X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=6c04c1255ab94010da7cacfb409d497b4f0354d4;hb=7c08fa69c0b89e7a08341af2aa724f206f182075;hp=96682af26b8bcb1b62c17987c82355856cfaf919;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp index 96682af..6c04c12 100644 --- a/deconvolutecommand.cpp +++ b/deconvolutecommand.cpp @@ -9,46 +9,125 @@ #include "deconvolutecommand.h" +//********************************************************************************************************************** +vector DeconvoluteCommand::getValidParameters(){ + try { + string Array[] = {"fasta", "name","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "DeconvoluteCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +DeconvoluteCommand::DeconvoluteCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector DeconvoluteCommand::getRequiredParameters(){ + try { + string Array[] = {"fasta"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "DeconvoluteCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector DeconvoluteCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "DeconvoluteCommand", "getRequiredFiles"); + exit(1); + } +} /**************************************************************************************/ -DeconvoluteCommand::DeconvoluteCommand(string option) { +DeconvoluteCommand::DeconvoluteCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { //valid paramters for this command - string Array[] = {"fasta"}; + string Array[] = {"fasta", "name","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - parser = new OptionParser(); - parser->parse(option, parameters); delete parser; + OptionParser parser(option); + map parameters = parser.getParameters(); - ValidParameters* validParameter = new ValidParameters(); + ValidParameters validParameter; + map::iterator it; //check to make sure all parameters are valid for command for (it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("fasta"); + //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["fasta"] = inputDir + it->second; } + } + + it = parameters.find("name"); + //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["name"] = inputDir + it->second; } + } } + //check for required parameters - filename = validParameter->validFile(parameters, "fasta", true); - if (filename == "not open") { abort = true; } - else if (filename == "not found") { filename = ""; cout << "fasta is a required parameter for the unique.seqs command." << endl; abort = true; } - else { globaldata->setFastaFile(filename); globaldata->setFormat("fasta"); } + inFastaName = validParameter.validFile(parameters, "fasta", true); + if (inFastaName == "not open") { abort = true; } + else if (inFastaName == "not found") { inFastaName = ""; m->mothurOut("fasta is a required parameter for the unique.seqs command."); m->mothurOutEndLine(); abort = true; } + + //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 = ""; + outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it + } - delete validParameter; + oldNameMapFName = validParameter.validFile(parameters, "name", true); + if (oldNameMapFName == "not open") { abort = true; } + else if (oldNameMapFName == "not found"){ oldNameMapFName = ""; } } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the DeconvoluteCommand class function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand"); exit(1); } } @@ -56,60 +135,54 @@ DeconvoluteCommand::DeconvoluteCommand(string option) { void DeconvoluteCommand::help(){ try { - cout << "The unique.seqs command reads a fastafile and creates a namesfile." << "\n"; - cout << "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. " << "\n"; - cout << "If the sequence is unique the second column will just contain its name. " << "\n"; - cout << "The unique.seqs command parameter is fasta and it is required." << "\n"; - cout << "The unique.seqs command should be in the following format: " << "\n"; - cout << "unique.seqs(fasta=yourFastaFile) " << "\n"; + m->mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n"); + m->mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n"); + m->mothurOut("If the sequence is unique the second column will just contain its name. \n"); + m->mothurOut("The unique.seqs command parameter is fasta and it is required.\n"); + m->mothurOut("The unique.seqs command should be in the following format: \n"); + m->mothurOut("unique.seqs(fasta=yourFastaFile) \n"); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "DeconvoluteCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the DeconvoluteCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /**************************************************************************************/ int DeconvoluteCommand::execute() { try { - if (abort == true) { return 0; } - + if (abort == true) { if (calledHelp) { return 0; } return 2; } + //prepare filenames and open files - outputFileName = (getRootName(filename) + "names"); - outFastafile = (getRootName(filename) + "unique.fasta"); + string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names"; + string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName); - openInputFile(filename, in); - openOutputFile(outputFileName, out); - openOutputFile(outFastafile, outFasta); - - //constructor reads in file and store internally - fastamap = new FastaMap(); + FastaMap fastamap; - //two columns separated by tabs sequence name and then sequence - fastamap->readFastaFile(in); + if(oldNameMapFName == "") { fastamap.readFastaFile(inFastaName); } + else { fastamap.readFastaFile(inFastaName, oldNameMapFName); } - //print out new names file - //file contains 2 columns separated by tabs. the first column is the groupname(name of first sequence found. - //the second column is the list of names of identical sequences separated by ','. - fastamap->printNamesFile(out); - fastamap->printCondensedFasta(outFasta); + if (m->control_pressed) { return 0; } + + fastamap.printCondensedFasta(outFastaFile); + fastamap.printNamesFile(outNameFile); + + if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + m->mothurOut(outFastaFile); m->mothurOutEndLine(); + m->mothurOut(outNameFile); m->mothurOutEndLine(); + outputNames.push_back(outFastaFile); outputNames.push_back(outNameFile); outputTypes["fasta"].push_back(outFastaFile); outputTypes["name"].push_back(outNameFile); + m->mothurOutEndLine(); + + - out.close(); - outFasta.close(); - return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "DeconvoluteCommand", "execute"); exit(1); } }