try {
CommandParameter pfasta("ffastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
CommandParameter prfasta("rfastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(prfasta);
- CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
+
+ CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "",false,false); parameters.push_back(palign);
+ CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pallfiles);
CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
+ CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "",false,false); parameters.push_back(pthreshold);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
try {
string helpString = "";
helpString += "The make.contigs command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.\n";
- helpString += "The make.contigs command parameters are ffastq, rfastq, align, match, mismatch, gapopen, gapextend and processors.\n";
- helpString += "The ffastq and rfastq parameter is required.\n";
- helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n";
+ helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n";
+ helpString += "The make.contigs command parameters are ffastq, rfastq, oligos, tdiffs, bdiffs, ldiffs, sdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, allfiles and processors.\n";
+ helpString += "The ffastq and rfastq parameters are required.\n";
+ helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh and needleman. The default is needleman.\n";
+ helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
+ helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
+ helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
+ helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
+ helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n";
+ helpString += "The threshold parameter allows you to set a quality scores threshold. In the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it. Default=40.\n";
helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
+ helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
helpString += "The make.contigs command should be in the following format: \n";
helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n";
helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n";
exit(1);
}
}
-
+//**********************************************************************************************************************
+string MakeContigsCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "fasta") { outputFileName = "contigs.fasta"; }
+ else if (type == "qfile") { outputFileName = "contigs.qual"; }
+ else if (type == "group") { outputFileName = "groups"; }
+ else if (type == "mismatch") { outputFileName = "contigs.mismatch"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
MakeContigsCommand::MakeContigsCommand(){
try {
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["mismatch"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
+ outputTypes["mismatch"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["rfastq"] = inputDir + it->second; }
}
+
+ it = parameters.find("oligos");
+ //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["oligos"] = inputDir + it->second; }
+ }
}
ffastqfile = validParameter.validFile(parameters, "ffastq", true);
if (rfastqfile == "not open") { rfastqfile = ""; abort = true; }
else if (rfastqfile == "not found") { rfastqfile = ""; abort=true; m->mothurOut("The rfastq parameter is required.\n"); }
+ oligosfile = validParameter.validFile(parameters, "oligos", true);
+ if (oligosfile == "not found") { oligosfile = ""; }
+ else if(oligosfile == "not open") { abort = true; }
+ else { m->setOligosFile(oligosfile); }
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(ffastqfile); }
m->mothurConvert(temp, gapExtend);
if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
+ temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "40"; }
+ m->mothurConvert(temp, threshold);
+ if ((threshold < 0) || (threshold > 40)) { m->mothurOut("[ERROR]: threshold must be between 0 and 40.\n"); abort=true; }
+
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
+
+ temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, bdiffs);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, pdiffs);
+
+ temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, ldiffs);
+
+ temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, sdiffs);
+
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
+ m->mothurConvert(temp, tdiffs);
+
+ if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
+
+ temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
+ allFiles = m->isTrue(temp);
align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
- if ((align != "needleman") && (align != "blast") && (align != "gotoh") && (align != "noalign")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman, blast, gotoh and noalign. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; }
+ if ((align != "needleman") && (align != "gotoh")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman or gotoh. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; }
}
}
//this function will create a forward and reverse, fasta and qual files for each processor.
//files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual
int numReads = 0;
- m->mothurOut("Reading fastq data..."); cout.flush();
+ int start = time(NULL);
+ longestBase = 1000;
+ m->mothurOut("Reading fastq data...\n");
vector< vector<string> > files = readFastqFiles(numReads);
m->mothurOut("Done.\n");
+
+ if (m->control_pressed) { return 0; }
+
+ string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("fasta");
+ string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("qfile");
+ string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("mismatch");
+ outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
+ outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
+ outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
+
+ m->mothurOut("Making contigs...\n");
+ createProcesses(files, outFastaFile, outQualFile, outMisMatchFile);
+ m->mothurOut("Done.\n");
+
+ //remove temp fasta and qual files
+ for (int i = 0; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
string currentFasta = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); }
}
+
+ string currentGroup = "";
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { currentGroup = (itTypes->second)[0]; m->setGroupFile(currentGroup); }
+ }
//output files created by command
m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
-
return 0;
}
catch(exception& e) {
}
}
//**********************************************************************************************************************
+int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputMisMatches) {
+ try {
+ int num = 0;
+ vector<int> processIDS;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ int process = 0;
+
+ //loop through and create all the processes you want
+ while (process != processors-1) {
+ int 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
+ process++;
+ }else if (pid == 0){
+ num = driver(files[process], outputFasta + toString(getpid()) + ".temp", outputQual + toString(getpid()) + ".temp", outputMisMatches + toString(getpid()) + ".temp");
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = outputFasta + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << endl;
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = outputFasta + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+ in.close(); m->mothurRemove(tempFile);
+ }
+ #else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the contigsData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<contigsData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++ ){
+ string extension = toString(i) + ".temp";
+
+ contigsData* tempcontig = new contigsData(files[i], (outputFasta + extension), (outputQual + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, threshold, i);
+ pDataArray.push_back(tempcontig);
+ processIDS.push_back(i);
+
+ hThreadArray[i] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+ #endif
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
+ m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
+ m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
+
+ m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
+ m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
+ }
+
+ return num;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "createProcesses");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputMisMatches){
+ try {
+
+ Alignment* alignment;
+ if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
+ else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
+
+ int num = 0;
+ string thisffastafile = files[0];
+ string thisfqualfile = files[1];
+ string thisrfastafile = files[2];
+ string thisrqualfile = files[3];
+
+ if (m->debug) { m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
+
+ ifstream inFFasta, inRFasta, inFQual, inRQual;
+ m->openInputFile(thisffastafile, inFFasta);
+ m->openInputFile(thisfqualfile, inFQual);
+ m->openInputFile(thisrfastafile, inRFasta);
+ m->openInputFile(thisrqualfile, inRQual);
+
+ ofstream outFasta, outQual, outMisMatch;
+ m->openOutputFile(outputFasta, outFasta);
+ m->openOutputFile(outputQual, outQual);
+ m->openOutputFile(outputMisMatches, outMisMatch);
+ outMisMatch << "Name\tLength\tMisMatches\n";
+
+ while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
+
+ if (m->control_pressed) { break; }
+
+ //read seqs and quality info
+ Sequence fSeq(inFFasta); m->gobble(inFFasta);
+ Sequence rSeq(inRFasta); m->gobble(inRFasta);
+ QualityScores fQual(inFQual); m->gobble(inFQual);
+ QualityScores rQual(inRQual); m->gobble(inRQual);
+
+ //flip the reverse reads
+ rSeq.reverseComplement();
+ rQual.flipQScores();
+
+ //pairwise align
+ alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
+ map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
+ map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
+ fSeq.setAligned(alignment->getSeqAAln());
+ rSeq.setAligned(alignment->getSeqBAln());
+ int length = fSeq.getAligned().length();
+
+ //traverse alignments merging into one contiguous seq
+ string contig = "";
+ vector<int> contigScores;
+ int numMismatches = 0;
+ string seq1 = fSeq.getAligned();
+ string seq2 = rSeq.getAligned();
+ vector<int> scores1 = fQual.getQualityScores();
+ vector<int> scores2 = rQual.getQualityScores();
+
+ // if (num < 5) { cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
+ int overlapStart = fSeq.getStartPos();
+ int seq2Start = rSeq.getStartPos();
+ //bigger of the 2 starting positions is the location of the overlapping start
+ if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
+ overlapStart = seq2Start;
+ for (int i = 0; i < overlapStart; i++) {
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ }
+ }else { //seq1 starts later so take from 0 to overlapStart from seq2
+ for (int i = 0; i < overlapStart; i++) {
+ contig += seq2[i];
+ contigScores.push_back(scores2[BBaseMap[i]]);
+ }
+ }
+
+ int seq1End = fSeq.getEndPos();
+ int seq2End = rSeq.getEndPos();
+ int overlapEnd = seq1End;
+ if (seq2End < overlapEnd) { overlapEnd = seq2End; } //smallest end position is where overlapping ends
+
+ for (int i = overlapStart; i < overlapEnd; i++) {
+ if (seq1[i] == seq2[i]) { //match, add base and choose highest score
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
+ }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base
+ if (scores2[BBaseMap[i]] < threshold) { } //
+ else {
+ contig += seq2[i];
+ contigScores.push_back(scores2[BBaseMap[i]]);
+ }
+ }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base
+ if (scores1[ABaseMap[i]] < threshold) { } //
+ else {
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ }
+ }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
+ char c = seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
+ contig += c;
+ numMismatches++;
+ }else { //should never get here
+ m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
+ }
+ }
+
+ if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
+ for (int i = overlapEnd; i < length; i++) {
+ contig += seq2[i];
+ contigScores.push_back(scores2[BBaseMap[i]]);
+ }
+ }else { //seq2 ends before seq1 so take from overlap to length from seq1
+ for (int i = overlapEnd; i < length; i++) {
+ contig += seq1[i];
+ contigScores.push_back(scores1[ABaseMap[i]]);
+ }
+
+ }
+ //if (num < 5) { cout << overlapStart << '\t' << overlapEnd << endl << seq1 << endl << seq2 << endl<< contig << endl; }
+ //output
+ outFasta << ">" << fSeq.getName() << endl << contig << endl;
+ outQual << ">" << fSeq.getName() << endl;
+ for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
+ outQual << endl;
+ outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
+
+ num++;
+
+ //report progress
+ if((num) % 1000 == 0){ m->mothurOut(toString(num)); m->mothurOutEndLine(); }
+ }
+
+ //report progress
+ if((num) % 1000 != 0){ m->mothurOut(toString(num)); m->mothurOutEndLine(); }
+
+ inFFasta.close();
+ inFQual.close();
+ inRFasta.close();
+ inRQual.close();
+ outFasta.close();
+ outQual.close();
+ outMisMatch.close();
+ delete alignment;
+
+ if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta); m->mothurRemove(outputMisMatches);}
+
+ return num;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
vector< vector<string> > MakeContigsCommand::readFastqFiles(int& count){
try {
vector< vector<string> > files;
//report progress
if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-
+
//close files, delete ofstreams
for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close(); delete (it->second)[i]; } }
exit(1);
}
}
-
//**********************************************************************************************************************
fastqRead MakeContigsCommand::readFastq(ifstream& in){
try {
exit(1);
}
}
+//***************************************************************************************************************
+//illumina data requires paired forward and reverse data
+//BARCODE atgcatgc atgcatgc groupName
+//PRIMER atgcatgc atgcatgc groupName
+//PRIMER atgcatgc atgcatgc
+bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames){
+ try {
+ ifstream in;
+ m->openInputFile(oligosfile, in);
+
+ ofstream test;
+
+ string type, foligo, roligo, group;
+
+ int indexPrimer = 0;
+ int indexBarcode = 0;
+ set<string> uniquePrimers;
+ set<string> uniqueBarcodes;
+
+ while(!in.eof()){
+
+ in >> type;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
+
+ if(type[0] == '#'){
+ while (!in.eof()) { char c = in.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ m->gobble(in);
+ }
+ else{
+ m->gobble(in);
+ //make type case insensitive
+ for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
+
+ in >> foligo;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reading - " + foligo + ".\n"); }
+
+ for(int i=0;i<foligo.length();i++){
+ foligo[i] = toupper(foligo[i]);
+ if(foligo[i] == 'U') { foligo[i] = 'T'; }
+ }
+
+ if(type == "PRIMER"){
+ m->gobble(in);
+
+ in >> 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 (!in.eof()) {
+ char c = in.get();
+ if (c == 10 || c == 13){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ oligosPair newPrimer(foligo, roligo);
+
+ //check for repeat barcodes
+ string tempPair = foligo+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"); } }
+
+ primers[indexPrimer]=newPrimer; indexPrimer++;
+ primerNameVector.push_back(group);
+ }else if(type == "BARCODE"){
+ m->gobble(in);
+
+ in >> roligo;
+
+ for(int i=0;i<roligo.length();i++){
+ roligo[i] = toupper(roligo[i]);
+ if(roligo[i] == 'U') { roligo[i] = 'T'; }
+ }
+ roligo = reverseOligo(roligo);
+
+ oligosPair newPair(foligo, roligo);
+
+ group = "";
+ while (!in.eof()) {
+ char c = in.get();
+ if (c == 10 || c == 13){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
+
+ //check for repeat barcodes
+ string tempPair = foligo+roligo;
+ 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); }
+
+ barcodes[indexBarcode]=newPair; indexBarcode++;
+ barcodeNameVector.push_back(group);
+ }else if(type == "LINKER"){
+ linker.push_back(foligo);
+ }else if(type == "SPACER"){
+ spacer.push_back(foligo);
+ }
+ else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are primer, barcode, linker and spacer. Ignoring " + foligo + "."); m->mothurOutEndLine(); }
+ }
+ m->gobble(in);
+ }
+ in.close();
+
+ if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
+
+ //add in potential combos
+ if(barcodeNameVector.size() == 0){
+ oligosPair temp("", "");
+ barcodes[0] = temp;
+ barcodeNameVector.push_back("");
+ }
+
+ if(primerNameVector.size() == 0){
+ oligosPair temp("", "");
+ primers[0] = temp;
+ primerNameVector.push_back("");
+ }
+
+ fastaFileNames.resize(barcodeNameVector.size());
+ for(int i=0;i<fastaFileNames.size();i++){
+ fastaFileNames[i].assign(primerNameVector.size(), "");
+ }
+ qualFileNames = fastaFileNames;
+
+ if(allFiles){
+ set<string> uniqueNames; //used to cleanup outputFileNames
+ 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 = primerNameVector[itPrimer->first];
+ string barcodeName = barcodeNameVector[itBar->first];
+
+ 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;
+ fastaFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + comboGroupName + ".fasta";
+ 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();
+
+
+ qualFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + comboGroupName + ".qual";
+ 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();
+ }
+ }
+ }
+
+ 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;
+ }
+
+ return true;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "getOligos");
+ exit(1);
+ }
+}
+//********************************************************************/
+string MakeContigsCommand::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, "MakeContigsCommand", "reverseOligo");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
projects / mothur.git / blobdiff