CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pfastq);
CommandParameter poligos("oligos", "InputTypes", "", "", "oligosGroup", "none", "none","",false,false); parameters.push_back(poligos);
CommandParameter pgroup("group", "InputTypes", "", "", "oligosGroup", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppdiffs);
CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pbdiffs);
CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
+ helpString += "The checkorient parameter will check look for the reverse compliment of the barcode or primer in the sequence. If found the sequence is flipped. The default is false.\n";
helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=sanger.\n";
helpString += "The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.\n";
helpString += "The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.\n";
}
if ((!fasta) && (!qual)) { m->mothurOut("[ERROR]: no outputs selected. Aborting."); m->mothurOutEndLine(); abort=true; }
+
+ temp = validParameter.validFile(parameters, "checkorient", false); if (temp == "not found") { temp = "F"; }
+ reorient = m->isTrue(temp);
}
}
if (fasta) { m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile); }
if (qual) { m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile); outputTypes["qfile"].push_back(qualFile); }
- TrimOligos* trimOligos = NULL;
- int numBarcodes, numPrimers; numBarcodes = 0; numPrimers = 0;
+ TrimOligos* trimOligos = NULL; TrimOligos* rtrimOligos = NULL;
+ pairedOligos = false; numBarcodes = 0; numPrimers= 0; numLinkers= 0; numSpacers = 0; numRPrimers = 0;
if (oligosfile != "") {
readOligos(oligosfile);
- numPrimers = primers.size(); numBarcodes = barcodes.size();
//find group read belongs to
- if (pairedOligos) { trimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, pairedPrimers, pairedBarcodes); numBarcodes = pairedBarcodes.size(); numPrimers = pairedPrimers.size(); }
- else { trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer); }
+ if (pairedOligos) { trimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos.getPairedPrimers(), oligos.getPairedBarcodes()); numBarcodes = oligos.getPairedBarcodes().size(); numPrimers = oligos.getPairedPrimers().size(); }
+ else { trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, oligos.getPrimers(), oligos.getBarcodes(), oligos.getReversePrimers(), oligos.getLinkers(), oligos.getSpacers()); numPrimers = oligos.getPrimers().size(); numBarcodes = oligos.getBarcodes().size(); }
+
+ if (reorient) {
+ rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos.getReorientedPairedPrimers(), oligos.getReorientedPairedBarcodes()); numBarcodes = oligos.getReorientedPairedBarcodes().size();
+ }
}
else if (groupfile != "") { readGroup(groupfile); }
if (split > 1) {
int barcodeIndex, primerIndex, trashCodeLength;
- if (oligosfile != "") { trashCodeLength = findGroup(thisRead, barcodeIndex, primerIndex, trimOligos, numBarcodes, numPrimers); }
+ if (oligosfile != "") { trashCodeLength = findGroup(thisRead, barcodeIndex, primerIndex, trimOligos, rtrimOligos, numBarcodes, numPrimers); }
else if (groupfile != "") { trashCodeLength = findGroup(thisRead, barcodeIndex, primerIndex, "groupMode"); }
else { m->mothurOut("[ERROR]: uh oh, we shouldn't be here...\n"); }
if (split > 1) {
if (groupfile != "") { delete groupMap; }
- else if (oligosfile != "") { delete trimOligos; }
+ else if (oligosfile != "") { delete trimOligos; if (reorient) { delete rtrimOligos; } }
map<string, string>::iterator it;
set<string> namesToRemove;
}
}
//**********************************************************************************************************************
-int ParseFastaQCommand::findGroup(fastqRead2 thisRead, int& barcode, int& primer, TrimOligos*& trimOligos, int numBarcodes, int numPrimers) {
+int ParseFastaQCommand::findGroup(fastqRead2 thisRead, int& barcode, int& primer, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos, int numBarcodes, int numPrimers) {
try {
int success = 1;
string trashCode = "";
Sequence currSeq(thisRead.seq.getName(), thisRead.seq.getAligned());
QualityScores currQual; currQual.setScores(convertQual(thisRead.quality));
- if(linker.size() != 0){
+ //for reorient
+ Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
+ QualityScores savedQual(currQual.getName(), currQual.getScores());
+
+ if(numLinkers != 0){
success = trimOligos->stripLinker(currSeq, currQual);
if(success > ldiffs) { trashCode += 'k'; }
else{ currentSeqsDiffs += success; }
else{ currentSeqsDiffs += success; }
}
- if(spacer.size() != 0){
+ if(numSpacers != 0){
success = trimOligos->stripSpacer(currSeq, currQual);
if(success > sdiffs) { trashCode += 's'; }
else{ currentSeqsDiffs += success; }
if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
- if(revPrimer.size() != 0){
+ if(numRPrimers != 0){
success = trimOligos->stripReverse(currSeq, currQual);
if(!success) { trashCode += 'r'; }
}
- if (trashCode.length() == 0) { //is this sequence in the ignore group
- string thisGroup = "";
+ if (reorient && (trashCode != "")) { //if you failed and want to check the reverse
+ int thisSuccess = 0;
+ string thisTrashCode = "";
+ int thisCurrentSeqsDiffs = 0;
- if(barcodes.size() != 0){
- thisGroup = barcodeNameVector[barcode];
- if (numPrimers != 0) {
- if (primerNameVector[primer] != "") {
- if(thisGroup != "") {
- thisGroup += "." + primerNameVector[primer];
- }else {
- thisGroup = primerNameVector[primer];
- }
- }
- }
+ 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(numPrimers != 0){
+ thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, true);
+ if(thisSuccess > pdiffs) { thisTrashCode += "f"; }
+ else{ thisCurrentSeqsDiffs += thisSuccess; }
}
+ if (thisCurrentSeqsDiffs > tdiffs) { thisTrashCode += 't'; }
+
+ if (thisTrashCode == "") {
+ trashCode = thisTrashCode;
+ success = thisSuccess;
+ currentSeqsDiffs = thisCurrentSeqsDiffs;
+ barcode = thisBarcodeIndex;
+ primer = thisPrimerIndex;
+ savedSeq.reverseComplement();
+ currSeq.setAligned(savedSeq.getAligned());
+ savedQual.flipQScores();
+ currQual.setScores(savedQual.getScores());
+ }else { trashCode += "(" + thisTrashCode + ")"; }
+ }
+
+ if (trashCode.length() == 0) { //is this sequence in the ignore group
+ string thisGroup = oligos.getGroupName(barcode, primer);
+
int pos = thisGroup.find("ignore");
if (pos != string::npos) { trashCode += "i"; }
}
string group = groupMap->getGroup(thisRead.seq.getName());
if (group == "not found") { trashCode += "g"; } //scrap for group
- else { //find file group
- map<string, int>::iterator it = barcodes.find(group);
- if (it != barcodes.end()) {
- barcode = it->second;
- }else { trashCode += "g"; }
- }
-
+
return trashCode.length();
}
catch(exception& e) {
bool ParseFastaQCommand::readOligos(string oligoFile){
try {
- ifstream inOligos;
- m->openInputFile(oligoFile, inOligos);
-
- string type, oligo, roligo, group;
- bool hasPrimer = false; bool hasPairedBarcodes = false; pairedOligos = false;
-
- int indexPrimer = 0;
- int indexBarcode = 0;
- int indexPairedPrimer = 0;
- int indexPairedBarcode = 0;
- set<string> uniquePrimers;
- set<string> uniqueBarcodes;
-
- while(!inOligos.eof()){
-
- inOligos >> type;
-
- if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
-
- 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
- m->gobble(inOligos);
- }
- else{
- m->gobble(inOligos);
- //make type case insensitive
- for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
-
- inOligos >> oligo;
-
- if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }
-
- for(int i=0;i<oligo.length();i++){
- oligo[i] = toupper(oligo[i]);
- if(oligo[i] == 'U') { oligo[i] = 'T'; }
- }
-
- if(type == "FORWARD"){
- group = "";
-
- // get rest of line in case there is a primer name
- while (!inOligos.eof()) {
- char c = inOligos.get();
- if (c == 10 || c == 13 || c == -1){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- else { group += c; }
- }
-
- //check for repeat barcodes
- map<string, int>::iterator itPrime = primers.find(oligo);
- if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
-
- if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer " + oligo + ".\n"); } }
-
- primers[oligo]=indexPrimer; indexPrimer++;
- primerNameVector.push_back(group);
- }
- else if (type == "PRIMER"){
- m->gobble(inOligos);
-
- inOligos >> roligo;
-
- for(int i=0;i<roligo.length();i++){
- roligo[i] = toupper(roligo[i]);
- if(roligo[i] == 'U') { roligo[i] = 'T'; }
- }
- roligo = reverseOligo(roligo);
-
- group = "";
-
- // get rest of line in case there is a primer name
- while (!inOligos.eof()) {
- char c = inOligos.get();
- if (c == 10 || c == 13 || c == -1){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- else { group += c; }
- }
-
- oligosPair newPrimer(oligo, roligo);
-
- if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
-
- //check for repeat barcodes
- string tempPair = oligo+roligo;
- if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine(); }
- else { uniquePrimers.insert(tempPair); }
-
- if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } }
-
- pairedPrimers[indexPairedPrimer]=newPrimer; indexPairedPrimer++;
- primerNameVector.push_back(group);
- hasPrimer = true;
- }
- else if(type == "REVERSE"){
- //Sequence oligoRC("reverse", oligo);
- //oligoRC.reverseComplement();
- string oligoRC = reverseOligo(oligo);
- revPrimer.push_back(oligoRC);
- }
- else if(type == "BARCODE"){
- inOligos >> group;
-
- //barcode lines can look like BARCODE atgcatgc groupName - for 454 seqs
- //or BARCODE atgcatgc atgcatgc groupName - for illumina data that has forward and reverse info
-
- string temp = "";
- while (!inOligos.eof()) {
- char c = inOligos.get();
- if (c == 10 || c == 13 || c == -1){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- else { temp += c; }
- }
-
- //then this is illumina data with 4 columns
- if (temp != "") {
- hasPairedBarcodes = true;
- string reverseBarcode = group; //reverseOligo(group); //reverse barcode
- group = temp;
-
- for(int i=0;i<reverseBarcode.length();i++){
- reverseBarcode[i] = toupper(reverseBarcode[i]);
- if(reverseBarcode[i] == 'U') { reverseBarcode[i] = 'T'; }
- }
-
- reverseBarcode = reverseOligo(reverseBarcode);
- oligosPair newPair(oligo, reverseBarcode);
-
- if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
- //check for repeat barcodes
- string tempPair = oligo+reverseBarcode;
- if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse + " is in your oligos file already, disregarding."); m->mothurOutEndLine(); }
- else { uniqueBarcodes.insert(tempPair); }
-
- pairedBarcodes[indexPairedBarcode]=newPair; indexPairedBarcode++;
- barcodeNameVector.push_back(group);
- }else {
- //check for repeat barcodes
- map<string, int>::iterator itBar = barcodes.find(oligo);
- if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
-
- barcodes[oligo]=indexBarcode; indexBarcode++;
- barcodeNameVector.push_back(group);
- }
- }else if(type == "LINKER"){
- linker.push_back(oligo);
- }else if(type == "SPACER"){
- spacer.push_back(oligo);
- }
- else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
- }
- m->gobble(inOligos);
- }
- inOligos.close();
-
- if (hasPairedBarcodes || hasPrimer) {
+ bool allBlank = false;
+ oligos.read(oligosfile);
+
+ if (m->control_pressed) { return false; } //error in reading oligos
+
+ if (oligos.hasPairedBarcodes()) {
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; }
+ numPrimers = oligos.getPairedPrimers().size();
+ numBarcodes = oligos.getPairedBarcodes().size();
+ }else {
+ pairedOligos = false;
+ numPrimers = oligos.getPrimers().size();
+ numBarcodes = oligos.getBarcodes().size();
}
- //add in potential combos
- if(barcodeNameVector.size() == 0){
- barcodes[""] = 0;
- barcodeNameVector.push_back("");
- }
-
- if(primerNameVector.size() == 0){
- primers[""] = 0;
- primerNameVector.push_back("");
- }
-
- fastqFileNames.resize(barcodeNameVector.size());
+ numLinkers = oligos.getLinkers().size();
+ numSpacers = oligos.getSpacers().size();
+ numRPrimers = oligos.getReversePrimers().size();
+
+ vector<string> groupNames = oligos.getGroupNames();
+ if (groupNames.size() == 0) { allBlank = true; }
+
+
+ fastqFileNames.resize(oligos.getBarcodeNames().size());
for(int i=0;i<fastqFileNames.size();i++){
- fastqFileNames[i].assign(primerNameVector.size(), "");
+ for(int j=0;j<oligos.getPrimerNames().size();j++){ fastqFileNames[i].push_back(""); }
}
-
-
- set<string> uniqueNames; //used to cleanup outputFileNames
- if (pairedOligos) {
- for(map<int, oligosPair>::iterator itBar = pairedBarcodes.begin();itBar != pairedBarcodes.end();itBar++){
- for(map<int, oligosPair>::iterator itPrimer = pairedPrimers.begin();itPrimer != pairedPrimers.end(); itPrimer++){
-
- string primerName = primerNameVector[itPrimer->first];
- string barcodeName = barcodeNameVector[itBar->first];
+
+ set<string> uniqueNames; //used to cleanup outputFileNames
+ if (pairedOligos) {
+ map<int, oligosPair> barcodes = oligos.getPairedBarcodes();
+ map<int, oligosPair> primers = oligos.getPairedPrimers();
+ for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
+ for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
+
+ string primerName = oligos.getPrimerName(itPrimer->first);
+ string barcodeName = oligos.getBarcodeName(itBar->first);
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
- if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
- else {
- string comboGroupName = "";
- string fastqFileName = "";
-
- if(primerName == ""){
- comboGroupName = barcodeNameVector[itBar->first];
+ if(primerName == ""){
+ comboGroupName = barcodeName;
+ }else{
+ if(barcodeName == ""){
+ comboGroupName = primerName;
}
else{
- if(barcodeName == ""){
- comboGroupName = primerNameVector[itPrimer->first];
- }
- else{
- comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
- }
+ comboGroupName = barcodeName + "." + primerName;
}
-
-
- ofstream temp;
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
- variables["[group]"] = comboGroupName;
- fastqFileName = getOutputFileName("fastq", variables);
- if (uniqueNames.count(fastqFileName) == 0) {
- outputNames.push_back(fastqFileName);
- outputTypes["fastq"].push_back(fastqFileName);
- uniqueNames.insert(fastqFileName);
- }
-
- fastqFileNames[itBar->first][itPrimer->first] = fastqFileName;
- m->openOutputFile(fastqFileName, temp); temp.close();
-
}
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+ variables["[group]"] = comboGroupName;
+ string fastqFileName = getOutputFileName("fastq", variables);
+ if (uniqueNames.count(fastqFileName) == 0) {
+ outputNames.push_back(fastqFileName);
+ outputTypes["fastq"].push_back(fastqFileName);
+ uniqueNames.insert(fastqFileName);
+ }
+
+ fastqFileNames[itBar->first][itPrimer->first] = fastqFileName;
+ m->openOutputFile(fastqFileName, temp); temp.close();
}
}
- }else {
- for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
- for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
-
- string primerName = primerNameVector[itPrimer->second];
- string barcodeName = barcodeNameVector[itBar->second];
+ }
+ }else {
+ map<string, int> barcodes = oligos.getBarcodes() ;
+ map<string, int> primers = oligos.getPrimers();
+ for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
+ for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
+
+ string primerName = oligos.getPrimerName(itPrimer->second);
+ string barcodeName = oligos.getBarcodeName(itBar->second);
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
- if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
- else {
- string comboGroupName = "";
- string fastqFileName = "";
-
- if(primerName == ""){
- comboGroupName = barcodeNameVector[itBar->second];
+ if(primerName == ""){
+ comboGroupName = barcodeName;
+ }else{
+ if(barcodeName == ""){
+ comboGroupName = primerName;
}
else{
- if(barcodeName == ""){
- comboGroupName = primerNameVector[itPrimer->second];
- }
- else{
- comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
- }
+ comboGroupName = barcodeName + "." + primerName;
}
-
-
- ofstream temp;
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
- variables["[group]"] = comboGroupName;
- fastqFileName = getOutputFileName("fastq", variables);
- if (uniqueNames.count(fastqFileName) == 0) {
- outputNames.push_back(fastqFileName);
- outputTypes["fastq"].push_back(fastqFileName);
- uniqueNames.insert(fastqFileName);
- }
-
- fastqFileNames[itBar->second][itPrimer->second] = fastqFileName;
- m->openOutputFile(fastqFileName, temp); temp.close();
-
}
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+ variables["[group]"] = comboGroupName;
+ string fastqFileName = getOutputFileName("fastq", variables);
+ if (uniqueNames.count(fastqFileName) == 0) {
+ outputNames.push_back(fastqFileName);
+ outputTypes["fastq"].push_back(fastqFileName);
+ uniqueNames.insert(fastqFileName);
+ }
+
+ fastqFileNames[itBar->second][itPrimer->second] = fastqFileName;
+ m->openOutputFile(fastqFileName, temp); temp.close();
}
}
}
-
+ }
+
+ if (allBlank) {
+ m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine();
+ return false;
+ }
+
ofstream temp;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
variables["[group]"] = "scrap";
noMatchFile = getOutputFileName("fastq", variables);
m->openOutputFile(noMatchFile, temp); temp.close();
-
+
return true;
}
ofstream temp;
m->openOutputFileBinary(thisFilename, temp); temp.close();
fastqFileNames[i].push_back(thisFilename);
- barcodes[groups[i]] = i;
}
}
exit(1);
}
}
-//********************************************************************/
-string ParseFastaQCommand::reverseOligo(string oligo){
- try {
- string reverse = "";
-
- for(int i=oligo.length()-1;i>=0;i--){
-
- if(oligo[i] == 'A') { reverse += 'T'; }
- else if(oligo[i] == 'T'){ reverse += 'A'; }
- else if(oligo[i] == 'U'){ reverse += 'A'; }
-
- else if(oligo[i] == 'G'){ reverse += 'C'; }
- else if(oligo[i] == 'C'){ reverse += 'G'; }
-
- else if(oligo[i] == 'R'){ reverse += 'Y'; }
- else if(oligo[i] == 'Y'){ reverse += 'R'; }
-
- else if(oligo[i] == 'M'){ reverse += 'K'; }
- else if(oligo[i] == 'K'){ reverse += 'M'; }
-
- else if(oligo[i] == 'W'){ reverse += 'W'; }
- else if(oligo[i] == 'S'){ reverse += 'S'; }
-
- else if(oligo[i] == 'B'){ reverse += 'V'; }
- else if(oligo[i] == 'V'){ reverse += 'B'; }
-
- else if(oligo[i] == 'D'){ reverse += 'H'; }
- else if(oligo[i] == 'H'){ reverse += 'D'; }
-
- else { reverse += 'N'; }
- }
-
-
- return reverse;
- }
- catch(exception& e) {
- m->errorOut(e, "ParseFastaQCommand", "reverseOligo");
- exit(1);
- }
-}
-
-
//**********************************************************************************************************************
projects / mothur.git / blobdiff