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);
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, "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"; }
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 (countfile != "") {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, true, false);
nameCount = ct.getNameMap();
outputNames.push_back(trimCountFile);
outputNames.push_back(scrapCountFile);
}
}
- 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
if (countfile != "") { //create countfile with group info included
CountTable* ct = new CountTable();
- ct->readTable(trimCountFile);
+ ct->readTable(trimCountFile, true, false);
map<string, int> justTrimmedNames = ct->getNameMap();
delete ct;
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 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;
}
else{ currentSeqsDiffs += success; }
}
-
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
if(numSpacers != 0){
success = trimOligos->stripSpacer(currSeq, currQual);
if(success > sdiffs) { trashCode += 's'; }
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"; }
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);
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<string, int>::iterator it = firstSeqNames.find(sname);
projects / mothur.git / blobdiff