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qFileName)); + qualFileName = getOutputFileName("qfile", variables); + if (uniqueNames.count(qualFileName) == 0) { + outputNames.push_back(qualFileName); + outputTypes["qfile"].push_back(qualFileName); + } + + qualFileNames[itBar->second][itPrimer->second] = qualFileName; + m->openOutputFile(qualFileName, temp); temp.close(); + } + + if(nameFile != ""){ + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFile)); + nameFileName = getOutputFileName("name", variables); + if (uniqueNames.count(nameFileName) == 0) { + outputNames.push_back(nameFileName); + outputTypes["name"].push_back(nameFileName); + } + + nameFileNames[itBar->second][itPrimer->second] = nameFileName; + m->openOutputFile(nameFileName, 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(); + allFiles = false; + return false; + } + + + + /*ifstream inOligos; m->openInputFile(oligoFile, inOligos); ofstream test; @@ -1505,7 +1669,7 @@ bool TrimSeqsCommand::getOligos(vector >& fastaFileNames, vector< while(!inOligos.eof()){ - inOligos >> type; + inOligos >> type; if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); } @@ -1648,7 +1812,7 @@ bool TrimSeqsCommand::getOligos(vector >& fastaFileNames, vector< if (hasPairedBarcodes || hasPrimer) { pairedOligos = true; if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->control_pressed = true; m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting."); m->mothurOutEndLine(); return 0; } - }else if (reorient) { m->mothurOut("[Warning]: cannot use checkorient without paired barcodes or primers, ignoring.\n"); m->mothurOutEndLine(); reorient = false; } + } if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; } @@ -1810,33 +1974,8 @@ bool TrimSeqsCommand::getOligos(vector >& fastaFileNames, vector< } } } - numFPrimers = primers.size(); - if (pairedOligos) { numFPrimers = pairedPrimers.size(); } - numRPrimers = revPrimer.size(); - numLinkers = linker.size(); - numSpacers = spacer.size(); - - 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; + */ + return true; } catch(exception& e) { @@ -1936,46 +2075,6 @@ bool TrimSeqsCommand::cullHomoP(Sequence& seq){ } } -//********************************************************************/ -string TrimSeqsCommand::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, "TrimSeqsCommand", "reverseOligo"); - exit(1); - } -} //***************************************************************************************************************