X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.cpp;h=1331b7f47f4e131cb5a76913889d275b7ec93121;hb=5b72d1cf3fa48730e5bb70d59cced1e43e1fe424;hp=75d6fa01be65bcccf8f176bfd29dcce843efc0e3;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp index 75d6fa0..1331b7f 100644 --- a/parsefastaqcommand.cpp +++ b/parsefastaqcommand.cpp @@ -14,6 +14,8 @@ vector ParseFastaQCommand::setParameters(){ try { CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfastq); + CommandParameter pfasta("fasta", "Bool", "", "T", "", "", "",false,false); parameters.push_back(pfasta); + CommandParameter pqual("qfile", "Bool", "", "T", "", "", "",false,false); parameters.push_back(pqual); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); @@ -31,8 +33,10 @@ 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 parameters are fastq, fasta and qfile; fastq is required.\n"; helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\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 +46,28 @@ 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 { @@ -62,6 +88,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){ abort = false; calledHelp = false; if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -103,6 +130,15 @@ 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); + + if ((!fasta) && (!qual)) { m->mothurOut("[ERROR]: no outputs selected. Aborting."); m->mothurOutEndLine(); abort=true; } } } @@ -118,16 +154,19 @@ 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); while (!in.eof()) { + + if (m->control_pressed) { break; } //read sequence name string name = m->getline(in); m->gobble(in); @@ -146,29 +185,29 @@ 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(); remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; } //set fasta file as new current fastafile string current = ""; @@ -199,7 +238,7 @@ vector ParseFastaQCommand::convertQual(string qual) { try { vector qualScores; - int controlChar = int('!'); + int controlChar = int('@'); for (int i = 0; i < qual.length(); i++) { int temp = int(qual[i]);