X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=4b2ee4eee99d3d38c2e5cd4f77ad2c0b90af4b81;hb=6e81846c8e5b2614f6b06643a9f558fb0e6669fa;hp=944e2cdc0a110828157301f14f2470a06ac3e052;hpb=a86aff4f80701bf0d436f02c0095920114e1cba2;p=mothur.git diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp index 944e2cd..4b2ee4e 100644 --- a/trimseqscommand.cpp +++ b/trimseqscommand.cpp @@ -24,7 +24,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option) { else { //valid paramters for this command string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", - "qthreshold", "qaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"}; + "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"}; vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); @@ -81,6 +81,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option) { outputDir += hasPath(fastaFile); //if user entered a file with a path then preserve it } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... string temp; @@ -105,7 +106,6 @@ TrimSeqsCommand::TrimSeqsCommand(string option) { temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; } convert(temp, maxLength); - temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; } convert(temp, bdiffs); @@ -125,16 +125,28 @@ TrimSeqsCommand::TrimSeqsCommand(string option) { temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; } convert(temp, qThreshold); - temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "F"; } + temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "F"; } qtrim = isTrue(temp); + temp = validParameter.validFile(parameters, "rollaverage", false); if (temp == "not found") { temp = "0"; } + convert(temp, qRollAverage); + + temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; } + convert(temp, qWindowAverage); + + temp = validParameter.validFile(parameters, "qwindowsize", false); if (temp == "not found") { temp = "100"; } + convert(temp, qWindowSize); + + temp = validParameter.validFile(parameters, "qstepsize", false); if (temp == "not found") { temp = "10"; } + convert(temp, qWindowStep); + temp = validParameter.validFile(parameters, "qaverage", false); if (temp == "not found") { temp = "0"; } convert(temp, qAverage); temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; } allFiles = isTrue(temp); - temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; } convert(temp, processors); if(allFiles && oligoFile == ""){ @@ -211,87 +223,123 @@ int TrimSeqsCommand::execute(){ outputNames.push_back(trimSeqFile); string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta"; outputNames.push_back(scrapSeqFile); + string trimQualFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.qual"; + outputNames.push_back(trimQualFile); + string scrapQualFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.qual"; + outputNames.push_back(scrapQualFile); string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups"; vector fastaFileNames; + vector qualFileNames; if(oligoFile != ""){ outputNames.push_back(groupFile); - getOligos(fastaFileNames); + getOligos(fastaFileNames, qualFileNames); } - - if(qFileName != "") { setLines(qFileName, qLines); } + vector fastaFilePos; + vector qFilePos; + + setLines(fastaFile, qFileName, fastaFilePos, qFilePos); + + for (int i = 0; i < (fastaFilePos.size()-1); i++) { + lines.push_back(new linePair(fastaFilePos[i], fastaFilePos[(i+1)])); + if (qFileName != "") { qLines.push_back(new linePair(qFilePos[i], qFilePos[(i+1)])); } + } + if(qFileName == "") { qLines = lines; } //files with duds #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) if(processors == 1){ - ifstream inFASTA; - int numSeqs; - openInputFile(fastaFile, inFASTA); - getNumSeqs(inFASTA, numSeqs); - inFASTA.close(); - - lines.push_back(new linePair(0, numSeqs)); - - driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]); + + driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]); for (int j = 0; j < fastaFileNames.size(); j++) { rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str()); } + if(qFileName != ""){ + for (int j = 0; j < qualFileNames.size(); j++) { + rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str()); + } + } }else{ - setLines(fastaFile, lines); - if(qFileName == "") { qLines = lines; } - - createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames); + createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames); rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str()); rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str()); rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str()); + + if(qFileName != ""){ + rename((trimQualFile + toString(processIDS[0]) + ".temp").c_str(), trimQualFile.c_str()); + rename((scrapQualFile + toString(processIDS[0]) + ".temp").c_str(), scrapQualFile.c_str()); + } + + for (int j = 0; j < fastaFileNames.size(); j++) { rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str()); } + if(qFileName != ""){ + for (int j = 0; j < qualFileNames.size(); j++) { + rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str()); + } + } + //append files for(int i=1;icontrol_pressed) { return 0; } #else - ifstream inFASTA; - int numSeqs; - openInputFile(fastaFile, inFASTA); - getNumSeqs(inFASTA, numSeqs); - inFASTA.close(); - - lines.push_back(new linePair(0, numSeqs)); - - driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]); + driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qlines[0]); + for (int j = 0; j < fastaFileNames.size(); j++) { + rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str()); + } + if(qFileName != ""){ + for (int j = 0; j < qualFileNames.size(); j++) { + rename((qualFileNames[j] + toString(j) + ".temp").c_str(), qualFileNames[j].c_str()); + } + } + if (m->control_pressed) { return 0; } #endif for(int i=0;i 0) { remove(fastaFileNames[i].c_str()); } else { ifstream inFASTA; string seqName; - //openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA); openInputFile(fastaFileNames[i], inFASTA); ofstream outGroups; string outGroupFilename = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "groups"; openOutputFile(outGroupFilename, outGroups); - //openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups); outputNames.push_back(outGroupFilename); string thisGroup = ""; @@ -314,6 +362,31 @@ int TrimSeqsCommand::execute(){ } } + if(qFileName != ""){ + for(int i=0;i 0) { remove(qualFileNames[i].c_str()); } + else { + ifstream inQual; + string seqName; + openInputFile(qualFileNames[i], inQual); +// ofstream outGroups; +// +// string thisGroup = ""; +// if (i > comboStarts) { +// map::iterator itCombo; +// for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){ +// if(itCombo->second == i){ thisGroup = itCombo->first; combos.erase(itCombo); break; } +// } +// } +// else{ thisGroup = groupVector[i]; } + + inQual.close(); + } + } + } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; @@ -334,7 +407,9 @@ int TrimSeqsCommand::execute(){ } /**************************************************************************************/ -int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector fastaNames, linePair* line, linePair* qline) { + +int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector fastaNames, vector qualNames, linePair* line, linePair* qline) { + try { ofstream outFASTA; @@ -343,95 +418,128 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string ofstream scrapFASTA; openOutputFile(scrapFile, scrapFASTA); + ofstream outQual; + ofstream scrapQual; + if(qFileName != ""){ + openOutputFile(trimQFile, outQual); + openOutputFile(scrapQFile, scrapQual); + } + ofstream outGroups; vector fastaFileNames; + vector qualFileNames; + + if (oligoFile != "") { openOutputFile(groupFile, outGroups); for (int i = 0; i < fastaNames.size(); i++) { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); + if(qFileName != ""){ + qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate)); + } #else fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate)); + if(qFileName != ""){ + qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate)); + } #endif } } ifstream inFASTA; openInputFile(filename, inFASTA); + inFASTA.seekg(line->start); ifstream qFile; - if(qFileName != "") { openInputFile(qFileName, qFile); } + if(qFileName != "") { openInputFile(qFileName, qFile); qFile.seekg(qline->start); } - qFile.seekg(qline->start); - inFASTA.seekg(line->start); - - for(int i=0;inum;i++){ + bool done = false; + int count = 0; + + while (!done) { if (m->control_pressed) { - inFASTA.close(); outFASTA.close(); scrapFASTA.close(); if (oligoFile != "") { outGroups.close(); } if(qFileName != "") { qFile.close(); } + inFASTA.close(); outFASTA.close(); scrapFASTA.close(); + if (oligoFile != "") { outGroups.close(); } + for(int i=0;iclose(); delete fastaFileNames[i]; } + + if(qFileName != ""){ + qFile.close(); + for(int i=0;iclose(); delete qualFileNames[i]; } + } for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; } int success = 1; - Sequence currSeq(inFASTA); - + Sequence currSeq(inFASTA); gobble(inFASTA); + QualityScores currQual; + if(qFileName != ""){ + currQual = QualityScores(qFile, currSeq.getNumBases()); gobble(qFile); + } + string origSeq = currSeq.getUnaligned(); if (origSeq != "") { int groupBar, groupPrime; string trashCode = ""; int currentSeqsDiffs = 0; - + if(qFileName != ""){ - if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); } - else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); } - + 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); } + if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) { success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap } - if(!success) { trashCode += 'q'; } + if(!success) { trashCode += 'q'; } } if(barcodes.size() != 0){ - success = stripBarcode(currSeq, groupBar); - if(success > bdiffs){ trashCode += 'b'; } + success = stripBarcode(currSeq, currQual, groupBar); + if(success > bdiffs) { trashCode += 'b'; } else{ currentSeqsDiffs += success; } } if(numFPrimers != 0){ - success = stripForward(currSeq, groupPrime); - if(success > pdiffs){ trashCode += 'f'; } + success = stripForward(currSeq, currQual, groupPrime); + if(success > pdiffs) { trashCode += 'f'; } else{ currentSeqsDiffs += success; } } - if (currentSeqsDiffs > tdiffs) { trashCode += 't'; } + if (currentSeqsDiffs > tdiffs) { trashCode += 't'; } if(numRPrimers != 0){ - success = stripReverse(currSeq); - if(!success){ trashCode += 'r'; } + success = stripReverse(currSeq, currQual); + if(!success) { trashCode += 'r'; } } if(minLength > 0 || maxLength > 0){ success = cullLength(currSeq); - if(!success){ trashCode += 'l'; } + if(!success) { trashCode += 'l'; } } if(maxHomoP > 0){ success = cullHomoP(currSeq); - if(!success){ trashCode += 'h'; } + if(!success) { trashCode += 'h'; } } if(maxAmbig != -1){ success = cullAmbigs(currSeq); - if(!success){ trashCode += 'n'; } + if(!success) { trashCode += 'n'; } } - if(flip){ currSeq.reverseComplement(); } // should go last + if(flip){ currSeq.reverseComplement(); currQual.flipQScores(); } // should go last if(trashCode.length() == 0){ currSeq.setAligned(currSeq.getUnaligned()); currSeq.printSequence(outFASTA); + currQual.printQScores(outQual); + if(barcodes.size() != 0){ string thisGroup = groupVector[groupBar]; int indexToFastaFile = groupBar; @@ -443,9 +551,12 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string } } outGroups << currSeq.getName() << '\t' << thisGroup << endl; - if(allFiles){ - currSeq.printSequence(*fastaFileNames[indexToFastaFile]); + currSeq.printSequence(*fastaFileNames[indexToFastaFile]); + + if(qFileName != ""){ + currQual.printQScores(*qualFileNames[indexToFastaFile]); + } } } } @@ -454,31 +565,51 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string currSeq.setUnaligned(origSeq); currSeq.setAligned(origSeq); currSeq.printSequence(scrapFASTA); + currQual.printQScores(scrapQual); } + count++; } - gobble(inFASTA); + + unsigned long int pos = inFASTA.tellg(); + if ((pos == -1) || (pos >= line->end)) { break; } + + //report progress + if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } + } + //report progress + if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } + inFASTA.close(); outFASTA.close(); scrapFASTA.close(); if (oligoFile != "") { outGroups.close(); } - if(qFileName != "") { qFile.close(); } + if(qFileName != "") { qFile.close(); scrapQual.close(); outQual.close(); } for(int i=0;iclose(); delete fastaFileNames[i]; } - return 0; + if(qFileName != ""){ + for(int i=0;iclose(); + delete qualFileNames[i]; + } + } + + return count; } catch(exception& e) { m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim"); exit(1); } } + /**************************************************************************************************/ -int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector fastaNames) { + +int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector fastaNames, vector qualNames) { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 0; @@ -493,7 +624,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName 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){ - driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, lines[process], qLines[process]); + driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (trimQFile + toString(getpid()) + ".temp"), (scrapQFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, qualNames, lines[process], qLines[process]); exit(0); }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); } } @@ -512,35 +643,73 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName exit(1); } } + /**************************************************************************************************/ -int TrimSeqsCommand::setLines(string filename, vector& lines) { +int TrimSeqsCommand::setLines(string filename, string qfilename, vector& fastaFilePos, vector& qfileFilePos) { try { - lines.clear(); + //set file positions for fasta file + fastaFilePos = divideFile(filename, processors); - vector positions; + if (qfilename == "") { return processors; } - ifstream inFASTA; - openInputFile(filename, inFASTA); + //get name of first sequence in each chunk + map firstSeqNames; + for (int i = 0; i < (fastaFilePos.size()-1); i++) { + ifstream in; + openInputFile(filename, in); + in.seekg(fastaFilePos[i]); + + Sequence temp(in); + firstSeqNames[temp.getName()] = i; + + in.close(); + } + + //seach for filePos of each first name in the qfile and save in qfileFilePos + ifstream inQual; + openInputFile(qfilename, inQual); string input; - while(!inFASTA.eof()){ - input = getline(inFASTA); + while(!inQual.eof()){ + input = getline(inQual); if (input.length() != 0) { - if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } + if(input[0] == '>'){ //this is a sequence name line + istringstream nameStream(input); + + string sname = ""; nameStream >> sname; + sname = sname.substr(1); + + map::iterator it = firstSeqNames.find(sname); + + if(it != firstSeqNames.end()) { //this is the start of a new chunk + unsigned long int pos = inQual.tellg(); + qfileFilePos.push_back(pos - input.length() - 1); + firstSeqNames.erase(it); + } + } } + + if (firstSeqNames.size() == 0) { break; } } - inFASTA.close(); + inQual.close(); - int numFastaSeqs = positions.size(); - + if (firstSeqNames.size() != 0) { + for (map::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) { + m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine(); + } + qFileName = ""; + return processors; + } + + //get last file position of qfile FILE * pFile; - long size; + unsigned long int size; //get num bytes in file - pFile = fopen (filename.c_str(),"rb"); + pFile = fopen (qfilename.c_str(),"rb"); if (pFile==NULL) perror ("Error opening file"); else{ fseek (pFile, 0, SEEK_END); @@ -548,20 +717,9 @@ int TrimSeqsCommand::setLines(string filename, vector& lines) { fclose (pFile); } - int numSeqsPerProcessor = numFastaSeqs / processors; + qfileFilePos.push_back(size); - for (int i = 0; i < processors; i++) { - - long int startPos = positions[ i * numSeqsPerProcessor ]; - if(i == processors - 1){ - numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; - }else{ - long int myEnd = positions[ (i+1) * numSeqsPerProcessor ]; - } - lines.push_back(new linePair(startPos, numSeqsPerProcessor)); - } - - return numFastaSeqs; + return processors; } catch(exception& e) { m->errorOut(e, "TrimSeqsCommand", "setLines"); @@ -570,7 +728,7 @@ int TrimSeqsCommand::setLines(string filename, vector& lines) { } //*************************************************************************************************************** -void TrimSeqsCommand::getOligos(vector& outFASTAVec){ //vector& outFASTAVec +void TrimSeqsCommand::getOligos(vector& outFASTAVec, vector& outQualVec){ try { ifstream inOligos; openInputFile(oligoFile, inOligos); @@ -583,11 +741,14 @@ void TrimSeqsCommand::getOligos(vector& outFASTAVec){ //vector> type; - + if(type[0] == '#'){ while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there } else{ + //make type case insensitive + for(int i=0;i> oligo; for(int i=0;i& outFASTAVec){ //vector& outFASTAVec){ //vector> group; //check for repeat barcodes @@ -636,8 +809,12 @@ void TrimSeqsCommand::getOligos(vector& outFASTAVec){ //vectormothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); } } @@ -652,9 +829,14 @@ void TrimSeqsCommand::getOligos(vector& outFASTAVec){ //vector::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) { for (map::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) { if (groupVector[itPrime->second] != "") { //there is a group for this primer - outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(itBar->second) + "." + groupVector[itBar->second] + "." + toString(itPrime->second) + "." + groupVector[itPrime->second] + ".fasta")); - outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + toString(itBar->second) + "." + groupVector[itBar->second] + "." + toString(itPrime->second) + "." + groupVector[itPrime->second] + ".fasta")); + outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta")); + outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta")); combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1; + + if(qFileName != ""){ + outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual")); + outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual")); + } } } } @@ -671,7 +853,7 @@ void TrimSeqsCommand::getOligos(vector& outFASTAVec){ //vectorsecond; seq.setUnaligned(rawSequence.substr(oligo.length())); + + if(qual.getName() != ""){ + qual.trimQScores(oligo.length(), -1); + } + success = 0; break; } @@ -770,6 +957,10 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){ else{ //use the best match group = minGroup; seq.setUnaligned(rawSequence.substr(minPos)); + + if(qual.getName() != ""){ + qual.trimQScores(minPos, -1); + } success = minDiff; } @@ -790,7 +981,7 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){ //*************************************************************************************************************** -int TrimSeqsCommand::stripForward(Sequence& seq, int& group){ +int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){ try { string rawSequence = seq.getUnaligned(); int success = pdiffs + 1; //guilty until proven innocent @@ -806,6 +997,10 @@ int TrimSeqsCommand::stripForward(Sequence& seq, int& group){ if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){ group = it->second; seq.setUnaligned(rawSequence.substr(oligo.length())); + if(qual.getName() != ""){ + qual.trimQScores(oligo.length(), -1); + + } success = 0; break; } @@ -888,6 +1083,9 @@ int TrimSeqsCommand::stripForward(Sequence& seq, int& group){ else{ //use the best match group = minGroup; seq.setUnaligned(rawSequence.substr(minPos)); + if(qual.getName() != ""){ + qual.trimQScores(minPos, -1); + } success = minDiff; } @@ -906,7 +1104,7 @@ int TrimSeqsCommand::stripForward(Sequence& seq, int& group){ //*************************************************************************************************************** -bool TrimSeqsCommand::stripReverse(Sequence& seq){ +bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){ try { string rawSequence = seq.getUnaligned(); bool success = 0; //guilty until proven innocent @@ -921,6 +1119,9 @@ bool TrimSeqsCommand::stripReverse(Sequence& seq){ if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){ seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length())); + if(qual.getName() != ""){ + qual.trimQScores(-1, rawSequence.length()-oligo.length()); + } success = 1; break; } @@ -1054,9 +1255,9 @@ int TrimSeqsCommand::countDiffs(string oligo, string seq){ else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; } else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; } else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { countDiffs++; } - else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; } - + else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; } } + } return countDiffs; @@ -1069,102 +1270,76 @@ int TrimSeqsCommand::countDiffs(string oligo, string seq){ } //*************************************************************************************************************** -bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){ - try { +//bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){ +// try { +// // string rawSequence = seq.getUnaligned(); -// int seqLength; // = rawSequence.length(); -// string name, temp, temp2; +// int seqLength = seq.getNumBases(); +// bool success = 0; //guilty until proven innocent +// string name; // // qFile >> name; +// if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } } +// +// while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } } +// +// int score; +// int end = seqLength; // -// //get rest of line -// temp = ""; -// while (!qFile.eof()) { -// char c = qFile.get(); -// if (c == 10 || c == 13){ break; } -// else { temp += c; } -// } -// -// int pos = temp.find("length"); -// if (pos == temp.npos) { m->mothurOut("Cannot find length in qfile for " + seq.getName()); m->mothurOutEndLine(); seqLength = 0; } -// else { -// string tempLength = temp.substr(pos); -// istringstream iss (tempLength,istringstream::in); -// iss >> temp; +// for(int i=0;i> score; +// +// if(score < qThreshold){ +// end = i; +// break; +// } +// } +// for(int i=end+1;i> score; // } // -// splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242 -// convert(temp, seqLength); //converts string to int -// -// if (name.length() != 0) { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); } } - - string rawSequence = seq.getUnaligned(); - int seqLength = seq.getNumBases(); - bool success = 0; //guilty until proven innocent - string name; - - qFile >> name; - if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } } - - while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } } - - int score; - int end = seqLength; - - for(int i=0;i> score; - - if(score < qThreshold){ - end = i; - break; - } - } - for(int i=end+1;i> score; - } - - seq.setUnaligned(rawSequence.substr(0,end)); - - return 1; - } - catch(exception& e) { - m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold"); - exit(1); - } -} +// seq.setUnaligned(rawSequence.substr(0,end)); +// +// return 1; +// } +// catch(exception& e) { +// m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold"); +// exit(1); +// } +//} //*************************************************************************************************************** -bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){ - try { - string rawSequence = seq.getUnaligned(); - int seqLength = seq.getNumBases(); - bool success = 0; //guilty until proven innocent - string name; - - qFile >> name; - if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } } - - while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } } - - float score; - float average = 0; - - for(int i=0;i> score; - average += score; - } - average /= seqLength; - - if(average >= qAverage) { success = 1; } - else { success = 0; } - - return success; - } - catch(exception& e) { - m->errorOut(e, "TrimSeqsCommand", "cullQualAverage"); - exit(1); - } -} +//bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){ +// try { +// string rawSequence = seq.getUnaligned(); +// int seqLength = seq.getNumBases(); +// bool success = 0; //guilty until proven innocent +// string name; +// +// qFile >> name; +// if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } } +// +// while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } } +// +// float score; +// float average = 0; +// +// for(int i=0;i> score; +// average += score; +// } +// average /= seqLength; +// +// if(average >= qAverage) { success = 1; } +// else { success = 0; } +// +// return success; +// } +// catch(exception& e) { +// m->errorOut(e, "TrimSeqsCommand", "cullQualAverage"); +// exit(1); +// } +//} //***************************************************************************************************************