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 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);
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";
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; }
}
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
outputTypes["mismatch"] = tempOutNames;
}
catch(exception& e) {
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); }
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 != "gotoh")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman or gotoh. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; }
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("mismatches");
+ vector<vector<string> > fastaFileNames;
+ vector<vector<string> > qualFileNames;
+ createGroup = false;
+ string outputGroupFileName;
+ if(oligosfile != ""){
+ createGroup = getOligos(fastaFileNames, qualFileNames);
+ if (createGroup) {
+ outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("group");
+ outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
+ }
+ }
+
+ string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "trim." + getOutputFileNameTag("fasta");
+ string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "trim." + getOutputFileNameTag("qfile");
+ string outScrapFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "scrap." + getOutputFileNameTag("fasta");
+ string outScrapQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "scrap." + 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(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
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ if(allFiles){
+ map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
+ map<string, string>::iterator it;
+ set<string> namesToRemove;
+ for(int i=0;i<fastaFileNames.size();i++){
+ for(int j=0;j<fastaFileNames[0].size();j++){
+ if (fastaFileNames[i][j] != "") {
+ if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
+ if(m->isBlank(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<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);
+
+ ofstream out;
+ string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first));
+ thisGroupName += getOutputFileNameTag("group"); 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<string, string>::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<string, int>::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()) {
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) {
+int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames) {
try {
int num = 0;
vector<int> processIDS;
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<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+
+ if(allFiles){
+ ofstream temp;
+
+ 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();
+
+ 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<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+ out << it->first << '\t' << it->second << endl;
+ }
+
+ out << groupMap.size() << endl;
+ for (map<string, string>::iterator it = groupMap.begin(); it != groupMap.end(); it++) {
+ out << it->first << '\t' << it->second << endl;
+ }
+ }
+ out.close();
exit(0);
}else {
}
}
+ 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<processIDS.size();i++) {
}
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<string, int>::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<string, string>::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
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);
+ for( int h=0; h<processors-1; h++ ){
+ string extension = "";
+ if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
+ vector<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+
+ if(allFiles){
+ ofstream temp;
+
+ for(int i=0;i<tempFASTAFileNames.size();i++){
+ for(int j=0;j<tempFASTAFileNames[i].size();j++){
+ if (tempFASTAFileNames[i][j] != "") {
+ tempFASTAFileNames[i][j] += extension;
+ m->openOutputFile(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<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+
+ if(allFiles){
+ ofstream temp;
+ string extension = toString(processors-1) + ".temp";
+
+ for(int i=0;i<tempFASTAFileNames.size();i++){
+ for(int j=0;j<tempFASTAFileNames[i].size();j++){
+ if (tempFASTAFileNames[i][j] != "") {
+ tempFASTAFileNames[i][j] += extension;
+ m->openOutputFile(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);
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
num += pDataArray[i]->count;
+ for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
+ map<string, int>::iterator it2 = groupCounts.find(it->first);
+ if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
+ else { groupCounts[it->first] += it->second; }
+ }
+ for (map<string, string>::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) {
+ map<string, string>::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];
}
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;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]);
+ 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;
}
}
//**********************************************************************************************************************
-int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputMisMatches){
+int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames){
try {
Alignment* alignment;
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<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
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;
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; }
+
+ // 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
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<string, int>::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
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;
}
m->openInputFile(rfastqfile, inReverse);
count = 0;
- while ((!inForward.eof()) && (!inReverse.eof())) {
+ map<string, fastqRead> uniques;
+ map<string, fastqRead>::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<pairFastqRead> 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]; } }
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);
}
}
//**********************************************************************************************************************
-fastqRead MakeContigsCommand::readFastq(ifstream& in){
+vector<pairFastqRead> MakeContigsCommand::getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques){
+ try {
+ vector<pairFastqRead> reads;
+ map<string, fastqRead>::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<string> 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<int> 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;
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<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 == "FORWARD"){
+ 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);
+ 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<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