CommandParameter prfastq("rfastq", "InputTypes", "", "", "none", "none", "fastqGroup","fasta-qfile",false,false,true); parameters.push_back(prfastq);
CommandParameter pfasta("ffasta", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "fastaGroup","fasta",false,false,true); parameters.push_back(pfasta);
CommandParameter prfasta("rfasta", "InputTypes", "", "", "none", "none", "none","fastaGroup",false,false,true); parameters.push_back(prfasta);
- CommandParameter pfqual("fqfile", "InputTypes", "", "", "none", "none", "qfileGroup","qfile",false,false,true); parameters.push_back(pfqual);
- CommandParameter prqual("rqfile", "InputTypes", "", "", "none", "none", "qfileGroup","qfile",false,false,true); parameters.push_back(prqual);
+ CommandParameter pfqual("fqfile", "InputTypes", "", "", "none", "none", "qfileGroup","",false,false,true); parameters.push_back(pfqual);
+ CommandParameter prqual("rqfile", "InputTypes", "", "", "none", "none", "qfileGroup","",false,false,true); parameters.push_back(prqual);
CommandParameter pfile("file", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "none","fasta-qfile",false,false,true); parameters.push_back(pfile);
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 ptrimoverlap("trimoverlap", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptrimoverlap);
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 pthreshold("insert", "Number", "", "20", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter pdeltaq("deltaq", "Number", "", "6", "", "", "","",false,false); parameters.push_back(pdeltaq);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
string helpString = "";
helpString += "The make.contigs command reads a file, forward fastq file and a reverse fastq file or forward fasta and reverse fasta files and outputs new fasta. It will also provide new quality files if the fastq or file parameter is used.\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 make.contigs command parameters are file, ffastq, rfastq, ffasta, rfasta, fqfile, rqfile, oligos, format, tdiffs, bdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, insert, deltaq, allfiles and processors.\n";
helpString += "The ffastq and rfastq, file, or ffasta and rfasta parameters are required.\n";
- helpString += "The file parameter is 2 column file containing the forward fastq files in the first column and their matching reverse fastq files in the second column. Mothur will process each pair and create a combined fasta and qual file with all the sequences.\n";
+ helpString += "The file parameter is 2 or 3 column file containing the forward fastq files in the first column and their matching reverse fastq files in the second column, or a groupName then forward fastq file and reverse fastq file. Mothur will process each pair and create a combined fasta and report file with all the sequences.\n";
helpString += "The ffastq and rfastq parameters are used to provide a forward fastq and reverse fastq file to process. If you provide one, you must provide the other.\n";
helpString += "The ffasta and rfasta parameters are used to provide a forward fasta and reverse fasta file to process. If you provide one, you must provide the other.\n";
helpString += "The fqfile and rqfile parameters are used to provide a forward quality and reverse quality files to process with the ffasta and rfasta parameters. If you provide one, you must provide the other.\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 format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=illumina1.8+.\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 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 deltaq parameter allows you to specify the delta allowed between quality scores of a mismatched base. For example in the overlap, if deltaq=5 and in the alignment seqA, pos 200 has a quality score of 30 and the same position in seqB has a quality score of 20, you take the base from seqA (30-20 >= 5). If the quality score in seqB is 28 then the base in the consensus will be an N (30-28<5) The default is 6.\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 insert 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 equal to or below the threshold we eliminate it. Default=20.\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 trimoverlap parameter allows you to trim the sequences to only the overlapping section. 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";
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 if (type == "group") { pattern = "[filename],[tag],contigs.groups"; }
+ else if (type == "report") { pattern = "[filename],[tag],contigs.report"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- outputTypes["qfile"] = tempOutNames;
outputTypes["group"] = tempOutNames;
- outputTypes["mismatch"] = tempOutNames;
- }
+ outputTypes["report"] = tempOutNames;
+ }
catch(exception& e) {
m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
exit(1);
//**********************************************************************************************************************
MakeContigsCommand::MakeContigsCommand(string option) {
try {
- abort = false; calledHelp = false;
+ abort = false; calledHelp = false;
+ createFileGroup = false; createOligosGroup = false;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- outputTypes["qfile"] = tempOutNames;
- outputTypes["mismatch"] = tempOutNames;
+ outputTypes["report"] = tempOutNames;
outputTypes["group"] = tempOutNames;
if (file == "not open") { abort = true; }
else if (file == "not found") { file = ""; }
- if ((file == "") && (ffastafile == "") && (ffastqfile == "")) { abort = true; m->mothurOut("[ERROR]: ffastq and rfastq parameters are required.\n"); }
- if ((ffastqfile != "") && (rfastqfile == "")) { abort = true; }
- if ((ffastqfile == "") && (rfastqfile != "")) { abort = true; }
+ //provide at least
+ if ((file == "") && (ffastafile == "") && (ffastqfile == "")) { abort = true; m->mothurOut("[ERROR]: The file, ffastq and rfastq or ffasta and rfasta parameters are required.\n"); }
+ if ((file != "") && ((ffastafile != "") || (ffastqfile != ""))) { abort = true; m->mothurOut("[ERROR]: The file, ffastq and rfastq or ffasta and rfasta parameters are required.\n"); }
+ if ((ffastqfile != "") && (rfastqfile == "")) { abort = true; m->mothurOut("[ERROR]: If you provide use the ffastq, you must provide a rfastq file.\n"); }
+ if ((ffastqfile == "") && (rfastqfile != "")) { abort = true; m->mothurOut("[ERROR]: If you provide use the rfastq, you must provide a ffastq file.\n"); }
+ if ((ffastafile != "") && (rfastafile == "")) { abort = true; m->mothurOut("[ERROR]: If you provide use the ffasta, you must provide a rfasta file.\n"); }
+ if ((ffastafile == "") && (rfastafile != "")) { abort = true; m->mothurOut("[ERROR]: If you provide use the rfasta, you must provide a ffasta file.\n"); }
+ if ((fqualfile != "") && (rqualfile == "")) { abort = true; m->mothurOut("[ERROR]: If you provide use the fqfile, you must provide a rqfile file.\n"); }
+ if ((fqualfile == "") && (rqualfile != "")) { abort = true; m->mothurOut("[ERROR]: If you provide use the rqfile, you must provide a fqfile file.\n"); }
+ if (((fqualfile != "") || (rqualfile != "")) && ((ffastafile == "") || (rfastafile == ""))) {
+ abort = true; m->mothurOut("[ERROR]: If you provide use the rqfile or fqfile file, you must provide the ffasta and rfasta parameters.\n");
+ }
oligosfile = validParameter.validFile(parameters, "oligos", true);
if (oligosfile == "not found") { oligosfile = ""; }
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); }
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ }
//check for optional parameter and set defaults
m->mothurConvert(temp, gapExtend);
if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
- temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "40"; }
- m->mothurConvert(temp, threshold);
- if ((threshold < 0) || (threshold > 40)) { m->mothurOut("[ERROR]: threshold must be between 0 and 40.\n"); abort=true; }
+ temp = validParameter.validFile(parameters, "insert", false); if (temp == "not found"){ temp = "20"; }
+ m->mothurConvert(temp, insert);
+ if ((insert < 0) || (insert > 40)) { m->mothurOut("[ERROR]: insert must be between 0 and 40.\n"); abort=true; }
+ temp = validParameter.validFile(parameters, "deltaq", false); if (temp == "not found"){ temp = "6"; }
+ m->mothurConvert(temp, deltaq);
+
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
allFiles = m->isTrue(temp);
+
+
+ temp = validParameter.validFile(parameters, "trimoverlap", false); if (temp == "not found") { temp = "F"; }
+ trimOverlap = 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"; }
+
+ format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "illumina1.8+"; }
+
+ if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+") && (format != "solexa")) {
+ m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa, illumina1.8+ and illumina, aborting." ); m->mothurOutEndLine();
+ abort=true;
+ }
+
+ //fill convert table - goes from solexa to sanger. Used fq_all2std.pl as a reference.
+ for (int i = -64; i < 65; i++) {
+ char temp = (char) ((int)(33 + 10*log(1+pow(10,(i/10.0)))/log(10)+0.499));
+ convertTable.push_back(temp);
+ }
}
}
//read ffastq and rfastq files creating fasta and qual files.
//this function will create a forward and reverse, fasta and qual files for each processor.
- //files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual
+ //files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual. filesToProcess is for each filepair in the file parameter file. for ffastq and rfastq this will be size 1.
unsigned long int numReads = 0;
int start = time(NULL);
longestBase = 1000;
m->mothurOut("Reading fastq data...\n");
- vector< vector<string> > files = readFastqFiles(numReads);
+ vector < vector< vector<string> > > filesToProcess = preProcessData(numReads);
m->mothurOut("Done.\n");
if (m->control_pressed) { return 0; }
- vector<vector<string> > fastaFileNames;
- vector<vector<string> > qualFileNames;
- createGroup = false;
- string outputGroupFileName;
- map<string, string> 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, outScrapFastaFile, outScrapQualFile, outMisMatchFile, fastaFileNames, qualFileNames);
- m->mothurOut("Done.\n");
+ map<string, string> cvars;
+ string compOutputDir = outputDir;
+ if (outputDir == "") { compOutputDir = m->hasPath(file); }
+ cvars["[filename]"] = compOutputDir + m->getRootName(m->getSimpleName(file));
+ cvars["[tag]"] = "";
+ string compositeGroupFile = getOutputFileName("group",cvars);
+ cvars["[tag]"] = "trim";
+ string compositeFastaFile = getOutputFileName("fasta",cvars);
+ cvars["[tag]"] = "scrap";
+ string compositeScrapFastaFile = getOutputFileName("fasta",cvars);
+ cvars["[tag]"] = "";
+ string compositeMisMatchFile = getOutputFileName("report",cvars);
- //remove temp fasta and qual files
- for (int i = 0; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } }
+ if (filesToProcess.size() > 1) { //clear files for append below
+ ofstream outCTFasta, outCTQual, outCSFasta, outCSQual, outCMisMatch;
+ m->openOutputFile(compositeFastaFile, outCTFasta); outCTFasta.close();
+ m->openOutputFile(compositeScrapFastaFile, outCSFasta); outCSFasta.close();
+ m->openOutputFile(compositeMisMatchFile, outCMisMatch); outCMisMatch.close();
+ outputNames.push_back(compositeFastaFile); outputTypes["fasta"].push_back(compositeFastaFile);
+ outputNames.push_back(compositeMisMatchFile); outputTypes["report"].push_back(compositeMisMatchFile);
+ outputNames.push_back(compositeScrapFastaFile); outputTypes["fasta"].push_back(compositeScrapFastaFile);
+ }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ map<string, int> totalGroupCounts;
- 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);
+ for (int l = 0; l < filesToProcess.size(); l++) {
+
+ m->mothurOut("\n>>>>>\tProcessing " + filesToProcess[l][0][0] + " (file " + toString(l+1) + " of " + toString(filesToProcess.size()) + ")\t<<<<<\n");
+
+ groupCounts.clear();
+ groupMap.clear();
+ vector<vector<string> > fastaFileNames;
+ createOligosGroup = false;
+ string outputGroupFileName;
+ map<string, string> variables;
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir = m->hasPath(filesToProcess[l][0][0]); }
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(filesToProcess[l][0][0]));
+ variables["[tag]"] = "";
+ if(oligosfile != ""){ createOligosGroup = getOligos(fastaFileNames, variables["[filename]"]); }
+ if (createOligosGroup || createFileGroup) {
+ outputGroupFileName = getOutputFileName("group",variables);
+ }
+
+ //give group in file file precedence
+ if (createFileGroup) { createOligosGroup = false; }
+
+ variables["[tag]"] = "trim";
+ string outFastaFile = getOutputFileName("fasta",variables);
+ variables["[tag]"] = "scrap";
+ string outScrapFastaFile = getOutputFileName("fasta",variables);
+ variables["[tag]"] = "";
+ string outMisMatchFile = getOutputFileName("report",variables);
+
+ m->mothurOut("Making contigs...\n");
+ createProcesses(filesToProcess[l], outFastaFile, outScrapFastaFile, outMisMatchFile, fastaFileNames, l);
+ m->mothurOut("Here...\n");
+
+ //remove temp fasta and qual files
+ for (int i = 0; i < processors; i++) { for(int j = 0; j < filesToProcess[l][i].size(); j++) { m->mothurRemove(filesToProcess[l][i][j]); } }
+
+ 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]);
+ }else{
+ it = uniqueFastaNames.find(fastaFileNames[i][j]);
+ if (it == uniqueFastaNames.end()) {
+ uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
+ }
+ }
+ }
+ }
+ }
+ }
- 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; }
+ //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);
- Sequence currSeq(in); m->gobble(in);
- out << currSeq.getName() << '\t' << it->second << endl;
+ ofstream out;
+ string thisGroupName = thisOutputDir + 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;
+ }
+ out.close();
+ in.close();
}
- 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;
+
+ if (createFileGroup || createOligosGroup) {
+ 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();
+ }
+
+ if (filesToProcess.size() > 1) { //merge into large combo files
+ if (createFileGroup || createOligosGroup) {
+ if (l == 0) {
+ ofstream outCGroup;
+ m->openOutputFile(compositeGroupFile, outCGroup); outCGroup.close();
+ outputNames.push_back(compositeGroupFile); outputTypes["group"].push_back(compositeGroupFile);
+ }
+ m->appendFiles(outputGroupFileName, compositeGroupFile);
+ if (!allFiles) { m->mothurRemove(outputGroupFileName); }
+ else { outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); }
+
+ for (map<string, int>::iterator itGroups = groupCounts.begin(); itGroups != groupCounts.end(); itGroups++) {
+ map<string, int>::iterator itTemp = totalGroupCounts.find(itGroups->first);
+ if (itTemp == totalGroupCounts.end()) { totalGroupCounts[itGroups->first] = itGroups->second; } //new group create it in totalGroups
+ else { itTemp->second += itGroups->second; } //existing group, update total
+ }
+ }
+ if (l == 0) { m->appendFiles(outMisMatchFile, compositeMisMatchFile); }
+ else { m->appendFilesWithoutHeaders(outMisMatchFile, compositeMisMatchFile); }
+ m->appendFiles(outFastaFile, compositeFastaFile);
+ m->appendFiles(outScrapFastaFile, compositeScrapFastaFile);
+ if (!allFiles) {
+ m->mothurRemove(outMisMatchFile);
+ m->mothurRemove(outFastaFile);
+ m->mothurRemove(outScrapFastaFile);
+ }else {
+ outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
+ outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
+ outputNames.push_back(outMisMatchFile); outputTypes["report"].push_back(outMisMatchFile);
+ }
+ }else {
+ totalGroupCounts = groupCounts;
+ outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
+ outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
+ outputNames.push_back(outMisMatchFile); outputTypes["report"].push_back(outMisMatchFile);
+ if (createFileGroup || createOligosGroup) {
+ outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
+ }
}
- outGroup.close();
+ m->mothurOut("Done.\n");
}
+
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++) {
+ if (totalGroupCounts.size() != 0) { m->mothurOut("Group count: \n"); }
+ for (map<string, int>::iterator it = totalGroupCounts.begin(); it != totalGroupCounts.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 ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
}
- string currentQual = "";
- itTypes = outputTypes.find("qfile");
- 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()) {
}
}
//**********************************************************************************************************************
-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) {
+vector< vector< vector<string> > > MakeContigsCommand::preProcessData(unsigned long int& numReads) {
+ try {
+ vector< vector< vector<string> > > filesToProcess;
+
+ if (ffastqfile != "") { //reading one file
+ vector< vector<string> > files = readFastqFiles(numReads, ffastqfile, rfastqfile);
+ //adjust for really large processors or really small files
+ if (numReads == 0) { m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
+ if (numReads < processors) {
+ for (int i = numReads; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
+ files.resize(numReads);
+ processors = numReads;
+ }
+ filesToProcess.push_back(files);
+ }else if (file != "") { //reading multiple files
+ //return only valid pairs
+ vector< vector<string> > filePairsToProcess = readFileNames(file);
+
+ if (m->control_pressed) { return filesToProcess; }
+
+ if (filePairsToProcess.size() != 0) {
+ for (int i = 0; i < filePairsToProcess.size(); i++) {
+
+ if (m->control_pressed) { for (int l = 0; l < filesToProcess.size(); l++) { for (int k = 0; k < filesToProcess[l].size(); k++) { for(int j = 0; j < filesToProcess[l][k].size(); j++) { m->mothurRemove(filesToProcess[l][k][j]); } filesToProcess[l][k].clear(); } return filesToProcess; } }
+
+ unsigned long int thisFilesReads;
+ vector< vector<string> > files = readFastqFiles(thisFilesReads, filePairsToProcess[i][0], filePairsToProcess[i][1]);
+
+ //adjust for really large processors or really small files
+ if (thisFilesReads < processors) {
+ m->mothurOut("[ERROR]: " + filePairsToProcess[i][0] + " has less than " + toString(processors) + " good reads, skipping\n");
+ for (int k = 0; k < files.size(); k++) { for(int j = 0; j < files[k].size(); j++) { m->mothurRemove(files[k][j]); } files[k].clear(); }
+ }else {
+ filesToProcess.push_back(files);
+ numReads += thisFilesReads;
+ }
+ }
+ //all files are bad
+ if (numReads == 0) { m->control_pressed = true; }
+ }
+ }else if (ffastafile != "") {
+ vector< vector<string> > files = readFastaFiles(numReads, ffastafile, rfastafile);
+ //adjust for really large processors or really small files
+ if (numReads == 0) { m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
+ if (numReads < processors) {
+ for (int i = numReads; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
+ files.resize(numReads);
+ processors = numReads;
+ }
+ filesToProcess.push_back(files);
+ }else { m->control_pressed = true; } //should not get here
+
+ return filesToProcess;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "preProcessData");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputScrapFasta, string outputMisMatches, vector<vector<string> > fastaFileNames, int index) {
try {
int num = 0;
vector<int> processIDS;
+ string group = "";
+ map<int, string>::iterator it = file2Group.find(index);
+ if (it != file2Group.end()) { group = it->second; }
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 0;
process++;
}else if (pid == 0){
vector<vector<string> > tempFASTAFileNames = fastaFileNames;
- vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
if(allFiles){
ofstream temp;
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);
+ tempFASTAFileNames, process, group);
//pass groupCounts to parent
ofstream out;
string tempFile = toString(getpid()) + ".num.temp";
m->openOutputFile(tempFile, out);
out << num << endl;
- if(createGroup){
+ if (createFileGroup || createOligosGroup) {
out << groupCounts.size() << endl;
for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
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, outputScrapFasta, outputScrapQual, outputMisMatches, fastaFileNames, qualFileNames);
+ num = driver(files[processors-1], outputFasta, outputScrapFasta, outputMisMatches, fastaFileNames, processors-1, group);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
int tempNum;
in >> tempNum; num += tempNum; m->gobble(in);
- if(createGroup){
+ if (createFileGroup || createOligosGroup) {
string group;
in >> tempNum; m->gobble(in);
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;
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);
+
+ contigsData* tempcontig = new contigsData(group, files[h], (outputFasta + extension), (outputScrapFasta + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, insert, deltaq, barcodes, primers, tempFASTAFileNames, barcodeNameVector, primerNameVector, pdiffs, bdiffs, tdiffs, createOligosGroup, createFileGroup, allFiles, trimOverlap, h);
pDataArray.push_back(tempcontig);
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;
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();
-
//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);
+ processIDS.push_back(processors-1);
+ num = driver(files[processors-1], (outputFasta+ toString(processors-1) + ".temp"), (outputScrapFasta+ toString(processors-1) + ".temp"), (outputMisMatches+ toString(processors-1) + ".temp"), tempFASTAFileNames, processors-1, group);
//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;
+ if (!pDataArray[i]->done) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
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; }
m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
- m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
- m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
-
- m->appendFiles((outputScrapFasta + toString(processIDS[i]) + ".temp"), outputScrapFasta);
+ 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->appendFilesWithoutHeaders((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
if(allFiles){
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"));
}
}
}
}
}
//**********************************************************************************************************************
-int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames){
+int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputScrapFasta, string outputMisMatches, vector<vector<string> > fastaFileNames, int process, string group){
try {
Alignment* alignment;
if (m->debug) { m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
ifstream inFFasta, inRFasta, inFQual, inRQual;
+ ofstream outFasta, outMisMatch, outScrapFasta;
m->openInputFile(thisffastafile, inFFasta);
- m->openInputFile(thisfqualfile, inFQual);
m->openInputFile(thisrfastafile, inRFasta);
- m->openInputFile(thisrqualfile, inRQual);
-
- ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
+ if (thisfqualfile != "") {
+ m->openInputFile(thisfqualfile, inFQual);
+ m->openInputFile(thisrqualfile, inRQual);
+ }
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";
+ outMisMatch << "Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns\n";
TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes);
- while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
+ while ((!inFFasta.eof()) && (!inRFasta.eof())) {
if (m->control_pressed) { break; }
//read seqs and quality info
Sequence fSeq(inFFasta); m->gobble(inFFasta);
Sequence rSeq(inRFasta); m->gobble(inRFasta);
- QualityScores fQual(inFQual); m->gobble(inFQual);
- QualityScores rQual(inRQual); m->gobble(inRQual);
+ QualityScores* fQual = NULL; QualityScores* rQual = NULL;
+ if (thisfqualfile != "") {
+ fQual = new QualityScores(inFQual); m->gobble(inFQual);
+ rQual = new QualityScores(inRQual); m->gobble(inRQual);
+ }
int barcodeIndex = 0;
int primerIndex = 0;
if(barcodes.size() != 0){
- success = trimOligos.stripBarcode(fSeq, rSeq, fQual, rQual, barcodeIndex);
+ if (thisfqualfile != "") {
+ success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
+ }else {
+ success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
+ }
if(success > bdiffs) { trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
if(primers.size() != 0){
- success = trimOligos.stripForward(fSeq, rSeq, fQual, rQual, primerIndex);
+ if (thisfqualfile != "") {
+ success = trimOligos.stripForward(fSeq, rSeq, *fQual, *rQual, primerIndex);
+ }else {
+ success = trimOligos.stripForward(fSeq, rSeq, primerIndex);
+ }
if(success > pdiffs) { trashCode += 'f'; }
else{ currentSeqsDiffs += success; }
}
//flip the reverse reads
rSeq.reverseComplement();
- rQual.flipQScores();
+ if (thisfqualfile != "") { rQual->flipQScores(); }
//pairwise align
alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
//traverse alignments merging into one contiguous seq
string contig = "";
- vector<int> contigScores;
int numMismatches = 0;
string seq1 = fSeq.getAligned();
string seq2 = rSeq.getAligned();
- vector<int> scores1 = fQual.getQualityScores();
- vector<int> scores2 = rQual.getQualityScores();
+ vector<int> scores1, scores2;
+ if (thisfqualfile != "") {
+ scores1 = fQual->getQualityScores();
+ scores2 = rQual->getQualityScores();
+ delete fQual; delete rQual;
+ }
// if (num < 5) { cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
int overlapStart = fSeq.getStartPos();
int seq2Start = rSeq.getStartPos();
+
//bigger of the 2 starting positions is the location of the overlapping start
if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
overlapStart = seq2Start;
- for (int i = 0; i < overlapStart; i++) {
- contig += seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
- }
+ for (int i = 0; i < overlapStart; i++) { contig += seq1[i]; }
}else { //seq1 starts later so take from 0 to overlapStart from seq2
- for (int i = 0; i < overlapStart; i++) {
- contig += seq2[i];
- contigScores.push_back(scores2[BBaseMap[i]]);
- }
+ for (int i = 0; i < overlapStart; i++) { contig += seq2[i]; }
}
int seq1End = fSeq.getEndPos();
int overlapEnd = seq1End;
if (seq2End < overlapEnd) { overlapEnd = seq2End; } //smallest end position is where overlapping ends
+ int oStart = contig.length();
for (int i = overlapStart; i < overlapEnd; i++) {
if (seq1[i] == seq2[i]) { //match, add base and choose highest score
contig += seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
- if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
- }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base
- if (scores2[BBaseMap[i]] < threshold) { } //
- else {
- contig += seq2[i];
- contigScores.push_back(scores2[BBaseMap[i]]);
- }
- }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base
- if (scores1[ABaseMap[i]] < threshold) { } //
- else {
- contig += seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
- }
+ }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below insert. In that case eliminate base
+ if (thisfqualfile != "") {
+ if (scores2[BBaseMap[i]] <= insert) { } //
+ else { contig += seq2[i]; }
+ }else { contig += seq2[i]; } //with no quality info, then we keep it?
+ }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below insert. In that case eliminate base
+ if (thisfqualfile != "") {
+ if (scores1[ABaseMap[i]] <= insert) { } //
+ else { contig += seq1[i]; }
+ }else { contig += seq1[i]; } //with no quality info, then we keep it?
}else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
- char c = seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
- if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
- contig += c;
- numMismatches++;
+ if (thisfqualfile != "") {
+ if (abs(scores1[ABaseMap[i]] - scores2[BBaseMap[i]]) >= deltaq) { //is the difference in qual scores >= deltaq, if yes choose base with higher score
+ char c = seq1[i];
+ if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { c = seq2[i]; }
+ contig += c;
+ }else { //if no, base becomes n
+ contig += 'N';
+ }
+ numMismatches++;
+ }else { numMismatches++; } //cant decide, so eliminate and mark as mismatch
}else { //should never get here
m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
}
}
-
+ int oend = contig.length();
if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
- for (int i = overlapEnd; i < length; i++) {
- contig += seq2[i];
- contigScores.push_back(scores2[BBaseMap[i]]);
- }
+ for (int i = overlapEnd; i < length; i++) { contig += seq2[i]; }
}else { //seq2 ends before seq1 so take from overlap to length from seq1
- for (int i = overlapEnd; i < length; i++) {
- contig += seq1[i];
- contigScores.push_back(scores1[ABaseMap[i]]);
- }
-
+ for (int i = overlapEnd; i < length; i++) { contig += seq1[i]; }
}
-
+
+ if (trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart); if (contig.length() == 0) { trashCode += "l"; } }
+
if(trashCode.length() == 0){
- if (createGroup) {
+ bool ignore = false;
+
+ if (m->debug) { m->mothurOut(fSeq.getName()); }
+
+ if (createOligosGroup) {
if(barcodes.size() != 0){
string thisGroup = barcodeNameVector[barcodeIndex];
if (primers.size() != 0) {
if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
- groupMap[fSeq.getName()] = thisGroup;
+ int pos = thisGroup.find("ignore");
+ if (pos == string::npos) {
+ groupMap[fSeq.getName()] = thisGroup;
- map<string, int>::iterator it = groupCounts.find(thisGroup);
- if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; }
- else { groupCounts[it->first] ++; }
+ map<string, int>::iterator it = groupCounts.find(thisGroup);
+ if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; }
+ else { groupCounts[it->first] ++; }
+ }else { ignore = true; }
}
+ }else if (createFileGroup) {
+ int pos = group.find("ignore");
+ if (pos == string::npos) {
+ groupMap[fSeq.getName()] = group;
+
+ map<string, int>::iterator it = groupCounts.find(group);
+ if (it == groupCounts.end()) { groupCounts[group] = 1; }
+ else { groupCounts[it->first] ++; }
+ }else { ignore = true; }
}
+ if (m->debug) { m->mothurOut("\n"); }
- if(allFiles){
+ if(allFiles && !ignore){
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;
+ int numNs = 0;
+ for (int i = 0; i < contig.length(); i++) { if (contig[i] == 'N') { numNs++; } }
+ outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << (oend-oStart) << '\t' << oStart << '\t' << oend << '\t' << numMismatches << '\t' << numNs << 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;
}
num++;
if((num) % 1000 != 0){ m->mothurOut(toString(num)); m->mothurOutEndLine(); }
inFFasta.close();
- inFQual.close();
inRFasta.close();
- inRQual.close();
outFasta.close();
- outQual.close();
outScrapFasta.close();
- outScrapQual.close();
outMisMatch.close();
+ if (thisfqualfile != "") {
+ inFQual.close();
+ inRQual.close();
+ }
delete alignment;
- if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta); m->mothurRemove(outputScrapQual); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches);}
-
+ if (m->control_pressed) { m->mothurRemove(outputFasta); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches); }
+
return num;
}
catch(exception& e) {
}
}
//**********************************************************************************************************************
-vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& count){
+vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& count, string ffastq, string rfastq){
try {
vector< vector<string> > files;
-
//maps processors number to file pointer
map<int, vector<ofstream*> > tempfiles; //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
map<int, vector<ofstream*> >::iterator it;
tempfiles[i] = temp;
vector<string> names;
- string ffastafilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "ffasta.temp";
- string rfastafilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rfasta.temp";
- string fqualfilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "fqual.temp";
- string rqualfilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rqual.temp";
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir = m->hasPath(ffastq); }
+ string ffastafilename = thisOutputDir + m->getRootName(m->getSimpleName(ffastq)) + toString(i) + "ffastatemp";
+ string rfastafilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rfastatemp";
+ string fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(ffastq)) + toString(i) + "fqualtemp";
+ string rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rqualtemp";
names.push_back(ffastafilename); names.push_back(fqualfilename);
names.push_back(rfastafilename); names.push_back(rqualfilename);
files.push_back(names);
}
ifstream inForward;
- m->openInputFile(ffastqfile, inForward);
+ m->openInputFile(ffastq, inForward);
ifstream inReverse;
- m->openInputFile(rfastqfile, inReverse);
+ m->openInputFile(rfastq, inReverse);
count = 0;
map<string, fastqRead> uniques;
if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
- if (checkReads(fread, rread)) {
+ //if (checkReads(fread, rread, ffastq, rfastq)) {
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
//report progress
if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
- }
+ //}
}
}
//report progress
inForward.close();
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);
- processors = count;
+ return files;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector< vector<string> > MakeContigsCommand::readFastaFiles(unsigned long int& count, string ffasta, string rfasta){
+ try {
+ vector< vector<string> > files;
+ //maps processors number to file pointer
+ map<int, vector<ofstream*> > tempfiles; //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
+ map<int, vector<ofstream*> >::iterator it;
+
+ //create files to write to
+ for (int i = 0; i < processors; i++) {
+ vector<ofstream*> temp;
+ ofstream* outFF = new ofstream; temp.push_back(outFF);
+ ofstream* outFQ = new ofstream; temp.push_back(outFQ);
+ ofstream* outRF = new ofstream; temp.push_back(outRF);
+ ofstream* outRQ = new ofstream; temp.push_back(outRQ);
+ tempfiles[i] = temp;
+
+ vector<string> names;
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir = m->hasPath(ffasta); }
+ string ffastafilename = thisOutputDir + m->getRootName(m->getSimpleName(ffasta)) + toString(i) + "ffastatemp";
+ string rfastafilename = thisOutputDir + m->getRootName(m->getSimpleName(rfasta)) + toString(i) + "rfastatemp";
+ string fqualfilename = "";
+ if (fqualfile != "") { fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(fqualfile)) + toString(i) + "fqual.temp"; m->openOutputFile(fqualfilename, *outFQ); }
+ string rqualfilename = "";
+ if (rqualfile != "") { rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rqualfile)) + toString(i) + "rqual.temp"; m->openOutputFile(rqualfilename, *outRQ); }
+ names.push_back(ffastafilename); names.push_back(fqualfilename);
+ names.push_back(rfastafilename); names.push_back(rqualfilename);
+ files.push_back(names);
+
+ m->openOutputFile(ffastafilename, *outFF);
+ m->openOutputFile(rfastafilename, *outRF);
}
+ if (m->control_pressed) {
+ //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]; } }
+ //remove files
+ for (int i = 0; i < files.size(); i++) {
+ for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
+ }
+ }
+
+ ifstream inForwardFasta;
+ m->openInputFile(ffasta, inForwardFasta);
+
+ ifstream inReverseFasta;
+ m->openInputFile(rfasta, inReverseFasta);
+
+ ifstream inForwardQual, inReverseQual;
+ if (fqualfile != "") { m->openInputFile(fqualfile, inForwardQual); m->openInputFile(rqualfile, inReverseQual); }
+
+ count = 0;
+ map<string, fastqRead> uniques;
+ map<string, fastqRead>::iterator itUniques;
+ while ((!inForwardFasta.eof()) || (!inReverseFasta.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]); } } inReverseFasta.close(); inForwardFasta.close(); if (fqualfile != "") { inReverseQual.close(); inReverseQual.close(); } return files; }
+
+ //get a reads from forward and reverse fasta files
+ bool ignoref, ignorer;
+ fastqRead thisFread, thisRread;
+ if (!inForwardFasta.eof()) {
+ ignoref = false;
+ Sequence temp(inForwardFasta); m->gobble(inForwardFasta);
+ thisFread.name = temp.getName();
+ thisFread.sequence = temp.getUnaligned();
+ }else { ignoref = true; }
+ if (!inReverseFasta.eof()) {
+ ignorer = false;
+ Sequence temp(inReverseFasta); m->gobble(inReverseFasta);
+ thisRread.name = temp.getName();
+ thisRread.sequence = temp.getUnaligned();
+ }else { ignorer = true; }
+
+ //get qual reads if given
+ if (fqualfile != "") {
+ if (!inForwardQual.eof() && !ignoref) {
+ QualityScores temp(inForwardQual); m->gobble(inForwardQual);
+ //if forward files dont match ignore read
+ if (thisFread.name != temp.getName()) { ignoref = true; }
+ else { thisFread.scores = temp.getQualityScores(); }
+ }else { ignoref = true; }
+ if (!inReverseQual.eof() && !ignorer) {
+ QualityScores temp(inReverseQual); m->gobble(inReverseQual);
+ //if reverse files dont match ignore read
+ if (thisRread.name != temp.getName()) { ignorer = true; }
+ else { thisRread.scores = temp.getQualityScores(); }
+ }else { ignorer = true; }
+ }
+
+ vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
+
+ for (int i = 0; i < reads.size(); i++) {
+ fastqRead fread = reads[i].forward;
+ fastqRead rread = reads[i].reverse;
+
+ if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
+
+ // if (checkReads(fread, rread, ffasta, rfasta)) {
+ 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]); } } inReverseFasta.close(); inForwardFasta.close(); if (fqualfile != "") { inReverseQual.close(); inReverseQual.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][2]) << ">" << rread.name << endl << rread.sequence << endl;
+ if (fqualfile != "") { //if you have quality info, print it
+ *(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][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]; } }
+ inReverseFasta.close();
+ inForwardFasta.close();
+ if (fqualfile != "") { inReverseQual.close(); inReverseQual.close(); }
+
return files;
}
catch(exception& e) {
- m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
+ m->errorOut(e, "MakeContigsCommand", "readFastaFiles");
exit(1);
}
}
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('!');
- for (int i = 0; i < quality.length(); i++) {
- int temp = int(quality[i]);
- temp -= controlChar;
-
- qualScores.push_back(temp);
- }
-
+ vector<int> qualScores = convertQual(quality);
+
read.name = name;
read.sequence = sequence;
read.scores = qualScores;
exit(1);
}
}
-//**********************************************************************************************************************
-bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse){
+/**********************************************************************************************************************
+bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse, string ffile, string rfile){
try {
bool good = true;
//do sequence lengths match
if (forward.sequence.length() != reverse.sequence.length()) {
- 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");
+ m->mothurOut("[WARNING]: For sequence " + forward.name + " I read a sequence of length " + toString(forward.sequence.length()) + " from " + ffile + ", but read a sequence of length " + toString(reverse.sequence.length()) + " from " + rfile + ", ignoring.\n");
good = false;
}
//do number of qual scores match
if (forward.scores.size() != reverse.scores.size()) {
- 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");
+ m->mothurOut("[WARNING]: For sequence " + forward.name + " I read " + toString(forward.scores.size()) + " quality scores from " + ffile + ", but read " + toString(reverse.scores.size()) + " quality scores from " + rfile + ", ignoring.\n");
good = false;
}
m->errorOut(e, "MakeContigsCommand", "checkReads");
exit(1);
}
+}*/
+//***************************************************************************************************************
+vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
+ try {
+ vector< vector<string> > files;
+ string forward, reverse;
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ while(!in.eof()) {
+
+ if (m->control_pressed) { return files; }
+
+ in >> forward; m->gobble(in);
+ in >> reverse;
+
+ string group = "";
+ while (!in.eof()) { //do we have a group assigned to this pair
+ char c = in.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ if (group != "") {
+ //line in file look like: group forward reverse
+ string temp = forward;
+ forward = reverse;
+ reverse = group;
+ group = temp;
+ createFileGroup = true;
+ }
+ m->gobble(in);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ", forward = " + forward + ", reverse = " + reverse + ".\n"); }
+
+ //check to make sure both are able to be opened
+ ifstream in2;
+ int openForward = m->openInputFile(forward, in2, "noerror");
+
+ //if you can't open it, try default location
+ if (openForward == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(forward);
+ m->mothurOut("Unable to open " + forward + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in3;
+ openForward = m->openInputFile(tryPath, in3, "noerror");
+ in3.close();
+ forward = tryPath;
+ }
+ }
+
+ //if you can't open it, try output location
+ if (openForward == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(forward);
+ m->mothurOut("Unable to open " + forward + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in4;
+ openForward = m->openInputFile(tryPath, in4, "noerror");
+ forward = tryPath;
+ in4.close();
+ }
+ }
+
+ if (openForward == 1) { //can't find it
+ m->mothurOut("[WARNING]: can't find " + forward + ", ignoring pair.\n");
+ }else{ in2.close(); }
+
+ ifstream in3;
+ int openReverse = m->openInputFile(reverse, in3, "noerror");
+
+ //if you can't open it, try default location
+ if (openReverse == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(reverse);
+ m->mothurOut("Unable to open " + reverse + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in3;
+ openReverse = m->openInputFile(tryPath, in3, "noerror");
+ in3.close();
+ reverse = tryPath;
+ }
+ }
+
+ //if you can't open it, try output location
+ if (openReverse == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(reverse);
+ m->mothurOut("Unable to open " + reverse + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in4;
+ openReverse = m->openInputFile(tryPath, in4, "noerror");
+ reverse = tryPath;
+ in4.close();
+ }
+ }
+
+ if (openReverse == 1) { //can't find it
+ m->mothurOut("[WARNING]: can't find " + reverse + ", ignoring pair.\n");
+ }else{ in3.close(); }
+
+ if ((openForward != 1) && (openReverse != 1)) { //good pair
+ file2Group[files.size()] = group;
+ vector<string> pair;
+ pair.push_back(forward);
+ pair.push_back(reverse);
+ files.push_back(pair);
+ }
+ }
+ in.close();
+
+ return files;
+ }
+ catch(exception& e) {
+ 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){
+bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, string rootname){
try {
ifstream in;
m->openInputFile(oligosfile, in);
while(!in.eof()){
in >> type;
-
+
if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
if(type[0] == '#'){
if(foligo[i] == 'U') { foligo[i] = 'T'; }
}
- if(type == "FORWARD"){
+ if(type == "PRIMER"){
m->gobble(in);
in >> roligo;
}
//roligo = reverseOligo(roligo);
+ if (m->debug) { m->mothurOut("[DEBUG]: reading - " + roligo + ".\n"); }
+
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; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
else { group += c; }
}
oligosPair newPrimer(foligo, roligo);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
//check for repeat barcodes
string tempPair = foligo+roligo;
group = "";
while (!in.eof()) {
char c = in.get();
- if (c == 10 || c == 13){ break; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
else { group += c; }
}
for(int i=0;i<fastaFileNames.size();i++){
fastaFileNames[i].assign(primerNameVector.size(), "");
}
- qualFileNames = fastaFileNames;
if(allFiles){
set<string> uniqueNames; //used to cleanup outputFileNames
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);
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ 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 = rootname + 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();
}
-
- qualFileNames[itBar->first][itPrimer->first] = qualFileName;
- m->openOutputFile(qualFileName, temp); temp.close();
}
}
}
}
}
//**********************************************************************************************************************
+vector<int> MakeContigsCommand::convertQual(string qual) {
+ try {
+ vector<int> qualScores;
+ bool negativeScores = false;
+
+ for (int i = 0; i < qual.length(); i++) {
+
+ int temp = 0;
+ temp = int(qual[i]);
+ if (format == "illumina") {
+ temp -= 64; //char '@'
+ }else if (format == "illumina1.8+") {
+ temp -= int('!'); //char '!'
+ }else if (format == "solexa") {
+ temp = int(convertTable[temp]); //convert to sanger
+ temp -= int('!'); //char '!'
+ }else {
+ temp -= int('!'); //char '!'
+ }
+
+ if (temp < -5) { negativeScores = true; }
+ qualScores.push_back(temp);
+ }
+
+ if (negativeScores) { m->mothurOut("[ERROR]: finding negative quality scores, do you have the right format selected? http://en.wikipedia.org/wiki/FASTQ_format#Encoding \n"); m->control_pressed = true; }
+
+ return qualScores;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "convertQual");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
projects / mothur.git / blobdiff