X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;fp=chimeraccodecommand.cpp;h=0b6117a98efba24d95da9df73aa15062141a8cad;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=457eaf314bf304fe3d7f9e5eec67509f07236a35;hpb=36a867cbd85d9c276d3c8d13f25a150bbbe2466b;p=mothur.git diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp index 457eaf3..0b6117a 100644 --- a/chimeraccodecommand.cpp +++ b/chimeraccodecommand.cpp @@ -9,53 +9,69 @@ #include "chimeraccodecommand.h" #include "ccode.h" - //********************************************************************************************************************** -vector ChimeraCcodeCommand::getValidParameters(){ +vector ChimeraCcodeCommand::setParameters(){ try { - string AlignArray[] = {"fasta", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir" }; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); + CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter); + CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow); + CommandParameter pnumwanted("numwanted", "Number", "", "20", "", "", "",false,false); parameters.push_back(pnumwanted); + CommandParameter pmask("mask", "String", "", "", "", "", "",false,false); parameters.push_back(pmask); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); + 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, "ChimeraCcodeCommand", "getValidParameters"); + m->errorOut(e, "ChimeraCcodeCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -ChimeraCcodeCommand::ChimeraCcodeCommand(){ +string ChimeraCcodeCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["chimera"] = tempOutNames; - outputTypes["mapinfo"] = tempOutNames; - outputTypes["accnos"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand"); - exit(1); - } -} -//********************************************************************************************************************** -vector ChimeraCcodeCommand::getRequiredParameters(){ - try { - string AlignArray[] = {"template","fasta"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); - return myArray; + string helpString = ""; + helpString += "The chimera.ccode command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n"; + helpString += "This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n"; + helpString += "The chimera.ccode command parameters are fasta, reference, filter, mask, processors, window and numwanted.\n"; + helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required unless you have a valid current fasta file. \n"; + helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"; + helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. \n"; + helpString += "The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n"; + helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"; +#ifdef USE_MPI + helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n"; +#endif + helpString += "The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n"; + helpString += "The window parameter allows you to specify the window size for searching for chimeras. \n"; + helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n"; + helpString += "The chimera.ccode command should be in the following format: \n"; + helpString += "chimera.ccode(fasta=yourFastaFile, reference=yourTemplate) \n"; + helpString += "Example: chimera.ccode(fasta=AD.align, reference=core_set_aligned.imputed.fasta) \n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "ChimeraCcodeCommand", "getRequiredParameters"); + m->errorOut(e, "ChimeraCcodeCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector ChimeraCcodeCommand::getRequiredFiles(){ +ChimeraCcodeCommand::ChimeraCcodeCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["chimera"] = tempOutNames; + outputTypes["mapinfo"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "ChimeraCcodeCommand", "getRequiredFiles"); + m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand"); exit(1); } } @@ -68,9 +84,7 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { if(option == "help") { help(); abort = true; calledHelp = true; } else { - //valid paramters for this command - string Array[] = {"fasta", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -93,19 +107,22 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { if (inputDir == "not found"){ inputDir = ""; } else { string path; - it = parameters.find("template"); + it = parameters.find("reference"); //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["template"] = inputDir + it->second; } + if (path == "") { parameters["reference"] = inputDir + it->second; } } } //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", false); - if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; } - else { + if (fastafile == "not found") { //if there is a current fasta file, use it + string filename = m->getFastaFile(); + if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " 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->splitAtDash(fastafile, fastaFileNames); //go through files and make sure they are good, if not, then disregard them @@ -162,9 +179,9 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(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 = ""; } - templatefile = validParameter.validFile(parameters, "template", true); + templatefile = validParameter.validFile(parameters, "reference", true); if (templatefile == "not open") { abort = true; } - else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; } + else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; } maskfile = validParameter.validFile(parameters, "mask", false); if (maskfile == "not found") { maskfile = ""; } @@ -185,7 +202,8 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; } filter = m->isTrue(temp); - temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; } + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); convert(temp, processors); temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; } @@ -201,42 +219,7 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { exit(1); } } -//********************************************************************************************************************** - -void ChimeraCcodeCommand::help(){ - try { - - m->mothurOut("The chimera.ccode command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n"); - m->mothurOut("This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n"); - m->mothurOut("The chimera.ccode command parameters are fasta, template, filter, mask, processors, window and numwanted.\n"); - m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n"); - m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); - m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n"); - m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n"); - m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"); - #ifdef USE_MPI - m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n"); - #endif - m->mothurOut("The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n"); - m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras. \n"); - m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n"); - m->mothurOut("The chimera.ccode command should be in the following format: \n"); - m->mothurOut("chimera.ccode(fasta=yourFastaFile, template=yourTemplate) \n"); - m->mothurOut("Example: chimera.ccode(fasta=AD.align, template=core_set_aligned.imputed.fasta) \n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "ChimeraCcodeCommand", "help"); - exit(1); - } -} - //*************************************************************************************************************** - -ChimeraCcodeCommand::~ChimeraCcodeCommand(){ /* do nothing */ } - -//*************************************************************************************************************** - int ChimeraCcodeCommand::execute(){ try{