//**********************************************************************************************************************
vector<string> TrimSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
- 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 pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
- 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);
- CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
- CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); 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 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);
- CommandParameter prollaverage("rollaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(prollaverage);
- CommandParameter pqwindowaverage("qwindowaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqwindowaverage);
- CommandParameter pqstepsize("qstepsize", "Number", "", "1", "", "", "",false,false); parameters.push_back(pqstepsize);
- CommandParameter pqwindowsize("qwindowsize", "Number", "", "50", "", "", "",false,false); parameters.push_back(pqwindowsize);
- CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "",false,false); parameters.push_back(pkeepfirst);
- CommandParameter premovelast("removelast", "Number", "", "0", "", "", "",false,false); parameters.push_back(premovelast);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","qfile",false,false,true); parameters.push_back(pqfile);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(pflip);
+ 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 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 pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
+ 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 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);
+ CommandParameter prollaverage("rollaverage", "Number", "", "0", "", "", "","",false,false); parameters.push_back(prollaverage);
+ CommandParameter pqwindowaverage("qwindowaverage", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pqwindowaverage);
+ CommandParameter pqstepsize("qstepsize", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pqstepsize);
+ CommandParameter pqwindowsize("qwindowsize", "Number", "", "50", "", "", "","",false,false); parameters.push_back(pqwindowsize);
+ CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pkeepfirst);
+ CommandParameter premovelast("removelast", "Number", "", "0", "", "", "","",false,false); parameters.push_back(premovelast);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string TrimSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string TrimSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "qfile") { outputFileName = "qual"; }
- else if (type == "fasta") { outputFileName = "fasta"; }
- else if (type == "group") { outputFileName = "groups"; }
- else if (type == "name") { outputFileName = "names"; }
- else if (type == "count") { outputFileName = "count_table"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "qfile") { pattern = "[filename],[tag],qual"; }
+ else if (type == "fasta") { pattern = "[filename],[tag],fasta"; }
+ else if (type == "group") { pattern = "[filename],groups"; }
+ else if (type == "name") { pattern = "[filename],[tag],names"; }
+ else if (type == "count") { pattern = "[filename],[tag],count_table-[filename],count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
-
//**********************************************************************************************************************
TrimSeqsCommand::TrimSeqsCommand(){
vector<vector<string> > qualFileNames;
vector<vector<string> > nameFileNames;
- string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
+ variables["[tag]"] = "trim";
+ string trimSeqFile = getOutputFileName("fasta",variables);
+ string trimQualFile = getOutputFileName("qfile",variables);
outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
-
- string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("fasta");
+
+ variables["[tag]"] = "scrap";
+ string scrapSeqFile = getOutputFileName("fasta",variables);
+ string scrapQualFile = getOutputFileName("qfile",variables);
outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
- string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("qfile");
- string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("qfile");
-
if (qFileName != "") {
outputNames.push_back(trimQualFile);
outputNames.push_back(scrapQualFile);
outputTypes["qfile"].push_back(scrapQualFile);
}
- string trimNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "trim." + getOutputFileNameTag("name");
- string scrapNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "scrap." + getOutputFileNameTag("name");
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFile));
+ variables["[tag]"] = "trim";
+ string trimNameFile = getOutputFileName("name",variables);
+ variables["[tag]"] = "scrap";
+ string scrapNameFile = getOutputFileName("name",variables);
if (nameFile != "") {
m->readNames(nameFile, nameMap);
outputTypes["name"].push_back(scrapNameFile);
}
- string trimCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + "trim." + getOutputFileNameTag("count");
- string scrapCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + "scrap." + getOutputFileNameTag("count");
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[tag]"] = "trim";
+ string trimCountFile = getOutputFileName("count",variables);
+ variables["[tag]"] = "scrap";
+ string scrapCountFile = getOutputFileName("count",variables);
if (countfile != "") {
CountTable ct;
if(oligoFile != ""){
createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
if ((createGroup) && (countfile == "")){
- outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + getOutputFileNameTag("group");
+ map<string, string> myvariables;
+ myvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
+ outputGroupFileName = getOutputFileName("group",myvariables);
outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
}
}
m->openInputFile(it->first, in);
ofstream out;
- string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first));
- if (countfile == "") { thisGroupName += getOutputFileNameTag("group"); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); }
- else { thisGroupName += getOutputFileNameTag("count"); outputNames.push_back(thisGroupName); outputTypes["count"].push_back(thisGroupName); }
+ map<string, string> myvariables;
+ myvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(it->first));
+ string thisGroupName = "";
+ if (countfile == "") { thisGroupName = getOutputFileName("group",myvariables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); }
+ else { thisGroupName = getOutputFileName("count",myvariables); outputNames.push_back(thisGroupName); outputTypes["count"].push_back(thisGroupName); }
m->openOutputFile(thisGroupName, out);
if (countfile != "") { out << "Representative_Sequence\ttotal\t" << it->second << endl; }
if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + ", trashcode= " + trashCode); if (trashCode.length() != 0) { m->mothurOutEndLine(); } }
if(trashCode.length() == 0){
- currSeq.setAligned(currSeq.getUnaligned());
- currSeq.printSequence(trimFASTAFile);
-
- if(qFileName != ""){
- currQual.printQScores(trimQualFile);
- }
-
-
- if(nameFile != ""){
- map<string, string>::iterator itName = nameMap.find(currSeq.getName());
- if (itName != nameMap.end()) { trimNameFile << itName->first << '\t' << itName->second << endl; }
- else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
- }
-
- int numRedundants = 0;
- if (countfile != "") {
- map<string, int>::iterator itCount = nameCount.find(currSeq.getName());
- if (itCount != nameCount.end()) {
- trimCountFile << itCount->first << '\t' << itCount->second << endl;
- numRedundants = itCount->second-1;
- }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
- }
-
- if (createGroup) {
+ string thisGroup = "";
+ if (createGroup) {
if(barcodes.size() != 0){
- string thisGroup = barcodeNameVector[barcodeIndex];
+ thisGroup = barcodeNameVector[barcodeIndex];
if (primers.size() != 0) {
if (primerNameVector[primerIndex] != "") {
if(thisGroup != "") {
}
}
}
-
- if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
-
- if (countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
- else { groupMap[currSeq.getName()] = thisGroup; }
-
- if (nameFile != "") {
- map<string, string>::iterator itName = nameMap.find(currSeq.getName());
- if (itName != nameMap.end()) {
- vector<string> thisSeqsNames;
- m->splitAtChar(itName->second, thisSeqsNames, ',');
- numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
- for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
- outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
- }
- }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
- }
-
- map<string, int>::iterator it = groupCounts.find(thisGroup);
- if (it == groupCounts.end()) { groupCounts[thisGroup] = 1 + numRedundants; }
- else { groupCounts[it->first] += (1 + numRedundants); }
+ }
+ }
+
+ int pos = thisGroup.find("ignore");
+ if (pos == string::npos) {
+ currSeq.setAligned(currSeq.getUnaligned());
+ currSeq.printSequence(trimFASTAFile);
+
+ if(qFileName != ""){
+ currQual.printQScores(trimQualFile);
+ }
+
+
+ if(nameFile != ""){
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) { trimNameFile << itName->first << '\t' << itName->second << endl; }
+ else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
+
+ int numRedundants = 0;
+ if (countfile != "") {
+ map<string, int>::iterator itCount = nameCount.find(currSeq.getName());
+ if (itCount != nameCount.end()) {
+ trimCountFile << itCount->first << '\t' << itCount->second << endl;
+ numRedundants = itCount->second-1;
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
+ }
+
+ if (createGroup) {
+ if(barcodes.size() != 0){
+
+ if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
+
+ if (countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
+ else { groupMap[currSeq.getName()] = thisGroup; }
+
+ if (nameFile != "") {
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) {
+ vector<string> thisSeqsNames;
+ m->splitAtChar(itName->second, thisSeqsNames, ',');
+ numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
+ for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+ outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
+ }
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
+
+ map<string, int>::iterator it = groupCounts.find(thisGroup);
+ if (it == groupCounts.end()) { groupCounts[thisGroup] = 1 + numRedundants; }
+ else { groupCounts[it->first] += (1 + numRedundants); }
- }
- }
-
- if(allFiles){
- ofstream output;
- m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
- currSeq.printSequence(output);
- output.close();
-
- if(qFileName != ""){
- m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
- currQual.printQScores(output);
- output.close();
- }
-
- if(nameFile != ""){
- map<string, string>::iterator itName = nameMap.find(currSeq.getName());
- if (itName != nameMap.end()) {
- m->openOutputFileAppend(nameFileNames[barcodeIndex][primerIndex], output);
- output << itName->first << '\t' << itName->second << endl;
- output.close();
- }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
- }
- }
+ }
+ }
+
+ if(allFiles){
+ ofstream output;
+ m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
+ currSeq.printSequence(output);
+ output.close();
+
+ if(qFileName != ""){
+ m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
+ currQual.printQScores(output);
+ output.close();
+ }
+
+ if(nameFile != ""){
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) {
+ m->openOutputFileAppend(nameFileNames[barcodeIndex][primerIndex], output);
+ output << itName->first << '\t' << itName->second << endl;
+ output.close();
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
+ }
+ }
}
else{
if(nameFile != ""){ //needs to be before the currSeq name is changed
HANDLE hThreadArray[processors-1];
//Create processor worker threads.
- for( int i=0; i<processors-1; i++){
+ for( int h=0; h<processors-1; h++){
string extension = "";
- if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
+ if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
vector<vector<string> > tempFASTAFileNames = fastaFileNames;
vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
vector<vector<string> > tempNameFileNames = nameFileNames;
tempFASTAFileNames,
tempPrimerQualFileNames,
tempNameFileNames,
- lines[i].start, lines[i].end, qLines[i].start, qLines[i].end, m,
+ lines[h].start, lines[h].end, qLines[h].start, qLines[h].end, m,
pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer,
primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap, nameCount);
pDataArray.push_back(tempTrim);
- hThreadArray[i] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ hThreadArray[h] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
}
//parent do my part
m->openOutputFile(trimNameFileName, temp); temp.close();
m->openOutputFile(scrapNameFileName, temp); temp.close();
}
+ vector<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+ vector<vector<string> > tempNameFileNames = nameFileNames;
+ if(allFiles){
+ ofstream temp;
+ string extension = toString(processors-1) + ".temp";
+ for(int i=0;i<tempFASTAFileNames.size();i++){
+ for(int j=0;j<tempFASTAFileNames[i].size();j++){
+ if (tempFASTAFileNames[i][j] != "") {
+ tempFASTAFileNames[i][j] += extension;
+ m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
+
+ if(qFileName != ""){
+ tempPrimerQualFileNames[i][j] += extension;
+ m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
+ }
+ if(nameFile != ""){
+ tempNameFileNames[i][j] += extension;
+ m->openOutputFile(tempNameFileNames[i][j], temp); temp.close();
+ }
+ }
+ }
+ }
+ }
- driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (trimCountFileName + toString(processors-1) + ".temp"), (scrapCountFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), fastaFileNames, qualFileNames, nameFileNames, lines[processors-1], qLines[processors-1]);
+ driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (trimCountFileName + toString(processors-1) + ".temp"), (scrapCountFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames, tempNameFileNames, lines[processors-1], qLines[processors-1]);
processIDS.push_back(processors-1);
string primerName = primerNameVector[itPrimer->second];
string barcodeName = barcodeNameVector[itBar->second];
- string comboGroupName = "";
- string fastaFileName = "";
- string qualFileName = "";
- string nameFileName = "";
- string countFileName = "";
-
- if(primerName == ""){
- comboGroupName = barcodeNameVector[itBar->second];
- }
- else{
- if(barcodeName == ""){
- comboGroupName = primerNameVector[itPrimer->second];
- }
- else{
- comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
- }
- }
-
-
- ofstream temp;
- fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
- if (uniqueNames.count(fastaFileName) == 0) {
- outputNames.push_back(fastaFileName);
- outputTypes["fasta"].push_back(fastaFileName);
- uniqueNames.insert(fastaFileName);
- }
-
- fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
- m->openOutputFile(fastaFileName, temp); temp.close();
-
- if(qFileName != ""){
- qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
- if (uniqueNames.count(qualFileName) == 0) {
- outputNames.push_back(qualFileName);
- outputTypes["qfile"].push_back(qualFileName);
- }
-
- qualFileNames[itBar->second][itPrimer->second] = qualFileName;
- m->openOutputFile(qualFileName, temp); temp.close();
- }
-
- if(nameFile != ""){
- nameFileName = outputDir + m->getRootName(m->getSimpleName(nameFile)) + comboGroupName + ".names";
- if (uniqueNames.count(nameFileName) == 0) {
- outputNames.push_back(nameFileName);
- outputTypes["name"].push_back(nameFileName);
- }
-
- nameFileNames[itBar->second][itPrimer->second] = nameFileName;
- m->openOutputFile(nameFileName, temp); temp.close();
- }
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->second];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->second];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ }
+ }
+
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
+ variables["[tag]"] = comboGroupName;
+ fastaFileName = getOutputFileName("fasta", variables);
+ if (uniqueNames.count(fastaFileName) == 0) {
+ outputNames.push_back(fastaFileName);
+ outputTypes["fasta"].push_back(fastaFileName);
+ uniqueNames.insert(fastaFileName);
+ }
+
+ fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
+ m->openOutputFile(fastaFileName, temp); temp.close();
+
+ if(qFileName != ""){
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qFileName));
+ qualFileName = getOutputFileName("qfile", variables);
+ if (uniqueNames.count(qualFileName) == 0) {
+ outputNames.push_back(qualFileName);
+ outputTypes["qfile"].push_back(qualFileName);
+ }
+
+ qualFileNames[itBar->second][itPrimer->second] = qualFileName;
+ m->openOutputFile(qualFileName, temp); temp.close();
+ }
+
+ if(nameFile != ""){
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFile));
+ nameFileName = getOutputFileName("name", variables);
+ if (uniqueNames.count(nameFileName) == 0) {
+ outputNames.push_back(nameFileName);
+ outputTypes["name"].push_back(nameFileName);
+ }
+
+ nameFileNames[itBar->second][itPrimer->second] = nameFileName;
+ m->openOutputFile(nameFileName, temp); temp.close();
+ }
+ }
}
}
}
projects / mothur.git / blobdiff