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["qfile"] = tempOutNames;
outputTypes["group"] = tempOutNames;
}
catch(exception& e) {
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"};
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- outputTypes["qual"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
outputTypes["group"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
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);
temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
convert(temp, qThreshold);
- temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "F"; }
+ temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "t"; }
qtrim = m->isTrue(temp);
temp = validParameter.validFile(parameters, "rollaverage", false); if (temp == "not found") { temp = "0"; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
convert(temp, processors);
- if ((oligoFile != "") && (groupfile != "")) {
- m->mothurOut("You given both a oligos file and a groupfile, only one is allowed."); m->mothurOutEndLine(); abort = true;
- }
-
- if(allFiles && (oligoFile == "") && (groupfile == "")){
- m->mothurOut("You selected allfiles, but didn't enter an oligos or group file. Ignoring the allfiles request."); m->mothurOutEndLine();
+ if(allFiles && (oligoFile == "")){
+ m->mothurOut("You selected allfiles, but didn't enter an oligos. Ignoring the allfiles request."); m->mothurOutEndLine();
}
if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
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");
m->mothurOut("The rollaverage parameter allows you to set a minimum rolling average quality score allowed over a window. \n");
m->mothurOut("The qstepsize parameter allows you to set a number of bases to move the window over. Default=1.\n");
m->mothurOut("The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n");
- m->mothurOut("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 F.\n");
+ m->mothurOut("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");
m->mothurOut("The keepfirst parameter trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements. \n");
m->mothurOut("The removelast removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements.\n");
m->mothurOut("The trim.seqs command should be in the following format: \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["qfile"].push_back(trimQualFile);
+ outputTypes["qfile"].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["group"].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); }
+ 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++){
+ for(int j=0;j<fastaFileNames[0].size();j++){
+ if (fastaFileNames[i][j] != "") {
+ if(m->isBlank(fastaFileNames[i][j])){
+ remove(fastaFileNames[i][j].c_str());
+ namesToRemove.insert(fastaFileNames[i][j]);
+
+ if(qFileName != ""){
+ remove(qualFileNames[i][j].c_str());
+ namesToRemove.insert(qualFileNames[i][j]);
+ }
+ }else{
+ it = uniqueFastaNames.find(fastaFileNames[i][j]);
+ if (it == uniqueFastaNames.end()) {
+ uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
+ }
+ }
+ }
+ }
+ }
+
+ //remove names for outputFileNames, just cleans up the output
+ vector<string> outputNames2;
+ for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
+ outputNames = outputNames2;
+
+ for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
+ ifstream in;
+ m->openInputFile(it->first, in);
- m->openOutputFile(outGroupFilename, outGroups);
- outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);
+ ofstream out;
+ string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first)) + "groups";
+ outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
+ m->openOutputFile(thisGroupName, out);
- 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 (!in.eof()){
+ if (m->control_pressed) { break; }
- while(!inFASTA.eof()){
- if(inFASTA.get() == '>'){
- inFASTA >> seqName;
- outGroups << seqName << '\t' << thisGroup << endl;
- }
- while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
+ Sequence currSeq(in); m->gobble(in);
+ out << currSeq.getName() << '\t' << it->second << endl;
}
- outGroups.close();
- inFASTA.close();
+ in.close();
+ out.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()); } return 0; }
+
+ //output group counts
+ m->mothurOutEndLine();
+ int total = 0;
+// for (int i = 0; i < barcodeNameVector.size(); i++) {
+// if ((barcodeNameVector[i] != "") && (groupCounts[i] != 0)) { total += groupCounts[i]; m->mothurOut("Group " + barcodeNameVector[i] + " contains " + toString(groupCounts[i]) + " sequences."); m->mothurOutEndLine(); }
+// }
+// if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
- if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
/**************************************************************************************/
-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;
-
- if (oligoFile != "") {
- m->openOutputFile(groupFile, outGroups);
+ ofstream outGroupsFile;
+ if (oligoFile != ""){ m->openOutputFile(groupFileName, outGroupsFile); }
+ 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
+ if (fastaFileNames[i][j] != "") {
+ 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; }
}
else { success = 1; }
//you don't want to trim, if it fails above then scrap it
- if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
+ if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
if(!success) { trashCode += 'q'; }
}
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;
+ groupCounts[barcodeIndex]++;
}
- 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++){
+ if (tempFASTAFileNames[i][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]);
+
+ //pass groupCounts to parent
+ ofstream out;
+ string tempFile = filename + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ for(int i = 0; i < groupCounts.size(); i++) {
+ out << groupCounts[i] << endl;
+ }
+ out.close();
- 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();
- }
- }
-
- driverCreateTrim(filename, qFileName, trimFile, scrapFile, trimQFile, scrapQFile, groupFile, fastaNames, qualNames, lines[0], qLines[0]);
-
+ 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, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
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(allFiles){
+ for(int j=0;j<fastaFileNames.size();j++){
+ for(int k=0;k<fastaFileNames[j].size();k++){
+ if (fastaFileNames[j][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(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());
- }
+ ifstream in;
+ string tempFile = filename + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ int count = 0;
+ int tempNum;
+ while (!in.eof()) {
+ in >> tempNum; m->gobble(in);
+ groupCounts[count] += tempNum;
+ count++;
}
+ in.close(); remove(tempFile.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"));
+ 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 = "";
+
+ 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(fastaFileName) == 0) {
+ outputNames.push_back(qualFileName);
+ outputTypes["qfile"].push_back(qualFileName);
+ }
+
+ qualFileNames[itBar->second][itPrimer->second] = qualFileName;
+ m->openOutputFile(qualFileName, temp); temp.close();
}
}
}
}
-
numFPrimers = primers.size();
numRPrimers = revPrimer.size();
-
+ groupCounts.resize(barcodeNameVector.size(), 0);
+
}
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