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);
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 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";
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);
}
}
- 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
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<string, int>::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<string, int>::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) {
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
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);
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; }
projects / mothur.git / blobdiff