CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepprimer);
+ CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pkeepdots);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
temp = validParameter.validFile(parameters, "keepprimer", false); if (temp == "not found") { temp = "f"; }
keepprimer = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "keepdots", false); if (temp == "not found") { temp = "t"; }
+ keepdots = m->isTrue(temp);
+
temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found"){ oligosfile = ""; }
else if(temp == "not open"){ oligosfile = ""; abort = true; }
m->mothurOut("[ERROR]: You did not set any options. Please provide an oligos or ecoli file, or set start or end.\n"); abort = true;
}
- if ((oligosfile == "") && (ecolifile == "") && (start < 0) && (end != -1)) { m->mothurOut("[ERROR]: Invalid start value.\n"); abort = true; }
+ if ((oligosfile == "") && (ecolifile == "") && (start < 0) && (end == -1)) { m->mothurOut("[ERROR]: Invalid start value.\n"); abort = true; }
if ((ecolifile != "") && (start != -1) && (end != -1)) {
m->mothurOut("[ERROR]: You provided an ecoli file , but set the start or end parameters. Unsure what you intend. When you provide the ecoli file, mothur thinks you want to use the start and end of the sequence in the ecoli file.\n"); abort = true;
outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
string badSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pcr.scrap.fasta";
- outputNames.push_back(badSeqFile); outputTypes["fasta"].push_back(badSeqFile);
+
length = 0;
if(oligosfile != ""){ readOligos(); } if (m->control_pressed) { return 0; }
if (m->control_pressed) { return 0; }
- writeAccnos(badNames);
+ //don't write or keep if blank
+ if (badNames.size() != 0) { writeAccnos(badNames); }
+ if (m->isBlank(badSeqFile)) { m->mothurRemove(badSeqFile); }
+ else { outputNames.push_back(badSeqFile); outputTypes["fasta"].push_back(badSeqFile); }
+
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (namefile != "") { readName(badNames); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
// Allocate memory for thread data.
- pcrData* tempPcr = new pcrData(filename, goodFileName+extension, badFileName+extension, m, oligosfile, ecolifile, primers, revPrimer, nomatch, keepprimer, start, end, length, lines[i].start, lines[i].end);
+ pcrData* tempPcr = new pcrData(filename, goodFileName+extension, badFileName+extension, m, oligosfile, ecolifile, primers, revPrimer, nomatch, keepprimer, keepdots, start, end, length, lines[i].start, lines[i].end);
pDataArray.push_back(tempPcr);
//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
else{
//are you aligned
if (aligned) {
- if (!keepprimer) { currSeq.padToPos(mapAligned[primerEnd]); }
- else { currSeq.padToPos(mapAligned[primerStart]); }
+ if (!keepprimer) {
+ if (keepdots) { currSeq.filterToPos(mapAligned[primerEnd]); }
+ else { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerEnd])); }
+ }
+ else {
+ if (keepdots) { currSeq.filterToPos(mapAligned[primerStart]); }
+ else { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerStart])); }
+ }
}else {
if (!keepprimer) { currSeq.setAligned(currSeq.getUnaligned().substr(primerEnd)); }
else { currSeq.setAligned(currSeq.getUnaligned().substr(primerStart)); }
else{
//are you aligned
if (aligned) {
- if (!keepprimer) { currSeq.padFromPos(mapAligned[primerStart]); }
- else { currSeq.padFromPos(mapAligned[primerEnd]); }
+ if (!keepprimer) {
+ if (keepdots) { currSeq.filterFromPos(mapAligned[primerStart]); }
+ else { currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerStart])); }
+ }
+ else {
+ if (keepdots) { currSeq.filterFromPos(mapAligned[primerEnd]); }
+ else { currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerEnd])); }
+ }
}
else {
if (!keepprimer) { currSeq.setAligned(currSeq.getUnaligned().substr(0, primerStart)); }
else if (currSeq.getAligned().length() != length) {
m->mothurOut("[ERROR]: seqs are not the same length as ecoli seq. When using ecoli option your sequences must be aligned and the same length as the ecoli sequence.\n"); m->control_pressed = true; break;
}else {
- currSeq.padToPos(start);
- currSeq.padFromPos(end);
+ if (keepdots) {
+ currSeq.filterToPos(start);
+ currSeq.filterFromPos(end);
+ }else {
+ string seqString = currSeq.getAligned().substr(0, end);
+ seqString = seqString.substr(start);
+ currSeq.setAligned(seqString);
+ }
}
}else{ //using start and end to trim
//make sure the seqs are aligned
lengths.insert(currSeq.getAligned().length());
if (lengths.size() > 1) { m->mothurOut("[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.\n"); m->control_pressed = true; break; }
else {
- if (start != -1) { currSeq.padToPos(start); }
if (end != -1) {
if (end > currSeq.getAligned().length()) { m->mothurOut("[ERROR]: end is longer than your sequence length, aborting.\n"); m->control_pressed = true; break; }
else {
- currSeq.padFromPos(end);
+ if (keepdots) { currSeq.filterFromPos(end); }
+ else {
+ string seqString = currSeq.getAligned().substr(0, end);
+ currSeq.setAligned(seqString);
+ }
+ }
+ }
+ if (start != -1) {
+ if (keepdots) { currSeq.filterToPos(start); }
+ else {
+ string seqString = currSeq.getAligned().substr(start);
+ currSeq.setAligned(seqString);
}
}
}
}
-
+
+ //trimming removed all bases
+ if (currSeq.getUnaligned() == "") { goodSeq = false; }
+
if(goodSeq == 1) { currSeq.printSequence(goodFile); }
else {
badSeqNames.insert(currSeq.getName());
projects / mothur.git / blobdiff