X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.cpp;h=816bdb5d38c53afb849be7d5e65b458ac8582148;hb=035f86272c776e1cccaa47021e26782e49cd41e7;hp=9cba70b9d2772edba281cd5f03459d1fdc32a966;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp index 9cba70b..816bdb5 100644 --- a/parsefastaqcommand.cpp +++ b/parsefastaqcommand.cpp @@ -14,7 +14,10 @@ vector ParseFastaQCommand::setParameters(){ try { CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfastq); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter pfasta("fasta", "Bool", "", "T", "", "", "",false,false); parameters.push_back(pfasta); + CommandParameter pqual("qfile", "Bool", "", "T", "", "", "",false,false); parameters.push_back(pqual); + CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa", "sanger", "", "", "",false,false); parameters.push_back(pformat); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); vector myArray; @@ -31,8 +34,11 @@ string ParseFastaQCommand::getHelpString(){ try { string helpString = ""; helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n"; - helpString += "The fastq.info command parameter is fastq, and it is required.\n"; - helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n"; + helpString += "The fastq.info command parameters are fastq, fasta, qfile and format; fastq is required.\n"; + helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n"; + helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa or illumina, default=sanger.\n"; + helpString += "The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.\n"; + helpString += "The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.\n"; helpString += "Example fastq.info(fastaq=test.fastaq).\n"; helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n"; return helpString; @@ -42,6 +48,28 @@ string ParseFastaQCommand::getHelpString(){ exit(1); } } +//********************************************************************************************************************** +string ParseFastaQCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "fasta") { outputFileName = "fasta"; } + else if (type == "qfile") { outputFileName = "qual"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "ParseFastaQCommand", "getOutputFileNameTag"); + exit(1); + } +} + //********************************************************************************************************************** ParseFastaQCommand::ParseFastaQCommand(){ try { @@ -104,6 +132,22 @@ ParseFastaQCommand::ParseFastaQCommand(string option){ //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(fastaQFile); } + + string temp; + temp = validParameter.validFile(parameters, "fasta", false); if(temp == "not found"){ temp = "T"; } + fasta = m->isTrue(temp); + + temp = validParameter.validFile(parameters, "qfile", false); if(temp == "not found"){ temp = "T"; } + qual = m->isTrue(temp); + + format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "sanger"; } + + if ((format != "sanger") && (format != "illumina") && (format != "solexa")) { + m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa and illumina, aborting." ); m->mothurOutEndLine(); + abort=true; + } + + if ((!fasta) && (!qual)) { m->mothurOut("[ERROR]: no outputs selected. Aborting."); m->mothurOutEndLine(); abort=true; } } } @@ -119,16 +163,25 @@ int ParseFastaQCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } //open Output Files - string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta"; - string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual"; + string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("fasta"); + string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("qfile"); ofstream outFasta, outQual; - m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile); - m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile); outputTypes["qfile"].push_back(qualFile); + + if (fasta) { m->openOutputFile(fastaFile, outFasta); outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile); } + if (qual) { m->openOutputFile(qualFile, outQual); outputNames.push_back(qualFile); outputTypes["qfile"].push_back(qualFile); } ifstream in; m->openInputFile(fastaQFile, in); + + //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); + } while (!in.eof()) { + + if (m->control_pressed) { break; } //read sequence name string name = m->getline(in); m->gobble(in); @@ -147,27 +200,27 @@ int ParseFastaQCommand::execute(){ else { name2 = name2.substr(1); } //read quality scores - string qual = m->getline(in); m->gobble(in); - if (qual == "") { m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; } + string quality = m->getline(in); m->gobble(in); + if (quality == "") { m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; } //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; break; } } - if (qual.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(qual.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; } - - //convert quality scores - vector qualScores = convertQual(qual); + 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; break; } //print sequence info to files - outFasta << ">" << name << endl << sequence << endl; + if (fasta) { outFasta << ">" << name << endl << sequence << endl; } - outQual << ">" << name << endl; - for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; } - outQual << endl; + if (qual) { + vector qualScores = convertQual(quality); + outQual << ">" << name << endl; + for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; } + outQual << endl; + } } in.close(); - outFasta.close(); - outQual.close(); + if (fasta) { outFasta.close(); } + if (qual) { outQual.close(); } if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; } @@ -200,12 +253,18 @@ vector ParseFastaQCommand::convertQual(string qual) { try { vector qualScores; - int controlChar = int('!'); - for (int i = 0; i < qual.length(); i++) { - int temp = int(qual[i]); - temp -= controlChar; - + + int temp = 0; + temp = int(qual[i]); + if (format == "illumina") { + temp -= 64; //char '@' + }else if (format == "solexa") { + temp = int(convertTable[temp]); //convert to sanger + temp -= 33; //char '!' + }else { + temp -= 33; //char '!' + } qualScores.push_back(temp); }