X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makefastqcommand.cpp;h=5a66d9a4b7b23ccd9051803d0e817fc7cf89f315;hp=18ca8644a2f0bfffc1035706c7a6b46df8aba043;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=002421a439168e2610a2b62f1318f21c7202fe6d diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp index 18ca864..5a66d9a 100644 --- a/makefastqcommand.cpp +++ b/makefastqcommand.cpp @@ -12,49 +12,65 @@ #include "qualityscores.h" //********************************************************************************************************************** -vector MakeFastQCommand::getValidParameters(){ +vector MakeFastQCommand::setParameters(){ try { - string Array[] = {"fasta","qfile","outputdir","inputdir" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pfasta); + CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pqfile); + CommandParameter pformat("format", "Multiple", "sanger-illumina-illumina1.8+", "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; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "MakeFastQCommand", "getValidParameters"); + m->errorOut(e, "MakeFastQCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -MakeFastQCommand::MakeFastQCommand(){ +string MakeFastQCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["fastq"] = tempOutNames; + string helpString = ""; + helpString += "The make.fastq command reads a fasta and quality file and creates a fastq file.\n"; + helpString += "The make.fastq command parameters are fasta, qfile and format. fasta and qfile are required.\n"; + helpString += "The format parameter is used to indicate whether your sequences are sanger, illumina1.8+ or illumina, default=sanger.\n"; + helpString += "The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n"; + helpString += "Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand"); + m->errorOut(e, "MakeFastQCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector MakeFastQCommand::getRequiredParameters(){ - try { - string Array[] = {"fasta","qfile"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "MakeFastQCommand", "getRequiredParameters"); - exit(1); - } +string MakeFastQCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fastq") { pattern = "[filename],fastq"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "MakeFastQCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** -vector MakeFastQCommand::getRequiredFiles(){ +MakeFastQCommand::MakeFastQCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fastq"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "MakeFastQCommand", "getRequiredFiles"); + m->errorOut(e, "MakeFastQCommand", "MakeFastQCommand"); exit(1); } } @@ -65,11 +81,10 @@ MakeFastQCommand::MakeFastQCommand(string option) { //allow user to run help 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[] = {"fasta","qfile", "outputdir","inputdir" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -107,28 +122,36 @@ MakeFastQCommand::MakeFastQCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["qfile"] = inputDir + it->second; } } - - it = parameters.find("list"); - //user has given a template file - if(it != parameters.end()){ - path = m->hasPath(it->second); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["list"] = inputDir + it->second; } - } } //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", true); if (fastafile == "not open") { abort = true; fastafile = ""; } - else if (fastafile == "not found") { fastafile = ""; m->mothurOut("You must provide a fasta file."); m->mothurOutEndLine(); abort = true; } + else if (fastafile == "not found") { + fastafile = m->getFastaFile(); + if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setFastaFile(fastafile); } qualfile = validParameter.validFile(parameters, "qfile", true); if (qualfile == "not open") { abort = true; qualfile = ""; } - else if (qualfile == "not found") { qualfile = ""; m->mothurOut("You must provide a quality file."); m->mothurOutEndLine(); abort = true; } + else if (qualfile == "not found") { + qualfile = m->getQualFile(); + if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current qualfile and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setQualFile(qualfile); } //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(fastafile); } + + format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "sanger"; } + + if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+")) { + m->mothurOut(format + " is not a valid format. Your format choices are sanger, illumina1.8+ and illumina, aborting." ); m->mothurOutEndLine(); + abort=true; + } + } @@ -140,30 +163,14 @@ MakeFastQCommand::MakeFastQCommand(string option) { } //********************************************************************************************************************** -void MakeFastQCommand::help(){ - try { - m->mothurOut("The make.fastq command read a fasta and quality file and creates a fastq file.\n"); - m->mothurOut("The make.fastq command parameters are fasta and qfile, both are required.\n"); - m->mothurOut("You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n"); - m->mothurOut("The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n"); - m->mothurOut("Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "MakeFastQCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - int MakeFastQCommand::execute(){ try { if (abort == true) { if (calledHelp) { return 0; } return 2; } - - string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "fastq"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile)); + string outputFile = getOutputFileName("fastq",variables); outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile); ofstream out; @@ -174,7 +181,7 @@ int MakeFastQCommand::execute(){ ifstream fFile; m->openInputFile(fastafile, fFile); - + while (!fFile.eof() && !qFile.eof()) { if (m->control_pressed) { break; } @@ -199,7 +206,7 @@ int MakeFastQCommand::execute(){ qFile.close(); out.close(); - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -219,9 +226,10 @@ string MakeFastQCommand::convertQual(vector qual) { try { string qualScores; - int controlChar = int('!'); - - for (int i = 0; i < qual.size(); i++) { + for (int i = 0; i < qual.size(); i++) { + int controlChar = int('!'); + if (format == "illumina") { controlChar = int('@'); } + int temp = qual[i] + controlChar; char qualChar = (char) temp;