vector<string> TrimSeqsCommand::getValidParameters(){
try {
- string Array[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile",
+ string Array[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop","minlength", "maxlength", "qfile",
"qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
"keepfirst", "removelast",
"allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
TrimSeqsCommand::TrimSeqsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qual"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
TrimSeqsCommand::TrimSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
comboStarts = 0;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
- string AlignArray[] = { "fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile",
+ string AlignArray[] = { "fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
"qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
"keepfirst", "removelast",
"allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qual"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (path == "") { parameters["qfile"] = inputDir + it->second; }
}
- it = parameters.find("group");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["group"] = inputDir + it->second; }
- }
}
else if(temp == "not open"){ abort = true; }
else { oligoFile = temp; }
- temp = validParameter.validFile(parameters, "group", true);
- if (temp == "not found"){ groupfile = ""; }
- else if(temp == "not open"){ abort = true; }
- else { groupfile = temp; }
temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
convert(temp, maxAmbig);
try {
m->mothurOut("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");
m->mothurOut("The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.\n");
- m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, group, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n");
+ m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n");
m->mothurOut("The fasta parameter is required.\n");
- m->mothurOut("The group parameter allows you to enter a group file for your fasta file.\n");
m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
m->mothurOut("The oligos parameter allows you to provide an oligos file.\n");
m->mothurOut("The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n");
int TrimSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
numFPrimers = 0; //this needs to be initialized
numRPrimers = 0;
- vector<string> fastaFileNames;
- vector<string> qualFileNames;
+ vector<vector<string> > fastaFileNames;
+ vector<vector<string> > qualFileNames;
string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
+
string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
+
string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
- if (qFileName != "") { outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile); outputTypes["qual"].push_back(trimQualFile); outputTypes["qual"].push_back(scrapQualFile); }
- string groupFile = "";
- if (groupfile == "") { groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups"; }
- else{
- groupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "trim.groups";
- outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
-
- if(allFiles){
- for (int i = 0; i < groupMap->namesOfGroups.size(); i++) {
- groupToIndex[groupMap->namesOfGroups[i]] = i;
- groupVector.push_back(groupMap->namesOfGroups[i]);
- fastaFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupMap->namesOfGroups[i] + ".fasta"));
-
- //we append later, so we want to clear file
- ofstream outRemove;
- m->openOutputFile(fastaFileNames[i], outRemove);
- outRemove.close();
- if(qFileName != ""){
- qualFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupMap->namesOfGroups[i] + ".qual"));
- ofstream outRemove2;
- m->openOutputFile(qualFileNames[i], outRemove2);
- outRemove2.close();
- }
- }
- }
- comboStarts = fastaFileNames.size()-1;
+ if (qFileName != "") {
+ outputNames.push_back(trimQualFile);
+ outputNames.push_back(scrapQualFile);
+ outputTypes["qual"].push_back(trimQualFile);
+ outputTypes["qual"].push_back(scrapQualFile);
}
+ string outputGroupFileName;
+
if(oligoFile != ""){
- outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
+ outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
+ outputNames.push_back(outputGroupFileName); outputTypes["groups"].push_back(outputGroupFileName);
getOligos(fastaFileNames, qualFileNames);
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames, lines[0], qLines[0]);
}else{
- createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames);
+ createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames);
}
#else
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames, lines[0], qLines[0]);
#endif
if (m->control_pressed) { return 0; }
- set<string> blanks;
- for(int i=0;i<fastaFileNames.size();i++){
- if (m->isBlank(fastaFileNames[i])) { blanks.insert(fastaFileNames[i]); }
- else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
- else {
- ifstream inFASTA;
- string seqName;
- m->openInputFile(fastaFileNames[i], inFASTA);
- ofstream outGroups;
- string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
-
- //if the fastafile is on the blanks list then the groups file should be as well
- if (blanks.count(fastaFileNames[i]) != 0) { blanks.insert(outGroupFilename); }
-
- m->openOutputFile(outGroupFilename, outGroups);
- outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);
- string thisGroup = "";
- if (i > comboStarts) {
- map<string, int>::iterator itCombo;
- for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
- if(itCombo->second == i){ thisGroup = itCombo->first; combos.erase(itCombo); break; }
- }
- }else{ thisGroup = groupVector[i]; }
-
- while(!inFASTA.eof()){
- if(inFASTA.get() == '>'){
- inFASTA >> seqName;
- outGroups << seqName << '\t' << thisGroup << endl;
+ if(allFiles){
+ for(int i=0;i<fastaFileNames.size();i++){
+ for(int j=0;j<fastaFileNames[0].size();j++){
+ if(m->isBlank(fastaFileNames[i][j])){
+ remove(fastaFileNames[i][j].c_str());
+
+ if(qFileName != ""){
+ remove(fastaFileNames[i][j].c_str());
+ }
+
}
- while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
}
- outGroups.close();
- inFASTA.close();
}
}
- for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) { remove((*(itBlanks)).c_str()); }
-
- blanks.clear();
- if(qFileName != ""){
- for(int i=0;i<qualFileNames.size();i++){
- if (m->isBlank(qualFileNames[i])) { blanks.insert(qualFileNames[i]); }
- else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
- }
- }
- for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) { remove((*(itBlanks)).c_str()); }
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
/**************************************************************************************/
-int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames, linePair* line, linePair* qline) {
+int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, linePair* line, linePair* qline) {
try {
- ofstream outFASTA;
- m->openOutputFile(trimFile, outFASTA);
+ ofstream trimFASTAFile;
+ m->openOutputFile(trimFileName, trimFASTAFile);
- ofstream scrapFASTA;
- m->openOutputFile(scrapFile, scrapFASTA);
+ ofstream scrapFASTAFile;
+ m->openOutputFile(scrapFileName, scrapFASTAFile);
- ofstream outQual;
- ofstream scrapQual;
+ ofstream trimQualFile;
+ ofstream scrapQualFile;
if(qFileName != ""){
- m->openOutputFile(trimQFile, outQual);
- m->openOutputFile(scrapQFile, scrapQual);
+ m->openOutputFile(trimQFileName, trimQualFile);
+ m->openOutputFile(scrapQFileName, scrapQualFile);
}
- ofstream outGroups;
+ ofstream outGroupsFile;
+ if (oligoFile != ""){ m->openOutputFile(groupFileName, outGroupsFile); }
- if (oligoFile != "") {
- m->openOutputFile(groupFile, outGroups);
+ if(allFiles){
+ for (int i = 0; i < fastaFileNames.size(); i++) { //clears old file
+ for (int j = 0; j < fastaFileNames[i].size(); j++) { //clears old file
+ ofstream temp;
+ m->openOutputFile(fastaFileNames[i][j], temp); temp.close();
+ if(qFileName != ""){
+ m->openOutputFile(qualFileNames[i][j], temp); temp.close();
+ }
+ }
+ }
}
ifstream inFASTA;
inFASTA.seekg(line->start);
ifstream qFile;
- if(qFileName != "") { m->openInputFile(qFileName, qFile); qFile.seekg(qline->start); }
-
-
- for (int i = 0; i < fastaNames.size(); i++) { //clears old file
- ofstream temp;
- m->openOutputFile(fastaNames[i], temp);
- temp.close();
- }
- for (int i = 0; i < qualNames.size(); i++) { //clears old file
- ofstream temp;
- m->openOutputFile(qualNames[i], temp);
- temp.close();
+ if(qFileName != "") {
+ m->openInputFile(qFileName, qFile);
+ qFile.seekg(qline->start);
}
-
- bool done = false;
int count = 0;
+ bool moreSeqs = 1;
- while (!done) {
+ while (moreSeqs) {
if (m->control_pressed) {
- inFASTA.close(); outFASTA.close(); scrapFASTA.close();
- if (oligoFile != "") { outGroups.close(); }
+ inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
+ if (oligoFile != "") { outGroupsFile.close(); }
if(qFileName != ""){
qFile.close();
}
int success = 1;
-
+ string trashCode = "";
+ int currentSeqsDiffs = 0;
Sequence currSeq(inFASTA); m->gobble(inFASTA);
QualityScores currQual;
if(qFileName != ""){
- currQual = QualityScores(qFile, currSeq.getNumBases()); m->gobble(qFile);
+ currQual = QualityScores(qFile); m->gobble(qFile);
}
-
+
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
- int groupBar, groupPrime;
- string trashCode = "";
- int currentSeqsDiffs = 0;
-
+
+ int barcodeIndex = 0;
+ int primerIndex = 0;
+
if(barcodes.size() != 0){
- success = stripBarcode(currSeq, currQual, groupBar);
+ success = stripBarcode(currSeq, currQual, barcodeIndex);
if(success > bdiffs) { trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
if(numFPrimers != 0){
- success = stripForward(currSeq, currQual, groupPrime);
+ success = stripForward(currSeq, currQual, primerIndex);
if(success > pdiffs) { trashCode += 'f'; }
else{ currentSeqsDiffs += success; }
}
if(flip){ // should go last
currSeq.reverseComplement();
- currQual.flipQScores();
+ if(qFileName != ""){
+ currQual.flipQScores();
+ }
}
if(trashCode.length() == 0){
currSeq.setAligned(currSeq.getUnaligned());
- currSeq.printSequence(outFASTA);
- currQual.printQScores(outQual);
+ currSeq.printSequence(trimFASTAFile);
+
+ if(qFileName != ""){
+ currQual.printQScores(trimQualFile);
+ }
if(barcodes.size() != 0){
- string thisGroup = groupVector[groupBar];
- int indexToFastaFile = groupBar;
- if (primers.size() != 0){
- //does this primer have a group
- if (groupVector[groupPrime] != "") {
- thisGroup += "." + groupVector[groupPrime];
- indexToFastaFile = combos[thisGroup];
- }
- }
- outGroups << currSeq.getName() << '\t' << thisGroup << endl;
- if(allFiles){
- ofstream outTemp;
- m->openOutputFileAppend(fastaNames[indexToFastaFile], outTemp);
- //currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
- currSeq.printSequence(outTemp);
- outTemp.close();
-
- if(qFileName != ""){
- //currQual.printQScores(*qualFileNames[indexToFastaFile]);
- ofstream outTemp2;
- m->openOutputFileAppend(qualNames[indexToFastaFile], outTemp2);
- currQual.printQScores(outTemp2);
- outTemp2.close();
- }
- }
+ outGroupsFile << currSeq.getName() << '\t' << barcodeNameVector[barcodeIndex] << endl;
}
- if (groupfile != "") {
- string thisGroup = groupMap->getGroup(currSeq.getName());
+
+ if(allFiles){
+ ofstream output;
+ m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
+ currSeq.printSequence(output);
+ output.close();
- if (thisGroup != "not found") {
- outGroups << currSeq.getName() << '\t' << thisGroup << endl;
- if (allFiles) {
- ofstream outTemp;
- m->openOutputFileAppend(fastaNames[groupToIndex[thisGroup]], outTemp);
- currSeq.printSequence(outTemp);
- outTemp.close();
- if(qFileName != ""){
- ofstream outTemp2;
- m->openOutputFileAppend(qualNames[groupToIndex[thisGroup]], outTemp2);
- currQual.printQScores(outTemp2);
- outTemp2.close();
- }
- }
- }else{
- m->mothurOut(currSeq.getName() + " is not in your groupfile, adding to group XXX."); m->mothurOutEndLine();
- outGroups << currSeq.getName() << '\t' << "XXX" << endl;
- if (allFiles) {
- m->mothurOut("[ERROR]: " + currSeq.getName() + " will not be added to any .group.fasta or .group.qual file."); m->mothurOutEndLine();
- }
+ if(qFileName != ""){
+ m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
+ currQual.printQScores(output);
+ output.close();
}
}
}
currSeq.setName(currSeq.getName() + '|' + trashCode);
currSeq.setUnaligned(origSeq);
currSeq.setAligned(origSeq);
- currSeq.printSequence(scrapFASTA);
- currQual.printQScores(scrapQual);
+ currSeq.printSequence(scrapFASTAFile);
+ if(qFileName != ""){
+ currQual.printQScores(scrapQualFile);
+ }
}
count++;
}
inFASTA.close();
- outFASTA.close();
- scrapFASTA.close();
- if (oligoFile != "") { outGroups.close(); }
- if(qFileName != "") { qFile.close(); scrapQual.close(); outQual.close(); }
+ trimFASTAFile.close();
+ scrapFASTAFile.close();
+ if (oligoFile != "") { outGroupsFile.close(); }
+ if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
return count;
}
/**************************************************************************************************/
-int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
+int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- for (int i = 0; i < fastaNames.size(); i++) {
- fastaNames[i] = (fastaNames[i] + toString(getpid()) + ".temp");
- //clear old file if it exists
+
+ vector<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+
+ if(allFiles){
ofstream temp;
- m->openOutputFile(fastaNames[i], temp);
- temp.close();
- if(qFileName != ""){
- qualNames[i] = (qualNames[i] + toString(getpid()) + ".temp");
- //clear old file if it exists
- ofstream temp2;
- m->openOutputFile(qualNames[i], temp2);
- temp2.close();
+
+ for(int i=0;i<tempFASTAFileNames.size();i++){
+ for(int j=0;j<tempFASTAFileNames[i].size();j++){
+ tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
+ m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
+
+ if(qFileName != ""){
+ tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
+ m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
+ }
+ }
}
}
+
+ driverCreateTrim(filename,
+ qFileName,
+ (trimFASTAFileName + toString(getpid()) + ".temp"),
+ (scrapFASTAFileName + toString(getpid()) + ".temp"),
+ (trimQualFileName + toString(getpid()) + ".temp"),
+ (scrapQualFileName + toString(getpid()) + ".temp"),
+ (groupFile + toString(getpid()) + ".temp"),
+ tempFASTAFileNames,
+ tempPrimerQualFileNames,
+ lines[process],
+ qLines[process]);
- driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (trimQFile + toString(getpid()) + ".temp"), (scrapQFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, qualNames, lines[process], qLines[process]);
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
}
//parent do my part
- for (int i = 0; i < fastaNames.size(); i++) {
- //clear old file if it exists
- ofstream temp;
- m->openOutputFile(fastaNames[i], temp);
- temp.close();
- if(qFileName != ""){
- //clear old file if it exists
- ofstream temp2;
- m->openOutputFile(qualNames[i], temp2);
- temp2.close();
- }
- }
+ ofstream temp;
+ m->openOutputFile(trimFASTAFileName, temp); temp.close();
+ m->openOutputFile(scrapFASTAFileName, temp); temp.close();
+ m->openOutputFile(trimQualFileName, temp); temp.close();
+ m->openOutputFile(scrapQualFileName, temp); temp.close();
+
+
- driverCreateTrim(filename, qFileName, trimFile, scrapFile, trimQFile, scrapQFile, groupFile, fastaNames, qualNames, lines[0], qLines[0]);
+ driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
//force parent to wait until all the processes are done
m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
- m->appendFiles((trimFile + toString(processIDS[i]) + ".temp"), trimFile);
- remove((trimFile + toString(processIDS[i]) + ".temp").c_str());
- m->appendFiles((scrapFile + toString(processIDS[i]) + ".temp"), scrapFile);
- remove((scrapFile + toString(processIDS[i]) + ".temp").c_str());
-
- m->mothurOut("Done with fasta files"); m->mothurOutEndLine();
+ m->appendFiles((trimFASTAFileName + toString(processIDS[i]) + ".temp"), trimFASTAFileName);
+ remove((trimFASTAFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->appendFiles((scrapFASTAFileName + toString(processIDS[i]) + ".temp"), scrapFASTAFileName);
+ remove((scrapFASTAFileName + toString(processIDS[i]) + ".temp").c_str());
if(qFileName != ""){
- m->appendFiles((trimQFile + toString(processIDS[i]) + ".temp"), trimQFile);
- remove((trimQFile + toString(processIDS[i]) + ".temp").c_str());
- m->appendFiles((scrapQFile + toString(processIDS[i]) + ".temp"), scrapQFile);
- remove((scrapQFile + toString(processIDS[i]) + ".temp").c_str());
-
- m->mothurOut("Done with quality files"); m->mothurOutEndLine();
+ m->appendFiles((trimQualFileName + toString(processIDS[i]) + ".temp"), trimQualFileName);
+ remove((trimQualFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->appendFiles((scrapQualFileName + toString(processIDS[i]) + ".temp"), scrapQualFileName);
+ remove((scrapQualFileName + toString(processIDS[i]) + ".temp").c_str());
}
m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
- m->mothurOut("Done with group file"); m->mothurOutEndLine();
-
- for (int j = 0; j < fastaNames.size(); j++) {
- m->appendFiles((fastaNames[j] + toString(processIDS[i]) + ".temp"), fastaNames[j]);
- remove((fastaNames[j] + toString(processIDS[i]) + ".temp").c_str());
- }
- if(qFileName != ""){
- for (int j = 0; j < qualNames.size(); j++) {
- m->appendFiles((qualNames[j] + toString(processIDS[i]) + ".temp"), qualNames[j]);
- remove((qualNames[j] + toString(processIDS[i]) + ".temp").c_str());
+ if(allFiles){
+ for(int j=0;j<fastaFileNames.size();j++){
+ for(int k=0;k<fastaFileNames[j].size();k++){
+ m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
+ remove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+
+ if(qFileName != ""){
+ m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
+ remove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+ }
+ }
}
}
- if (allFiles) { m->mothurOut("Done with allfiles"); m->mothurOutEndLine(); }
}
return exitCommand;
//***************************************************************************************************************
-void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
+void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames){
try {
ifstream inOligos;
m->openInputFile(oligoFile, inOligos);
ofstream test;
string type, oligo, group;
- int index=0;
- //int indexPrimer = 0;
+
+ int indexPrimer = 0;
+ int indexBarcode = 0;
while(!inOligos.eof()){
+
inOligos >> type; m->gobble(inOligos);
if(type[0] == '#'){
map<string, int>::iterator itPrime = primers.find(oligo);
if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
- primers[oligo]=index; index++;
- groupVector.push_back(group);
-
- if(allFiles){
- outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- if(qFileName != ""){
- outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- }
- if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
- filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- if(qFileName != ""){
- filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- }
- }else {
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- if(qFileName != ""){
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- }
- }
- }
-
+ primers[oligo]=indexPrimer; indexPrimer++;
+ primerNameVector.push_back(group);
}
else if(type == "REVERSE"){
Sequence oligoRC("reverse", oligo);
//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]=index; index++;
- groupVector.push_back(group);
- if(allFiles){
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- if(qFileName != ""){
- outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- }
- }
-
- }else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
+ barcodes[oligo]=indexBarcode; indexBarcode++;
+ barcodeNameVector.push_back(group);
+ }
+ else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
}
m->gobble(inOligos);
- }
-
+ }
inOligos.close();
+ if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
+
//add in potential combos
+ if(barcodeNameVector.size() == 0){
+ barcodes[""] = 0;
+ barcodeNameVector.push_back("");
+ }
+
+ if(primerNameVector.size() == 0){
+ primers[""] = 0;
+ primerNameVector.push_back("");
+ }
+
+ fastaFileNames.resize(barcodeNameVector.size());
+ for(int i=0;i<fastaFileNames.size();i++){
+ fastaFileNames[i].assign(primerNameVector.size(), "");
+ }
+ if(qFileName != ""){ qualFileNames = fastaFileNames; }
+
if(allFiles){
- comboStarts = outFASTAVec.size()-1;
- for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
- for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
- if (groupVector[itPrime->second] != "") { //there is a group for this primer
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
- outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
- outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
- combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
-
- if(qFileName != ""){
- outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
- outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
+ 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 = "";
+
+ 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";
+ outputNames.push_back(fastaFileName);
+ outputTypes["fasta"].push_back(fastaFileName);
+ fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
+ m->openOutputFile(fastaFileName, temp); temp.close();
+
+ if(qFileName != ""){
+ qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
+ outputNames.push_back(qualFileName);
+ outputTypes["qual"].push_back(qualFileName);
+ qualFileNames[itBar->second][itPrimer->second] = qualFileName;
+ m->openOutputFile(qualFileName, temp); temp.close();
}
}
}
}
-
numFPrimers = primers.size();
numRPrimers = revPrimer.size();
-
+
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "getOligos");
exit(1);
}
}
+
//***************************************************************************************************************
int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
}
//if you found the barcode or if you don't want to allow for diffs
-// cout << success;
if ((bdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-// cout << endl;
int maxLength = 0;
int numDiff = countDiffs(oligo, temp);
-// cout << oligo << '\t' << temp << '\t' << numDiff << endl;
-
if(numDiff < minDiff){
minDiff = numDiff;
minCount = 1;
if (alignment != NULL) { delete alignment; }
}
-// cout << success << endl;
return success;
}
//if you found the barcode or if you don't want to allow for diffs
-// cout << success;
if ((pdiffs == 0) || (success == 0)) { return success; }
else { //try aligning and see if you can find it
-// cout << endl;
int maxLength = 0;
int numDiff = countDiffs(oligo, temp);
-// cout << oligo << '\t' << temp << '\t' << numDiff << endl;
-
if(numDiff < minDiff){
minDiff = numDiff;
minCount = 1;
projects / mothur.git / blobdiff