#include "trimoligos.h"
+
//**********************************************************************************************************************
vector<string> TrimSeqsCommand::setParameters(){
try {
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 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, 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 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 oligos parameter allows you to provide an oligos file.\n";
helpString += "The name parameter allows you to provide a names file with your fasta file.\n";
helpString += "The count parameter allows you to provide a count file with your fasta file.\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";
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],count_table"; }
+ 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;
TrimSeqsCommand::TrimSeqsCommand(){
try {
- abort = true; calledHelp = true;
+ abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
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);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ pairedOligos = false;
numFPrimers = 0; //this needs to be initialized
numRPrimers = 0;
numSpacers = 0;
vector<vector<string> > fastaFileNames;
vector<vector<string> > qualFileNames;
vector<vector<string> > nameFileNames;
+ map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
if (countfile != "") {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, true, false);
nameCount = ct.getNameMap();
outputNames.push_back(trimCountFile);
outputNames.push_back(scrapCountFile);
string outputGroupFileName;
if(oligoFile != ""){
- createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
+ createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames, uniqueFastaNames);
if ((createGroup) && (countfile == "")){
map<string, string> myvariables;
myvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
}
}
-
+
+ if (m->control_pressed) { return 0; }
+
//fills lines and qlines
setLines(fastaFile, qFileName);
if (m->control_pressed) { return 0; }
if(allFiles){
- map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
map<string, string>::iterator it;
set<string> namesToRemove;
for(int i=0;i<fastaFileNames.size();i++){
m->mothurRemove(nameFileNames[i][j]);
namesToRemove.insert(nameFileNames[i][j]);
}
- }else{
- it = uniqueFastaNames.find(fastaFileNames[i][j]);
- if (it == uniqueFastaNames.end()) {
- uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
- }
+ uniqueFastaNames.erase(fastaFileNames[i][j]); //remove from list for group file print
}
}
}
map<string, string> myvariables;
myvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(it->first));
string thisGroupName = "";
- if (countfile == "") { thisGroupName = getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); }
- else { thisGroupName = getOutputFileName("count",variables); outputNames.push_back(thisGroupName); outputTypes["count"].push_back(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 (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;
int count = 0;
bool moreSeqs = 1;
- TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
-
+ TrimOligos* trimOligos = NULL;
+ if (pairedOligos) { trimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos.getPairedPrimers(), oligos.getPairedBarcodes()); }
+ else { trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, oligos.getPrimers(), oligos.getBarcodes(), oligos.getReversePrimers(), oligos.getLinkers(), oligos.getSpacers()); }
+
+ TrimOligos* rtrimOligos = NULL;
+ if (reorient) {
+ rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, oligos.getReorientedPairedPrimers(), oligos.getReorientedPairedBarcodes()); numBarcodes = oligos.getReorientedPairedBarcodes().size();
+ }
+
while (moreSeqs) {
- if (m->control_pressed) {
+ if (m->control_pressed) {
+ delete trimOligos; if (reorient) { delete rtrimOligos; }
inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
if ((createGroup) && (countfile == "")) { outGroupsFile.close(); }
if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
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 currQual; QualityScores savedQual;
if(qFileName != ""){
currQual = QualityScores(qFile); m->gobble(qFile);
+ savedQual.setName(currQual.getName()); savedQual.setScores(currQual.getScores());
//cout << currQual.getName() << endl;
}
-
+
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
int primerIndex = 0;
if(numLinkers != 0){
- success = trimOligos.stripLinker(currSeq, currQual);
+ success = trimOligos->stripLinker(currSeq, currQual);
if(success > ldiffs) { trashCode += 'k'; }
else{ currentSeqsDiffs += success; }
}
- if(barcodes.size() != 0){
- success = trimOligos.stripBarcode(currSeq, currQual, barcodeIndex);
- if(success > bdiffs) { trashCode += 'b'; }
+ if(numBarcodes != 0){
+ success = trimOligos->stripBarcode(currSeq, currQual, barcodeIndex);
+ if(success > bdiffs) {
+ trashCode += 'b';
+ }
else{ currentSeqsDiffs += success; }
}
-
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
if(numSpacers != 0){
- success = trimOligos.stripSpacer(currSeq, currQual);
+ success = trimOligos->stripSpacer(currSeq, currQual);
if(success > sdiffs) { trashCode += 's'; }
else{ currentSeqsDiffs += success; }
}
if(numFPrimers != 0){
- success = trimOligos.stripForward(currSeq, currQual, primerIndex, keepforward);
- if(success > pdiffs) { trashCode += 'f'; }
+ success = trimOligos->stripForward(currSeq, currQual, primerIndex, keepforward);
+ if(success > pdiffs) {
+ trashCode += 'f';
+ }
else{ currentSeqsDiffs += success; }
}
if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
if(numRPrimers != 0){
- success = trimOligos.stripReverse(currSeq, currQual);
+ success = trimOligos->stripReverse(currSeq, currQual);
if(!success) { trashCode += 'r'; }
}
-
+
+ if (reorient && (trashCode != "")) { //if you failed and want to check the reverse
+ int thisSuccess = 0;
+ string thisTrashCode = "";
+ int thisCurrentSeqsDiffs = 0;
+
+ 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"; }
+ else{ thisCurrentSeqsDiffs += thisSuccess; }
+ }
+
+ if (thisCurrentSeqsDiffs > tdiffs) { thisTrashCode += 't'; }
+
+ if (thisTrashCode == "") {
+ trashCode = thisTrashCode;
+ success = thisSuccess;
+ currentSeqsDiffs = thisCurrentSeqsDiffs;
+ barcodeIndex = thisBarcodeIndex;
+ primerIndex = thisPrimerIndex;
+ savedSeq.reverseComplement();
+ currSeq.setAligned(savedSeq.getAligned());
+ if(qFileName != ""){
+ savedQual.flipQScores();
+ currQual.setScores(savedQual.getScores());
+ }
+ }else { trashCode += "(" + thisTrashCode + ")"; }
+ }
+
if(keepFirst != 0){
success = keepFirstTrim(currSeq, currQual);
}
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
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);
- }
-
+ string thisGroup = "";
+ if (createGroup) { thisGroup = oligos.getGroupName(barcodeIndex, primerIndex); }
- 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){
- string thisGroup = barcodeNameVector[barcodeIndex];
- if (primers.size() != 0) {
- if (primerNameVector[primerIndex] != "") {
- if(thisGroup != "") {
- thisGroup += "." + primerNameVector[primerIndex];
- }else {
- thisGroup = primerNameVector[primerIndex];
- }
- }
- }
-
- 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(numBarcodes != 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
//report progress
if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-
+ delete trimOligos;
+ if (reorient) { delete rtrimOligos; }
inFASTA.close();
trimFASTAFile.close();
scrapFASTAFile.close();
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
- int pid = fork();
+ pid_t pid = fork();
if (pid > 0) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
for(int i=0;i<tempFASTAFileNames.size();i++){
for(int j=0;j<tempFASTAFileNames[i].size();j++){
if (tempFASTAFileNames[i][j] != "") {
- tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
+ tempFASTAFileNames[i][j] += m->mothurGetpid(process) + ".temp";
m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
if(qFileName != ""){
- tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
+ tempPrimerQualFileNames[i][j] += m->mothurGetpid(process) + ".temp";
m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
}
if(nameFile != ""){
- tempNameFileNames[i][j] += toString(getpid()) + ".temp";
+ tempNameFileNames[i][j] += m->mothurGetpid(process) + ".temp";
m->openOutputFile(tempNameFileNames[i][j], temp); temp.close();
}
}
driverCreateTrim(filename,
qFileName,
- (trimFASTAFileName + toString(getpid()) + ".temp"),
- (scrapFASTAFileName + toString(getpid()) + ".temp"),
- (trimQualFileName + toString(getpid()) + ".temp"),
- (scrapQualFileName + toString(getpid()) + ".temp"),
- (trimNameFileName + toString(getpid()) + ".temp"),
- (scrapNameFileName + toString(getpid()) + ".temp"),
- (trimCountFileName + toString(getpid()) + ".temp"),
- (scrapCountFileName + toString(getpid()) + ".temp"),
- (groupFile + toString(getpid()) + ".temp"),
+ (trimFASTAFileName + m->mothurGetpid(process) + ".temp"),
+ (scrapFASTAFileName + m->mothurGetpid(process) + ".temp"),
+ (trimQualFileName + m->mothurGetpid(process) + ".temp"),
+ (scrapQualFileName + m->mothurGetpid(process) + ".temp"),
+ (trimNameFileName + m->mothurGetpid(process) + ".temp"),
+ (scrapNameFileName + m->mothurGetpid(process) + ".temp"),
+ (trimCountFileName + m->mothurGetpid(process) + ".temp"),
+ (scrapCountFileName + m->mothurGetpid(process) + ".temp"),
+ (groupFile + m->mothurGetpid(process) + ".temp"),
tempFASTAFileNames,
tempPrimerQualFileNames,
tempNameFileNames,
lines[process],
qLines[process]);
- if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + toString(getpid()) + '\n'); }
+ if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + m->mothurGetpid(process) + '\n'); }
//pass groupCounts to parent
if(createGroup){
ofstream out;
- string tempFile = filename + toString(getpid()) + ".num.temp";
+ string tempFile = filename + m->mothurGetpid(process) + ".num.temp";
m->openOutputFile(tempFile, out);
out << groupCounts.size() << endl;
tempPrimerQualFileNames,
tempNameFileNames,
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);
+ pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, oligoFile,
+ createGroup, allFiles, keepforward, keepFirst, removeLast,
+ qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage, logtransform,
+ minLength, maxAmbig, maxHomoP, maxLength, flip, reorient, nameMap, nameCount);
pDataArray.push_back(tempTrim);
hThreadArray[h] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
+ if (pDataArray[i]->count != pDataArray[i]->lineEnd) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->lineEnd) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
map<string, int>::iterator it2 = groupCounts.find(it->first);
if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
string sname = ""; nameStream >> sname;
sname = sname.substr(1);
+ m->checkName(sname);
+
map<string, int>::iterator it = firstSeqNames.find(sname);
if(it != firstSeqNames.end()) { //this is the start of a new chunk
//***************************************************************************************************************
-bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
+bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames, map<string, string>& fastaFile2Group){
try {
- ifstream inOligos;
+
+ bool allBlank = false;
+ oligos.read(oligoFile);
+
+ if (m->control_pressed) { return false; } //error in reading oligos
+
+ if (oligos.hasPairedBarcodes()) {
+ pairedOligos = true;
+ numFPrimers = oligos.getPairedPrimers().size();
+ numBarcodes = oligos.getPairedBarcodes().size();
+ }else {
+ pairedOligos = false;
+ numFPrimers = oligos.getPrimers().size();
+ numBarcodes = oligos.getBarcodes().size();
+ }
+
+ numLinkers = oligos.getLinkers().size();
+ numSpacers = oligos.getSpacers().size();
+ numRPrimers = oligos.getReversePrimers().size();
+
+ vector<string> groupNames = oligos.getGroupNames();
+ if (groupNames.size() == 0) { allFiles = 0; allBlank = true; }
+
+
+ fastaFileNames.resize(oligos.getBarcodeNames().size());
+ for(int i=0;i<fastaFileNames.size();i++){
+ for(int j=0;j<oligos.getPrimerNames().size();j++){ fastaFileNames[i].push_back(""); }
+ }
+
+ if(qFileName != "") { qualFileNames = fastaFileNames; }
+ if(nameFile != "") { nameFileNames = fastaFileNames; }
+
+
+ if (allFiles) {
+ 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 == ""){
+ comboGroupName = barcodeName;
+ }else{
+ if(barcodeName == ""){
+ comboGroupName = primerName;
+ }
+ else{
+ comboGroupName = barcodeName + "." + primerName;
+ }
+ }
+
+
+ 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);
+ fastaFile2Group[fastaFileName] = comboGroupName;
+ }
+
+ fastaFileNames[itBar->first][itPrimer->first] = 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->first][itPrimer->first] = 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->first][itPrimer->first] = nameFileName;
+ m->openOutputFile(nameFileName, temp); temp.close();
+ }
+ }
+ }
+ }
+ }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 == ""){
+ comboGroupName = barcodeName;
+ }else{
+ if(barcodeName == ""){
+ comboGroupName = primerName;
+ }
+ else{
+ comboGroupName = barcodeName + "." + primerName;
+ }
+ }
+
+
+
+ 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);
+ fastaFile2Group[fastaFileName] = comboGroupName;
+ }
+
+ 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();
+ }
+ }
+ }
+ }
+ }
+
+ }
+
+
+
+ if (allBlank) {
+ m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine();
+ allFiles = false;
+ return false;
+ }
+
+
+
+ /*ifstream inOligos;
m->openInputFile(oligoFile, inOligos);
ofstream test;
- string type, oligo, group;
+ string type, oligo, roligo, group;
+ bool hasPrimer = false; bool hasPairedBarcodes = false;
int indexPrimer = 0;
int indexBarcode = 0;
+ int indexPairedPrimer = 0;
+ int indexPairedBarcode = 0;
+ set<string> uniquePrimers;
+ set<string> uniqueBarcodes;
while(!inOligos.eof()){
- inOligos >> type;
+ inOligos >> type;
if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
// get rest of line in case there is a primer name
while (!inOligos.eof()) {
char c = inOligos.get();
- if (c == 10 || c == 13){ break; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
else { group += c; }
}
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();
}
else if(type == "BARCODE"){
inOligos >> group;
-
- //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);
+ //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"){
}
inOligos.close();
+ 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; }
+ }
+
if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
-
+
//add in potential combos
if(barcodeNameVector.size() == 0){
barcodes[""] = 0;
if(allFiles){
set<string> uniqueNames; //used to cleanup outputFileNames
- 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];
-
- 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();
- }
- }
- }
- }
- numFPrimers = primers.size();
- numRPrimers = revPrimer.size();
- numLinkers = linker.size();
- numSpacers = spacer.size();
-
- bool allBlank = true;
- for (int i = 0; i < barcodeNameVector.size(); i++) {
- if (barcodeNameVector[i] != "") {
- allBlank = false;
- break;
- }
- }
- for (int i = 0; i < primerNameVector.size(); i++) {
- if (primerNameVector[i] != "") {
- allBlank = false;
- break;
- }
- }
-
- if (allBlank) {
- m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine();
- allFiles = false;
- return false;
+ 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];
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->first];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->first];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
+ }
+ }
+
+
+ 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->first][itPrimer->first] = 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->first][itPrimer->first] = 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->first][itPrimer->first] = nameFileName;
+ m->openOutputFile(nameFileName, 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];
+
+ 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();
+ }
+ }
+ }
+ }
+ }
}
-
- return true;
+ */
+ return true;
}
catch(exception& e) {
if(qscores.getName() != ""){
qscores.trimQScores(-1, keepFirst);
}
+
+// sequence.printSequence(cout);cout << endl;
+
sequence.trim(keepFirst);
+
+// sequence.printSequence(cout);cout << endl << endl;;
+
return success;
}
catch(exception& e) {
}
}
-//********************************************************************/
-string TrimSeqsCommand::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, "TrimSeqsCommand", "reverseOligo");
- exit(1);
- }
-}
//***************************************************************************************************************
projects / mothur.git / blobdiff