X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimseqscommand.cpp;h=951ce65d400bb36afc60df92e56e148c14ee271c;hp=4128142448b8412314dc2b1d8ce057c6e8527519;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=372fb21ea66ced432b109225851a1b80ef0491a3 diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp index 4128142..951ce65 100644 --- a/trimseqscommand.cpp +++ b/trimseqscommand.cpp @@ -34,6 +34,7 @@ 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); @@ -61,7 +62,7 @@ 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"; @@ -84,6 +85,7 @@ 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"; @@ -329,6 +331,9 @@ 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); @@ -422,7 +427,7 @@ int TrimSeqsCommand::execute(){ if (countfile != "") { CountTable ct; - ct.readTable(countfile, true); + ct.readTable(countfile, true, false); nameCount = ct.getNameMap(); outputNames.push_back(trimCountFile); outputNames.push_back(scrapCountFile); @@ -444,8 +449,6 @@ 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 @@ -540,7 +543,7 @@ int TrimSeqsCommand::execute(){ if (countfile != "") { //create countfile with group info included CountTable* ct = new CountTable(); - ct->readTable(trimCountFile, true); + ct->readTable(trimCountFile, true, false); map justTrimmedNames = ct->getNameMap(); delete ct; @@ -695,7 +698,21 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string 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(); + int index = rpairedBarcodes.size(); + for (map::iterator it = barcodes.begin(); it != barcodes.end(); it++) { + oligosPair tempPair("", reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode + rpairedBarcodes[index] = tempPair; index++; + //cout << reverseOligo((it->second).reverse) << '\t' << (reverseOligo((it->second).forward)) << '\t' << barcodeNameVector[it->first] << endl; + } + + index = rpairedPrimers.size(); + for (map::iterator it = primers.begin(); it != primers.end(); it++) { + oligosPair tempPair("", reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode + rpairedPrimers[index] = tempPair; index++; + //cout << reverseOligo((it->second).reverse) << '\t' << (reverseOligo((it->second).forward)) << '\t' << primerNameVector[it->first] << endl; + } + + rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes); numBarcodes = rpairedBarcodes.size(); } while (moreSeqs) { @@ -819,9 +836,9 @@ 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 @@ -1174,7 +1191,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName 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, + qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage, logtransform, minLength, maxAmbig, maxHomoP, maxLength, flip, reorient, nameMap, nameCount); pDataArray.push_back(tempTrim); @@ -1646,7 +1663,7 @@ 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; }