X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=5a0124934bfaeb682914d62aff34a25f04b4a3ab;hb=0fb6d165c8dc8dc7153a101513a05f457431d0bc;hp=259adc1485222c2070e44c2f1b0bb32e3c86815d;hpb=21784ce4eb9b292db6f6191ed504f5e20754c810;p=mothur.git diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp index 259adc1..5a01249 100644 --- a/trimseqscommand.cpp +++ b/trimseqscommand.cpp @@ -8,48 +8,203 @@ */ #include "trimseqscommand.h" +#include "needlemanoverlap.hpp" //*************************************************************************************************************** -TrimSeqsCommand::TrimSeqsCommand(){ +TrimSeqsCommand::TrimSeqsCommand(string option) { try { - globaldata = GlobalData::getInstance(); + abort = false; + comboStarts = 0; - oligos = 0; - - if(globaldata->getFastaFile() == ""){ - cout << "you need to at least enter a fasta file name" << endl; - } - - if(isTrue(globaldata->getFlip())) { flip = 1; } - if(globaldata->getOligosFile() != "") { oligos = 1; } - - if(globaldata->getMaxAmbig() != "-1") { maxAmbig = atoi(globaldata->getMaxAmbig().c_str()); } - else { maxAmbig = -1; } - - if(globaldata->getMaxHomoPolymer() != "-1") { maxHomoP = atoi(globaldata->getMaxHomoPolymer().c_str()); } - else { maxHomoP = 0; } + //allow user to run help + if(option == "help") { help(); abort = true; } - if(globaldata->getMinLength() != "-1") { minLength = atoi(globaldata->getMinLength().c_str()); } - else { minLength = 0; } + else { + //valid paramters for this command + string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", + "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"}; + + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::iterator it; + + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //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); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("fasta"); + //user has given a template file + if(it != parameters.end()){ + path = hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["fasta"] = inputDir + it->second; } + } + + it = parameters.find("oligos"); + //user has given a template file + if(it != parameters.end()){ + path = 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("qfile"); + //user has given a template file + if(it != parameters.end()){ + path = hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["qfile"] = inputDir + it->second; } + } + } + + + //check for required parameters + fastaFile = validParameter.validFile(parameters, "fasta", true); + if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; } + else if (fastaFile == "not open") { 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 = ""; + outputDir += hasPath(fastaFile); //if user entered a file with a path then preserve it + } - if(globaldata->getMaxLength() != "-1") { maxLength = atoi(globaldata->getMaxLength().c_str()); } - else { maxLength = 0; } + + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + string temp; + temp = validParameter.validFile(parameters, "flip", false); + if (temp == "not found"){ flip = 0; } + else if(isTrue(temp)) { flip = 1; } - if(!flip && !oligos && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP ){ cout << "huh?" << endl; } + temp = validParameter.validFile(parameters, "oligos", true); + if (temp == "not found"){ oligoFile = ""; } + else if(temp == "not open"){ abort = true; } + else { oligoFile = temp; } + + temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; } + convert(temp, maxAmbig); + + temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "0"; } + convert(temp, maxHomoP); + + temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; } + convert(temp, minLength); + + 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); + + temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; } + convert(temp, pdiffs); + + temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs; temp = toString(tempTotal); } + convert(temp, tdiffs); + + if(tdiffs == 0){ tdiffs = bdiffs + pdiffs; } + + temp = validParameter.validFile(parameters, "qfile", true); + if (temp == "not found") { qFileName = ""; } + else if(temp == "not open") { abort = true; } + else { qFileName = temp; } + + 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"; } + 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"; } + convert(temp, processors); + + if(allFiles && oligoFile == ""){ + m->mothurOut("You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request."); m->mothurOutEndLine(); + } + if((qAverage != 0 && qThreshold != 0) && qFileName == ""){ + m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine(); + qAverage=0; + qThreshold=0; + } + if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){ + m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine(); + abort = true; + } + } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the TrimSeqsCommand class function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** + +void TrimSeqsCommand::help(){ + try { + m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n"); + m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n"); + m->mothurOut("The fasta parameter is required.\n"); + m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n"); + m->mothurOut("The oligos parameter .... The default is "".\n"); + m->mothurOut("The maxambig parameter .... The default is -1.\n"); + m->mothurOut("The maxhomop parameter .... The default is 0.\n"); + m->mothurOut("The minlength parameter .... The default is 0.\n"); + m->mothurOut("The maxlength parameter .... The default is 0.\n"); + m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n"); + m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n"); + m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n"); + m->mothurOut("The qfile parameter .....\n"); + m->mothurOut("The qthreshold parameter .... The default is 0.\n"); + m->mothurOut("The qaverage parameter .... The default is 0.\n"); + m->mothurOut("The allfiles parameter .... The default is F.\n"); + m->mothurOut("The qtrim parameter .... The default is F.\n"); + m->mothurOut("The trim.seqs command should be in the following format: \n"); + m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, \n"); + m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n"); + m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"); + m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n"); + + } + catch(exception& e) { + m->errorOut(e, "TrimSeqsCommand", "help"); exit(1); - } + } } + //*************************************************************************************************************** TrimSeqsCommand::~TrimSeqsCommand(){ /* do nothing */ } @@ -58,241 +213,1098 @@ TrimSeqsCommand::~TrimSeqsCommand(){ /* do nothing */ } int TrimSeqsCommand::execute(){ try{ - getOligos(); + + if (abort == true) { return 0; } - ifstream inFASTA; - openInputFile(globaldata->getFastaFile(), inFASTA); - - ofstream outFASTA; - string trimSeqFile = getRootName(globaldata->getFastaFile()) + "trim.fasta"; - openOutputFile(trimSeqFile, outFASTA); + numFPrimers = 0; //this needs to be initialized + numRPrimers = 0; - ofstream outGroups; - string groupFile = getRootName(globaldata->getFastaFile()) + "groups"; - openOutputFile(groupFile, outGroups); - - ofstream scrapFASTA; - string scrapSeqFile = getRootName(globaldata->getFastaFile()) + "scrap.fasta"; - openOutputFile(scrapSeqFile, scrapFASTA); + string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta"; + 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, qualFileNames); + } + + if(qFileName != "") { setLines(qFileName, qLines); } - bool success; - while(!inFASTA.eof()){ - Sequence currSeq(inFASTA); - string origSeq = currSeq.getUnaligned(); - string group; - string trashCode = ""; + #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, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[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()); + } + } - if(barcodes.size() != 0){ - success = stripBarcode(currSeq, group); - if(!success){ trashCode += 'b'; } - } - if(numFPrimers != 0){ - success = stripForward(currSeq); - if(!success){ trashCode += 'f'; } + }else{ + setLines(fastaFile, lines); + if(qFileName == "") { qLines = lines; } + + 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(); + qFile.close(); + lines.push_back(new linePair(0, numSeqs)); + + driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[0]); + + if (m->control_pressed) { return 0; } + #endif + + + for(int i=0;i 0) { remove(fastaFileNames[i].c_str()); } + else { + ifstream inFASTA; + string seqName; + openInputFile(fastaFileNames[i], inFASTA); + ofstream outGroups; + string outGroupFilename = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "groups"; + openOutputFile(outGroupFilename, outGroups); + outputNames.push_back(outGroupFilename); + + 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]; } + + while(!inFASTA.eof()){ + if(inFASTA.get() == '>'){ + inFASTA >> seqName; + outGroups << seqName << '\t' << thisGroup << endl; + } + while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } } + } + outGroups.close(); + inFASTA.close(); } - if(numRPrimers != 0){ - success = stripReverse(currSeq); - if(!success){ trashCode += 'r'; } + } + + 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(minLength > 0 || maxLength > 0){ - success = cullLength(currSeq); - if(!success){ trashCode += 'l'; } + } + + + if (m->control_pressed) { + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "TrimSeqsCommand", "execute"); + exit(1); + } +} + +/**************************************************************************************/ + +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; + int able = openOutputFile(trimFile, outFASTA); + + 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 } - if(maxHomoP > 0){ - success = cullHomoP(currSeq); - if(!success){ trashCode += 'h'; } + } + + ifstream inFASTA; + openInputFile(filename, inFASTA); + + ifstream qFile; + if(qFileName != "") { openInputFile(qFileName, qFile); } + + qFile.seekg(qline->start); + inFASTA.seekg(line->start); + + for(int i=0;inum;i++){ + + if (m->control_pressed) { + 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; } - if(maxAmbig != -1){ - success = cullAmbigs(currSeq); - if(!success){ trashCode += 'n'; } + + int success = 1; + + Sequence currSeq(inFASTA); + QualityScores currQual; + if(qFileName != ""){ + currQual = QualityScores(qFile); } - if(flip){ currSeq.reverseComplement(); } // should go last + string origSeq = currSeq.getUnaligned(); + if (origSeq != "") { + int groupBar, groupPrime; + string trashCode = ""; + int currentSeqsDiffs = 0; - if(trashCode.length() == 0){ - currSeq.printSequence(outFASTA); - outGroups << currSeq.getName() << '\t' << group << endl; - } - else{ - currSeq.setName(currSeq.getName() + '|' + trashCode); - currSeq.setUnaligned(origSeq); - currSeq.printSequence(scrapFASTA); - } + if(qFileName != ""){ + 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(barcodes.size() != 0){ + success = stripBarcode(currSeq, currQual, groupBar); + if(success > bdiffs) { trashCode += 'b'; } + else{ currentSeqsDiffs += success; } + } + + if(numFPrimers != 0){ + success = stripForward(currSeq, currQual, groupPrime); + if(success > pdiffs) { trashCode += 'f'; } + else{ currentSeqsDiffs += success; } + } + + if (currentSeqsDiffs > tdiffs) { trashCode += 't'; } + + if(numRPrimers != 0){ + success = stripReverse(currSeq, currQual); + if(!success) { trashCode += 'r'; } + } + + if(minLength > 0 || maxLength > 0){ + success = cullLength(currSeq); + if(!success) { trashCode += 'l'; } + } + if(maxHomoP > 0){ + success = cullHomoP(currSeq); + if(!success) { trashCode += 'h'; } + } + if(maxAmbig != -1){ + success = cullAmbigs(currSeq); + if(!success) { trashCode += 'n'; } + } + + 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; + if (primers.size() != 0){ + //does this primer have a group + if (groupVector[groupPrime] != "") { + thisGroup += "." + groupVector[groupPrime]; + indexToFastaFile = combos[thisGroup]; + } + } + outGroups << currSeq.getName() << '\t' << thisGroup << endl; + if(allFiles){ + currSeq.printSequence(*fastaFileNames[indexToFastaFile]); + + if(qFileName != ""){ + currQual.printQScores(*qualFileNames[indexToFastaFile]); + } + } + } + } + else{ + currSeq.setName(currSeq.getName() + '|' + trashCode); + currSeq.setUnaligned(origSeq); + currSeq.setAligned(origSeq); + currSeq.printSequence(scrapFASTA); + currQual.printQScores(scrapQual); + } + } gobble(inFASTA); + gobble(qFile); } + inFASTA.close(); outFASTA.close(); scrapFASTA.close(); - outGroups.close(); + if (oligoFile != "") { outGroups.close(); } + if(qFileName != "") { qFile.close(); scrapQual.close(); outQual.close(); } + + for(int i=0;iclose(); + delete fastaFileNames[i]; + } + + if(qFileName != ""){ + for(int i=0;iclose(); + delete qualFileNames[i]; + } + } - return 0; + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the TrimSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} + +/**************************************************************************************************/ + +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; + int exitCommand = 1; + processIDS.clear(); + + //loop through and create all the processes you want + while (process != processors) { + 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){ + 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); } + } + + //force parent to wait until all the processes are done + for (int i=0;ierrorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim"); exit(1); } } -//*************************************************************************************************************** +/**************************************************************************************************/ -void TrimSeqsCommand::getOligos(){ - - ifstream inOligos; - openInputFile(globaldata->getOligosFile(), inOligos); +int TrimSeqsCommand::setLines(string filename, vector& lines) { + try { + + lines.clear(); + + vector positions; + + ifstream inFASTA; + openInputFile(filename, inFASTA); + + string input; + while(!inFASTA.eof()){ + input = getline(inFASTA); - string type, oligo, group; + if (input.length() != 0) { + if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } + } + } + inFASTA.close(); + + int numFastaSeqs = positions.size(); - while(!inOligos.eof()){ - inOligos >> type; + FILE * pFile; + unsigned long int size; - if(type == "forward"){ - inOligos >> oligo; - forPrimer.push_back(oligo); + //get num bytes in file + pFile = fopen (filename.c_str(),"rb"); + if (pFile==NULL) perror ("Error opening file"); + else{ + fseek (pFile, 0, SEEK_END); + size=ftell (pFile); + fclose (pFile); } - else if(type == "reverse"){ - inOligos >> oligo; - revPrimer.push_back(oligo); + + int numSeqsPerProcessor = numFastaSeqs / processors; + + for (int i = 0; i < processors; i++) { + + unsigned long int startPos = positions[ i * numSeqsPerProcessor ]; + if(i == processors - 1){ + numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; + }else{ + unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ]; + } + lines.push_back(new linePair(startPos, numSeqsPerProcessor)); } - else if(type == "barcode"){ - inOligos >> oligo >> group; - barcodes[oligo]=group; + + return numFastaSeqs; + } + catch(exception& e) { + m->errorOut(e, "TrimSeqsCommand", "setLines"); + exit(1); + } +} +//*************************************************************************************************************** + +void TrimSeqsCommand::getOligos(vector& outFASTAVec, vector& outQualVec){ + try { + ifstream inOligos; + openInputFile(oligoFile, inOligos); + + ofstream test; + + string type, oligo, group; + int index=0; + //int indexPrimer = 0; + + while(!inOligos.eof()){ + inOligos >> 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::iterator itPrime = primers.find(oligo); + if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); } + + primers[oligo]=index; index++; + groupVector.push_back(group); + + if(allFiles){ + outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta")); + if(qFileName != ""){ + outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual")); + } + if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct + filesToRemove.insert((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta")); + if(qFileName != ""){ + filesToRemove.insert((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual")); + } + }else { + outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta")); + if(qFileName != ""){ + outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual")); + } + } + } + + } + else if(type == "REVERSE"){ + Sequence oligoRC("reverse", oligo); + oligoRC.reverseComplement(); + revPrimer.push_back(oligoRC.getUnaligned()); + } + else if(type == "BARCODE"){ + inOligos >> group; + + //check for repeat barcodes + map::iterator itBar = barcodes.find(oligo); + if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); } + + barcodes[oligo]=index; index++; + groupVector.push_back(group); + + if(allFiles){ + outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta")); + outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta")); + if(qFileName != ""){ + outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual")); + outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual")); + } + } + }else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); } + } + gobble(inOligos); } - else if(type[0] == '#'){ - char c; - while ((c = inOligos.get()) != EOF) { if (c == 10){ break; } } // get rest of line + + inOligos.close(); + + //add in potential combos + if(allFiles){ + comboStarts = outFASTAVec.size()-1; + for (map::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(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")); + } + } + } + } } - gobble(inOligos); + numFPrimers = primers.size(); + numRPrimers = revPrimer.size(); + + } + catch(exception& e) { + m->errorOut(e, "TrimSeqsCommand", "getOligos"); + exit(1); } - - numFPrimers = forPrimer.size(); - numRPrimers = revPrimer.size(); } - //*************************************************************************************************************** -bool TrimSeqsCommand::stripBarcode(Sequence& seq, string& group){ - - string rawSequence = seq.getUnaligned(); - bool success = 0; //guilty until proven innocent - - for(map::iterator it=barcodes.begin();it!=barcodes.end();it++){ - string oligo = it->first; +int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){ + try { - if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length - success = 0; - break; + string rawSequence = seq.getUnaligned(); + int success = bdiffs + 1; //guilty until proven innocent + + //can you find the barcode + for(map::iterator it=barcodes.begin();it!=barcodes.end();it++){ + string oligo = it->first; + if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length + success = bdiffs + 10; //if the sequence is shorter than the barcode then bail out + break; + } + + 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; + } } - if (rawSequence.compare(0,oligo.length(),oligo) == 0){ - group = it->second; - seq.setUnaligned(rawSequence.substr(oligo.length())); - success = 1; - break; + //if you found the barcode or if you don't want to allow for diffs +// cout << success; + if ((bdiffs == 0) || (success == 0)) { return success; } + + else { //try aligning and see if you can find it +// cout << endl; + + int maxLength = 0; + + Alignment* alignment; + if (barcodes.size() > 0) { + map::iterator it=barcodes.begin(); + + for(it;it!=barcodes.end();it++){ + if(it->first.length() > maxLength){ + maxLength = it->first.length(); + } + } + alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1)); + + }else{ alignment = NULL; } + + //can you find the barcode + int minDiff = 1e6; + int minCount = 1; + int minGroup = -1; + int minPos = 0; + + for(map::iterator it=barcodes.begin();it!=barcodes.end();it++){ + string oligo = it->first; +// int length = oligo.length(); + + if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length + success = bdiffs + 10; + break; + } + + //use needleman to align first barcode.length()+numdiffs of sequence to each barcode + alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs)); + oligo = alignment->getSeqAAln(); + string temp = alignment->getSeqBAln(); + + int alnLength = oligo.length(); + + for(int i=oligo.length()-1;i>=0;i--){ + if(oligo[i] != '-'){ alnLength = i+1; break; } + } + oligo = oligo.substr(0,alnLength); + temp = temp.substr(0,alnLength); + + int newStart=0; + int numDiff = countDiffs(oligo, temp); + +// cout << oligo << '\t' << temp << '\t' << numDiff << endl; + + if(numDiff < minDiff){ + minDiff = numDiff; + minCount = 1; + minGroup = it->second; + minPos = 0; + for(int i=0;i bdiffs) { success = minDiff; } //no good matches + else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes + else{ //use the best match + group = minGroup; + seq.setUnaligned(rawSequence.substr(minPos)); + + if(qual.getName() != ""){ + qual.trimQScores(minPos, -1); + } + success = minDiff; + } + + if (alignment != NULL) { delete alignment; } + } +// cout << success << endl; + + return success; + } - return success; - + catch(exception& e) { + m->errorOut(e, "TrimSeqsCommand", "stripBarcode"); + exit(1); + } + } //*************************************************************************************************************** -bool TrimSeqsCommand::stripForward(Sequence& seq){ - - string rawSequence = seq.getUnaligned(); - bool success = 0; //guilty until proven innocent - - for(int i=0;i::iterator it=primers.begin();it!=primers.end();it++){ + string oligo = it->first; + if(rawSequence.length() < oligo.length()){ //let's just assume that the primers are the same length + success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out + break; + } + + 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; + } } + + //if you found the barcode or if you don't want to allow for diffs +// cout << success; + if ((pdiffs == 0) || (success == 0)) { return success; } + + else { //try aligning and see if you can find it +// cout << endl; + + int maxLength = 0; + + Alignment* alignment; + if (primers.size() > 0) { + map::iterator it=primers.begin(); + + for(it;it!=primers.end();it++){ + if(it->first.length() > maxLength){ + maxLength = it->first.length(); + } + } + alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1)); + + }else{ alignment = NULL; } + + //can you find the barcode + int minDiff = 1e6; + int minCount = 1; + int minGroup = -1; + int minPos = 0; + + for(map::iterator it=primers.begin();it!=primers.end();it++){ + string oligo = it->first; +// int length = oligo.length(); + + if(rawSequence.length() < maxLength){ + success = pdiffs + 100; + break; + } + + //use needleman to align first barcode.length()+numdiffs of sequence to each barcode + alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs)); + oligo = alignment->getSeqAAln(); + string temp = alignment->getSeqBAln(); - if (rawSequence.compare(0,oligo.length(),oligo) == 0){ - seq.setUnaligned(rawSequence.substr(oligo.length())); - success = 1; - break; + int alnLength = oligo.length(); + + for(int i=oligo.length()-1;i>=0;i--){ + if(oligo[i] != '-'){ alnLength = i+1; break; } + } + oligo = oligo.substr(0,alnLength); + temp = temp.substr(0,alnLength); + + int newStart=0; + int numDiff = countDiffs(oligo, temp); + +// cout << oligo << '\t' << temp << '\t' << numDiff << endl; + + if(numDiff < minDiff){ + minDiff = numDiff; + minCount = 1; + minGroup = it->second; + minPos = 0; + for(int i=0;i pdiffs) { success = minDiff; } //no good matches + else if(minCount > 1) { success = pdiffs + 10; } //can't tell the difference between multiple primers + else{ //use the best match + group = minGroup; + seq.setUnaligned(rawSequence.substr(minPos)); + if(qual.getName() != ""){ + qual.trimQScores(minPos, -1); + } + success = minDiff; + } + + if (alignment != NULL) { delete alignment; } + } + + return success; + + } + catch(exception& e) { + m->errorOut(e, "TrimSeqsCommand", "stripForward"); + exit(1); } - - return success; - } //*************************************************************************************************************** -bool TrimSeqsCommand::stripReverse(Sequence& seq){ - - string rawSequence = seq.getUnaligned(); - bool success = 0; //guilty until proven innocent - - for(int i=0;ierrorOut(e, "TrimSeqsCommand", "stripReverse"); + exit(1); + } } //*************************************************************************************************************** bool TrimSeqsCommand::cullLength(Sequence& seq){ + try { - int length = seq.getNumBases(); - bool success = 0; //guilty until proven innocent - - if(length >= minLength && maxLength == 0) { success = 1; } - else if(length >= minLength && length <= maxLength) { success = 1; } - else { success = 0; } + int length = seq.getNumBases(); + bool success = 0; //guilty until proven innocent + + if(length >= minLength && maxLength == 0) { success = 1; } + else if(length >= minLength && length <= maxLength) { success = 1; } + else { success = 0; } + + return success; - return success; + } + catch(exception& e) { + m->errorOut(e, "TrimSeqsCommand", "cullLength"); + exit(1); + } } //*************************************************************************************************************** bool TrimSeqsCommand::cullHomoP(Sequence& seq){ - - int longHomoP = seq.getLongHomoPolymer(); - bool success = 0; //guilty until proven innocent - - if(longHomoP <= maxHomoP){ success = 1; } - else { success = 0; } - - return success; + try { + int longHomoP = seq.getLongHomoPolymer(); + bool success = 0; //guilty until proven innocent + + if(longHomoP <= maxHomoP){ success = 1; } + else { success = 0; } + + return success; + } + catch(exception& e) { + m->errorOut(e, "TrimSeqsCommand", "cullHomoP"); + exit(1); + } } //*************************************************************************************************************** bool TrimSeqsCommand::cullAmbigs(Sequence& seq){ - - int numNs = seq.getAmbigBases(); - bool success = 0; //guilty until proven innocent - - if(numNs <= maxAmbig){ success = 1; } - else { success = 0; } - - return success; + try { + int numNs = seq.getAmbigBases(); + bool success = 0; //guilty until proven innocent + + if(numNs <= maxAmbig) { success = 1; } + else { success = 0; } + + return success; + } + catch(exception& e) { + m->errorOut(e, "TrimSeqsCommand", "cullAmbigs"); + exit(1); + } } //*************************************************************************************************************** + +bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){ + try { + bool success = 1; + int length = oligo.length(); + + for(int i=0;ierrorOut(e, "TrimSeqsCommand", "compareDNASeq"); + exit(1); + } + +} +//*************************************************************************************************************** + +int TrimSeqsCommand::countDiffs(string oligo, string seq){ + try { + + int length = oligo.length(); + int countDiffs = 0; + + for(int i=0;ierrorOut(e, "TrimSeqsCommand", "countDiffs"); + exit(1); + } + +} +//*************************************************************************************************************** + +//bool TrimSeqsCommand::stripQualThreshold(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; } } +// +// 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); +// } +//} + +//*************************************************************************************************************** + +//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); +// } +//} + +//***************************************************************************************************************