X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makecontigscommand.cpp;h=bf55165dc96a6792a8f1de079dfb259b702df061;hb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;hp=523edd5e8ba1fd00f1bf5050a380b43e1549ee4f;hpb=01f6af90c907264686304a5c684c702e94ff40ae;p=mothur.git diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp index 523edd5..bf55165 100644 --- a/makecontigscommand.cpp +++ b/makecontigscommand.cpp @@ -11,17 +11,25 @@ //********************************************************************************************************************** vector MakeContigsCommand::setParameters(){ 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", "needleman", "", "", "",false,false); parameters.push_back(palign); - 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); + CommandParameter pfasta("ffastq", "InputTypes", "", "", "none", "none", "none","fasta-qfile",false,true,true); parameters.push_back(pfasta); + CommandParameter prfasta("rfastq", "InputTypes", "", "", "none", "none", "none","fasta-qfile",false,true,true); parameters.push_back(prfasta); + CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos); + CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs); + CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs); +// CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs); +// CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs); + CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs); + + CommandParameter 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,true); parameters.push_back(pprocessors); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -37,15 +45,22 @@ string MakeContigsCommand::getHelpString(){ 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"; @@ -56,7 +71,24 @@ string MakeContigsCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string MakeContigsCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],[tag],contigs.fasta"; } + else if (type == "qfile") { pattern = "[filename],[tag],contigs.qual"; } + else if (type == "group") { pattern = "[filename],[tag],groups"; } + else if (type == "mismatch") { pattern = "[filename],[tag],contigs.mismatch"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "MakeContigsCommand", "getOutputPattern"); + exit(1); + } +} //********************************************************************************************************************** MakeContigsCommand::MakeContigsCommand(){ try { @@ -65,6 +97,7 @@ MakeContigsCommand::MakeContigsCommand(){ vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["qfile"] = tempOutNames; + outputTypes["group"] = tempOutNames; outputTypes["mismatch"] = tempOutNames; } catch(exception& e) { @@ -100,6 +133,7 @@ MakeContigsCommand::MakeContigsCommand(string option) { 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 @@ -122,6 +156,14 @@ MakeContigsCommand::MakeContigsCommand(string option) { //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); @@ -132,6 +174,11 @@ MakeContigsCommand::MakeContigsCommand(string option) { 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); } @@ -161,6 +208,28 @@ MakeContigsCommand::MakeContigsCommand(string option) { 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); + ldiffs = 0; + + // temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; } + // m->mothurConvert(temp, sdiffs); + sdiffs = 0; + + temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs; 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 != "gotoh")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman or gotoh. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; } @@ -189,15 +258,38 @@ int MakeContigsCommand::execute(){ if (m->control_pressed) { return 0; } - string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.fasta"; - string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.qual"; - string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.mismatches"; + vector > fastaFileNames; + vector > qualFileNames; + createGroup = false; + string outputGroupFileName; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(ffastqfile)); + variables["[tag]"] = ""; + if(oligosfile != ""){ + createGroup = getOligos(fastaFileNames, qualFileNames); + if (createGroup) { + outputGroupFileName = getOutputFileName("group",variables); + outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); + } + } + + variables["[tag]"] = "trim"; + string outFastaFile = getOutputFileName("fasta",variables); + string outQualFile = getOutputFileName("qfile",variables); + variables["[tag]"] = "scrap"; + string outScrapFastaFile = getOutputFileName("fasta",variables); + string outScrapQualFile = getOutputFileName("qfile",variables); + + variables["[tag]"] = ""; + string outMisMatchFile = getOutputFileName("mismatch",variables); outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile); outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile); + outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile); + outputNames.push_back(outScrapQualFile); outputTypes["qfile"].push_back(outScrapQualFile); outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile); m->mothurOut("Making contigs...\n"); - createProcesses(files, outFastaFile, outQualFile, outMisMatchFile); + createProcesses(files, outFastaFile, outQualFile, outScrapFastaFile, outScrapQualFile, outMisMatchFile, fastaFileNames, qualFileNames); m->mothurOut("Done.\n"); //remove temp fasta and qual files @@ -205,8 +297,79 @@ int MakeContigsCommand::execute(){ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + if(allFiles){ + map uniqueFastaNames;// so we don't add the same groupfile multiple times + map::iterator it; + set namesToRemove; + for(int i=0;iisBlank(fastaFileNames[i][j])){ + m->mothurRemove(fastaFileNames[i][j]); + namesToRemove.insert(fastaFileNames[i][j]); + + m->mothurRemove(qualFileNames[i][j]); + 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 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); + + ofstream out; + string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first)); + thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); + m->openOutputFile(thisGroupName, out); + + while (!in.eof()){ + if (m->control_pressed) { break; } + + Sequence currSeq(in); m->gobble(in); + out << currSeq.getName() << '\t' << it->second << endl; + } + in.close(); + out.close(); + } + } + + if (createGroup) { + ofstream outGroup; + m->openOutputFile(outputGroupFileName, outGroup); + for (map::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) { + outGroup << itGroup->first << '\t' << itGroup->second << endl; + } + outGroup.close(); + } m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n"); + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + //output group counts + m->mothurOutEndLine(); + int total = 0; + if (groupCounts.size() != 0) { m->mothurOut("Group count: \n"); } + for (map::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) { + total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); 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++) { m->mothurRemove(outputNames[i]); } return 0; } + string currentFasta = ""; itTypes = outputTypes.find("fasta"); if (itTypes != outputTypes.end()) { @@ -218,6 +381,12 @@ int MakeContigsCommand::execute(){ 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(); @@ -225,7 +394,6 @@ int MakeContigsCommand::execute(){ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine(); - return 0; } catch(exception& e) { @@ -234,7 +402,7 @@ int MakeContigsCommand::execute(){ } } //********************************************************************************************************************** -int MakeContigsCommand::createProcesses(vector< vector > files, string outputFasta, string outputQual, string outputMisMatches) { +int MakeContigsCommand::createProcesses(vector< vector > files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector > fastaFileNames, vector > qualFileNames) { try { int num = 0; vector processIDS; @@ -249,14 +417,52 @@ int MakeContigsCommand::createProcesses(vector< vector > files, string o 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"); + vector > tempFASTAFileNames = fastaFileNames; + vector > tempPrimerQualFileNames = qualFileNames; + + if(allFiles){ + ofstream temp; + + for(int i=0;iopenOutputFile(tempFASTAFileNames[i][j], temp); temp.close(); + + tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp"; + m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close(); + } + } + } + } + + num = driver(files[process], + outputFasta + toString(getpid()) + ".temp", + outputQual + toString(getpid()) + ".temp", + outputScrapFasta + toString(getpid()) + ".temp", + outputScrapQual + toString(getpid()) + ".temp", + outputMisMatches + toString(getpid()) + ".temp", + tempFASTAFileNames, + tempPrimerQualFileNames); - //pass numSeqs to parent - ofstream out; - string tempFile = outputFasta + toString(getpid()) + ".num.temp"; - m->openOutputFile(tempFile, out); - out << num << endl; - out.close(); + //pass groupCounts to parent + ofstream out; + string tempFile = toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); + out << num << endl; + if(createGroup){ + out << groupCounts.size() << endl; + + for (map::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) { + out << it->first << '\t' << it->second << endl; + } + + out << groupMap.size() << endl; + for (map::iterator it = groupMap.begin(); it != groupMap.end(); it++) { + out << it->first << '\t' << it->second << endl; + } + } + out.close(); exit(0); }else { @@ -266,8 +472,14 @@ int MakeContigsCommand::createProcesses(vector< vector > files, string o } } + ofstream temp; + m->openOutputFile(outputFasta, temp); temp.close(); + m->openOutputFile(outputQual, temp); temp.close(); + m->openOutputFile(outputScrapFasta, temp); temp.close(); + m->openOutputFile(outputScrapQual, temp); temp.close(); + //do my part - num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches); + num = driver(files[processors-1], outputFasta, outputQual, outputScrapFasta, outputScrapQual, outputMisMatches, fastaFileNames, qualFileNames); //force parent to wait until all the processes are done for (int i=0;i > files, string o } 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); + ifstream in; + string tempFile = toString(processIDS[i]) + ".num.temp"; + m->openInputFile(tempFile, in); + int tempNum; + in >> tempNum; num += tempNum; m->gobble(in); + + if(createGroup){ + string group; + in >> tempNum; m->gobble(in); + + if (tempNum != 0) { + for (int j = 0; j < tempNum; j++) { + int groupNum; + in >> group >> groupNum; m->gobble(in); + + map::iterator it = groupCounts.find(group); + if (it == groupCounts.end()) { groupCounts[group] = groupNum; } + else { groupCounts[it->first] += groupNum; } + } + } + in >> tempNum; m->gobble(in); + if (tempNum != 0) { + for (int j = 0; j < tempNum; j++) { + string group, seqName; + in >> seqName >> group; m->gobble(in); + + map::iterator it = groupMap.find(seqName); + if (it == groupMap.end()) { groupMap[seqName] = group; } + else { m->mothurOut("[ERROR]: " + seqName + " is in your fasta file more than once. Sequence names must be unique. please correct.\n"); } + } + } + } + in.close(); m->mothurRemove(tempFile); } #else @@ -294,17 +534,67 @@ int MakeContigsCommand::createProcesses(vector< vector > files, string o HANDLE hThreadArray[processors-1]; //Create processor worker threads. - for( int i=0; i > tempFASTAFileNames = fastaFileNames; + vector > tempPrimerQualFileNames = qualFileNames; + + if(allFiles){ + ofstream temp; + + for(int i=0;iopenOutputFile(tempFASTAFileNames[i][j], temp); temp.close(); + + + tempPrimerQualFileNames[i][j] += extension; + m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close(); + } + } + } + } + + + contigsData* tempcontig = new contigsData(files[h], (outputFasta + extension), (outputQual + extension), (outputScrapFasta + extension), (outputScrapQual + extension),(outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, threshold, barcodes, primers, tempFASTAFileNames, tempPrimerQualFileNames, barcodeNameVector, primerNameVector, pdiffs, bdiffs, tdiffs, createGroup, allFiles, h); pDataArray.push_back(tempcontig); - processIDS.push_back(i); - hThreadArray[i] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]); + hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]); } + + vector > tempFASTAFileNames = fastaFileNames; + vector > tempPrimerQualFileNames = qualFileNames; + + if(allFiles){ + ofstream temp; + string extension = toString(processors-1) + ".temp"; + + for(int i=0;iopenOutputFile(tempFASTAFileNames[i][j], temp); temp.close(); + + + tempPrimerQualFileNames[i][j] += extension; + m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close(); + } + } + } + } + + //parent do my part + ofstream temp; + m->openOutputFile(outputFasta, temp); temp.close(); + m->openOutputFile(outputQual, temp); temp.close(); + m->openOutputFile(outputScrapFasta, temp); temp.close(); + m->openOutputFile(outputScrapQual, temp); temp.close(); - num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches); + + //do my part + num = driver(files[processors-1], (outputFasta+ toString(processors-1) + ".temp"), (outputQual+ toString(processors-1) + ".temp"), (outputScrapFasta+ toString(processors-1) + ".temp"), (outputScrapQual+ toString(processors-1) + ".temp"), (outputMisMatches+ toString(processors-1) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames); //Wait until all threads have terminated. WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE); @@ -312,6 +602,16 @@ int MakeContigsCommand::createProcesses(vector< vector > files, string o //Close all thread handles and free memory allocations. for(int i=0; i < pDataArray.size(); i++){ num += pDataArray[i]->count; + for (map::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) { + map::iterator it2 = groupCounts.find(it->first); + if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; } + else { groupCounts[it->first] += it->second; } + } + for (map::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) { + map::iterator it2 = groupMap.find(it->first); + if (it2 == groupMap.end()) { groupMap[it->first] = it->second; } + else { m->mothurOut("[ERROR]: " + it->first + " is in your fasta file more than once. Sequence names must be unique. please correct.\n"); } + } CloseHandle(hThreadArray[i]); delete pDataArray[i]; } @@ -325,8 +625,28 @@ int MakeContigsCommand::createProcesses(vector< vector > files, string o m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual); m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp")); + m->appendFiles((outputScrapFasta + toString(processIDS[i]) + ".temp"), outputScrapFasta); + m->mothurRemove((outputScrapFasta + toString(processIDS[i]) + ".temp")); + + m->appendFiles((outputScrapQual + toString(processIDS[i]) + ".temp"), outputScrapQual); + m->mothurRemove((outputScrapQual + toString(processIDS[i]) + ".temp")); + m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches); m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp")); + + if(allFiles){ + for(int j=0;jappendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]); + m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp")); + + m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]); + m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp")); + } + } + } + } } return num; @@ -337,7 +657,7 @@ int MakeContigsCommand::createProcesses(vector< vector > files, string o } } //********************************************************************************************************************** -int MakeContigsCommand::driver(vector files, string outputFasta, string outputQual, string outputMisMatches){ +int MakeContigsCommand::driver(vector files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector > fastaFileNames, vector > qualFileNames){ try { Alignment* alignment; @@ -358,26 +678,51 @@ int MakeContigsCommand::driver(vector files, string outputFasta, string m->openInputFile(thisrfastafile, inRFasta); m->openInputFile(thisrqualfile, inRQual); - ofstream outFasta, outQual, outMisMatch; + ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual; m->openOutputFile(outputFasta, outFasta); m->openOutputFile(outputQual, outQual); + m->openOutputFile(outputScrapFasta, outScrapFasta); + m->openOutputFile(outputScrapQual, outScrapQual); m->openOutputFile(outputMisMatches, outMisMatch); outMisMatch << "Name\tLength\tMisMatches\n"; + TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes); + while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) { if (m->control_pressed) { break; } + int success = 1; + string trashCode = ""; + int currentSeqsDiffs = 0; + //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); + int barcodeIndex = 0; + int primerIndex = 0; + + if(barcodes.size() != 0){ + success = trimOligos.stripBarcode(fSeq, rSeq, fQual, rQual, barcodeIndex); + if(success > bdiffs) { trashCode += 'b'; } + else{ currentSeqsDiffs += success; } + } + + if(primers.size() != 0){ + success = trimOligos.stripForward(fSeq, rSeq, fQual, rQual, primerIndex); + if(success > pdiffs) { trashCode += 'f'; } + else{ currentSeqsDiffs += success; } + } + + if (currentSeqsDiffs > tdiffs) { trashCode += 't'; } + //flip the reverse reads rSeq.reverseComplement(); rQual.flipQScores(); - + //pairwise align alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned()); map ABaseMap = alignment->getSeqAAlnBaseMap(); @@ -385,7 +730,7 @@ int MakeContigsCommand::driver(vector files, string outputFasta, string fSeq.setAligned(alignment->getSeqAAln()); rSeq.setAligned(alignment->getSeqBAln()); int length = fSeq.getAligned().length(); - + //traverse alignments merging into one contiguous seq string contig = ""; vector contigScores; @@ -394,8 +739,8 @@ int MakeContigsCommand::driver(vector files, string outputFasta, string string seq2 = rSeq.getAligned(); vector scores1 = fQual.getQualityScores(); vector scores2 = rQual.getQualityScores(); - - // if (num < 5) { cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; } + + // 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 @@ -455,16 +800,60 @@ int MakeContigsCommand::driver(vector files, string outputFasta, string contig += seq1[i]; contigScores.push_back(scores1[ABaseMap[i]]); } + + } + if(trashCode.length() == 0){ + if (createGroup) { + if(barcodes.size() != 0){ + string thisGroup = barcodeNameVector[barcodeIndex]; + if (primers.size() != 0) { + if (primerNameVector[primerIndex] != "") { + if(thisGroup != "") { + thisGroup += "." + primerNameVector[primerIndex]; + }else { + thisGroup = primerNameVector[primerIndex]; + } + } + } + + if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); } + + groupMap[fSeq.getName()] = thisGroup; + + map::iterator it = groupCounts.find(thisGroup); + if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; } + else { groupCounts[it->first] ++; } + + } + } + + if(allFiles){ + ofstream output; + m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output); + output << ">" << fSeq.getName() << endl << contig << endl; + output.close(); + + m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output); + output << ">" << fSeq.getName() << endl; + for (int i = 0; i < contigScores.size(); i++) { output << contigScores[i] << ' '; } + output << endl; + output.close(); + } + + //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; + }else { + //output + outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl; + outScrapQual << ">" << fSeq.getName() << " | " << trashCode << endl; + for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << ' '; } + outScrapQual << endl; } - //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 @@ -480,10 +869,12 @@ int MakeContigsCommand::driver(vector files, string outputFasta, string inRQual.close(); outFasta.close(); outQual.close(); + outScrapFasta.close(); + outScrapQual.close(); outMisMatch.close(); delete alignment; - if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta); m->mothurRemove(outputMisMatches);} + if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta); m->mothurRemove(outputScrapQual); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches);} return num; } @@ -541,39 +932,57 @@ vector< vector > MakeContigsCommand::readFastqFiles(int& count){ m->openInputFile(rfastqfile, inReverse); count = 0; - while ((!inForward.eof()) && (!inReverse.eof())) { + map uniques; + map::iterator itUniques; + while ((!inForward.eof()) || (!inReverse.eof())) { if (m->control_pressed) { 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]; } } for (int i = 0; i < files.size(); i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inForward.close(); inReverse.close(); return files; } //get a read from forward and reverse fastq files - fastqRead fread = readFastq(inForward); - fastqRead rread = readFastq(inReverse); - checkReads(fread, rread); - - if (m->control_pressed) { 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]; } } for (int i = 0; i < files.size(); i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inForward.close(); inReverse.close(); return files; } - - //if the reads are okay write to output files - int process = count % processors; + bool ignoref, ignorer; + fastqRead thisFread, thisRread; + if (!inForward.eof()) { thisFread = readFastq(inForward, ignoref); } + else { ignoref = true; } + if (!inReverse.eof()) { thisRread = readFastq(inReverse, ignorer); } + else { ignorer = true; } - *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl; - *(tempfiles[process][1]) << ">" << fread.name << endl; - for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; } - *(tempfiles[process][1]) << endl; - *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl; - *(tempfiles[process][3]) << ">" << rread.name << endl; - for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; } - *(tempfiles[process][3]) << endl; + vector reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques); - count++; - - //report progress - if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } - + for (int i = 0; i < reads.size(); i++) { + fastqRead fread = reads[i].forward; + fastqRead rread = reads[i].reverse; + + if (checkReads(fread, rread)) { + if (m->control_pressed) { 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]; } } for (int i = 0; i < files.size(); i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inForward.close(); inReverse.close(); return files; } + + //if the reads are okay write to output files + int process = count % processors; + + *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl; + *(tempfiles[process][1]) << ">" << fread.name << endl; + for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; } + *(tempfiles[process][1]) << endl; + *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl; + *(tempfiles[process][3]) << ">" << rread.name << endl; + for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; } + *(tempfiles[process][3]) << endl; + + count++; + + //report progress + if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } + } + } } //report progress if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } - + if (uniques.size() != 0) { + for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) { + m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n"); + } + 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]; } } @@ -581,6 +990,7 @@ vector< vector > MakeContigsCommand::readFastqFiles(int& count){ inReverse.close(); //adjust for really large processors or really small files + if (count == 0) { m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; } if (count < processors) { for (int i = count; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); } files.resize(count); @@ -595,43 +1005,110 @@ vector< vector > MakeContigsCommand::readFastqFiles(int& count){ } } //********************************************************************************************************************** -fastqRead MakeContigsCommand::readFastq(ifstream& in){ +vector MakeContigsCommand::getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map& uniques){ + try { + vector reads; + map::iterator itUniques; + + if (!ignoref && !ignorer) { + if (forward.name == reverse.name) { + pairFastqRead temp(forward, reverse); + reads.push_back(temp); + }else { + //look for forward pair + itUniques = uniques.find(forward.name); + if (itUniques != uniques.end()) { //we have the pair for this read + pairFastqRead temp(forward, itUniques->second); + reads.push_back(temp); + uniques.erase(itUniques); + }else { //save this read for later + uniques[forward.name] = forward; + } + + //look for reverse pair + itUniques = uniques.find(reverse.name); + if (itUniques != uniques.end()) { //we have the pair for this read + pairFastqRead temp(itUniques->second, reverse); + reads.push_back(temp); + uniques.erase(itUniques); + }else { //save this read for later + uniques[reverse.name] = reverse; + } + } + }else if (!ignoref && ignorer) { //ignore reverse keep forward + //look for forward pair + itUniques = uniques.find(forward.name); + if (itUniques != uniques.end()) { //we have the pair for this read + pairFastqRead temp(forward, itUniques->second); + reads.push_back(temp); + uniques.erase(itUniques); + }else { //save this read for later + uniques[forward.name] = forward; + } + + }else if (ignoref && !ignorer) { //ignore forward keep reverse + //look for reverse pair + itUniques = uniques.find(reverse.name); + if (itUniques != uniques.end()) { //we have the pair for this read + pairFastqRead temp(itUniques->second, reverse); + reads.push_back(temp); + uniques.erase(itUniques); + }else { //save this read for later + uniques[reverse.name] = reverse; + } + }//else ignore both and do nothing + + return reads; + } + catch(exception& e) { + m->errorOut(e, "MakeContigsCommand", "readFastqFiles"); + exit(1); + } +} +//********************************************************************************************************************** +fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){ try { fastqRead read; + ignore = false; + //read sequence name - string name = m->getline(in); m->gobble(in); - if (name == "") { m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; return read; } - else if (name[0] != '@') { m->mothurOut("[ERROR]: reading " + name + " expected a name with @ as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; return read; } + string line = m->getline(in); m->gobble(in); + vector pieces = m->splitWhiteSpace(line); + string name = ""; if (pieces.size() != 0) { name = pieces[0]; } + if (name == "") { m->mothurOut("[WARNING]: Blank fasta name, ignoring read."); m->mothurOutEndLine(); ignore=true; } + else if (name[0] != '@') { m->mothurOut("[WARNING]: reading " + name + " expected a name with @ as a leading character, ignoring read."); m->mothurOutEndLine(); ignore=true; } else { name = name.substr(1); } //read sequence string sequence = m->getline(in); m->gobble(in); - if (sequence == "") { m->mothurOut("[ERROR]: missing sequence for " + name); m->mothurOutEndLine(); m->control_pressed = true; return read; } + if (sequence == "") { m->mothurOut("[WARNING]: missing sequence for " + name + ", ignoring."); ignore=true; } //read sequence name - string name2 = m->getline(in); m->gobble(in); - if (name2 == "") { m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; return read; } - else if (name2[0] != '+') { m->mothurOut("[ERROR]: reading " + name2 + " expected a name with + as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; return read; } - else { name2 = name2.substr(1); } + line = m->getline(in); m->gobble(in); + pieces = m->splitWhiteSpace(line); + string name2 = ""; if (pieces.size() != 0) { name2 = pieces[0]; } + if (name2 == "") { m->mothurOut("[WARNING]: expected a name with + as a leading character, ignoring."); ignore=true; } + else if (name2[0] != '+') { m->mothurOut("[WARNING]: reading " + name2 + " expected a name with + as a leading character, ignoring."); ignore=true; } + else { name2 = name2.substr(1); if (name2 == "") { name2 = name; } } //read quality scores string quality = m->getline(in); m->gobble(in); - if (quality == "") { m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; return read; } - + if (quality == "") { m->mothurOut("[WARNING]: missing quality for " + name2 + ", ignoring."); ignore=true; } + //sanity check sequence length and number of quality scores match - if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; return read; } } - if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; return read; } + if (name2 != "") { if (name != name2) { m->mothurOut("[WARNING]: names do not match. read " + name + " for fasta and " + name2 + " for quality, ignoring."); ignore=true; } } + if (quality.length() != sequence.length()) { m->mothurOut("[WARNING]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores, ignoring read."); ignore=true; } vector qualScores; - int controlChar = int('@'); + int controlChar = int('!'); for (int i = 0; i < quality.length(); i++) { int temp = int(quality[i]); temp -= controlChar; qualScores.push_back(temp); } - + read.name = name; read.sequence = sequence; read.scores = qualScores; @@ -648,37 +1125,283 @@ bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse){ try { bool good = true; - //fix names - if ((forward.name.length() > 2) && (reverse.name.length() > 2)) { - forward.name = forward.name.substr(0, forward.name.length()-2); - reverse.name = reverse.name.substr(0, reverse.name.length()-2); - }else { good = false; m->control_pressed = true; } - - //do names match - if (forward.name != reverse.name) { - m->mothurOut("[ERROR]: read " + forward.name + " from " + ffastqfile + ", but read " + reverse.name + " from " + rfastqfile + ".\n"); - good = false; m->control_pressed = true; - } - //do sequence lengths match if (forward.sequence.length() != reverse.sequence.length()) { - m->mothurOut("[ERROR]: For sequence " + forward.name + " I read a sequence of length " + toString(forward.sequence.length()) + " from " + ffastqfile + ", but read a sequence of length " + toString(reverse.sequence.length()) + " from " + rfastqfile + ".\n"); - good = false; m->control_pressed = true; + m->mothurOut("[WARNING]: For sequence " + forward.name + " I read a sequence of length " + toString(forward.sequence.length()) + " from " + ffastqfile + ", but read a sequence of length " + toString(reverse.sequence.length()) + " from " + rfastqfile + ", ignoring.\n"); + good = false; } //do number of qual scores match if (forward.scores.size() != reverse.scores.size()) { - m->mothurOut("[ERROR]: For sequence " + forward.name + " I read " + toString(forward.scores.size()) + " quality scores from " + ffastqfile + ", but read " + toString(reverse.scores.size()) + " quality scores from " + rfastqfile + ".\n"); - good = false; m->control_pressed = true; + m->mothurOut("[WARNING]: For sequence " + forward.name + " I read " + toString(forward.scores.size()) + " quality scores from " + ffastqfile + ", but read " + toString(reverse.scores.size()) + " quality scores from " + rfastqfile + ", ignoring.\n"); + good = false; } return good; } catch(exception& e) { - m->errorOut(e, "MakeContigsCommand", "readFastq"); + m->errorOut(e, "MakeContigsCommand", "checkReads"); 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 >& fastaFileNames, vector >& qualFileNames){ + try { + ifstream in; + m->openInputFile(oligosfile, in); + + ofstream test; + + string type, foligo, roligo, group; + + int indexPrimer = 0; + int indexBarcode = 0; + set uniquePrimers; + set 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> foligo; + + if (m->debug) { m->mothurOut("[DEBUG]: reading - " + foligo + ".\n"); } + + for(int i=0;igobble(in); + + in >> roligo; + + for(int i=0;imothurOut("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;idebug) { 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); + m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n"); + }else if(type == "SPACER"){ + spacer.push_back(foligo); + m->mothurOut("[WARNING]: make.contigs is not setup to remove spacers, ignoring.\n"); + } + 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 uniqueNames; //used to cleanup outputFileNames + for(map::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){ + for(map::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); + } +} //**********************************************************************************************************************