X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.cpp;h=e6d7ce6d1aa30da836bb88f2833bd666ae11bd85;hb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;hp=87ec2d26651749f20153b7854ba7c3930eebd70c;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677;p=mothur.git diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp index 87ec2d2..e6d7ce6 100644 --- a/parsefastaqcommand.cpp +++ b/parsefastaqcommand.cpp @@ -11,50 +11,52 @@ #include "sequence.hpp" //********************************************************************************************************************** -vector ParseFastaQCommand::getValidParameters(){ +vector ParseFastaQCommand::setParameters(){ try { - string Array[] = {"fastq", "outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + 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); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "ParseFastaQCommand", "getValidParameters"); - exit(1); - } -} -//********************************************************************************************************************** -ParseFastaQCommand::ParseFastaQCommand(){ - try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["qfile"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand"); + m->errorOut(e, "ParseFastaQCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector ParseFastaQCommand::getRequiredParameters(){ +string ParseFastaQCommand::getHelpString(){ try { - string Array[] = {"fastq"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + string helpString = ""; + helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\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; } catch(exception& e) { - m->errorOut(e, "ParseFastaQCommand", "getRequiredParameters"); + m->errorOut(e, "ParseFastaQCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector ParseFastaQCommand::getRequiredFiles(){ +ParseFastaQCommand::ParseFastaQCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "ParseFastaQCommand", "getRequiredFiles"); + m->errorOut(e, "ParseFastaQCommand", "ParseFastaQCommand"); exit(1); } } @@ -64,11 +66,10 @@ 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 { - //valid paramters for this command - string Array[] = {"fastq", "outputdir", "inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -107,6 +108,15 @@ 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; } } } @@ -117,26 +127,6 @@ ParseFastaQCommand::ParseFastaQCommand(string option){ } //********************************************************************************************************************** -void ParseFastaQCommand::help(){ - try { - m->mothurOut("The fastq.info command reads a fastq file and creates a fasta and quality file.\n"); - m->mothurOut("The fastq.info command parameter is fastq, and it is required.\n"); - m->mothurOut("The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n"); - m->mothurOut("Example fastq.info(fastaq=test.fastaq).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n"); - m->mothurOutEndLine(); - } - catch(exception& e) { - m->errorOut(e, "ParseFastaQCommand", "help"); - exit(1); - } -} -//********************************************************************************************************************** - -ParseFastaQCommand::~ParseFastaQCommand() { /* do nothing */ } - -//********************************************************************************************************************** - int ParseFastaQCommand::execute(){ try { if (abort == true) { if (calledHelp) { return 0; } return 2; } @@ -145,13 +135,16 @@ int ParseFastaQCommand::execute(){ string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta"; string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual"; 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); @@ -170,29 +163,29 @@ 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 = "";