X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=df97fd88ad471ba97daaa593233d4177f1fe21a2;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=966fee03f90bf4fb87d39efdedf0189cc18f10be;hpb=16bea3130e36addc54e2116dfbcd02d706ebee45;p=mothur.git diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp index 966fee0..df97fd8 100644 --- a/deconvolutecommand.cpp +++ b/deconvolutecommand.cpp @@ -9,40 +9,176 @@ #include "deconvolutecommand.h" +//********************************************************************************************************************** +vector DeconvoluteCommand::setParameters(){ + try { + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); + 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, "DeconvoluteCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string DeconvoluteCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The unique.seqs command reads a fastafile and creates a namesfile.\n"; + helpString += "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"; + helpString += "If the sequence is unique the second column will just contain its name. \n"; + helpString += "The unique.seqs command parameters are fasta and name. fasta is required, unless there is a valid current fasta file.\n"; + helpString += "The unique.seqs command should be in the following format: \n"; + helpString += "unique.seqs(fasta=yourFastaFile) \n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "DeconvoluteCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +DeconvoluteCommand::DeconvoluteCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand"); + exit(1); + } +} +/**************************************************************************************/ +DeconvoluteCommand::DeconvoluteCommand(string option) { + try { + abort = false; calledHelp = false; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + 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; } + } + + //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 + inFastaName = validParameter.validFile(parameters, "fasta", true); + if (inFastaName == "not open") { abort = true; } + else if (inFastaName == "not found") { + inFastaName = m->getFastaFile(); + if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " 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; } + } + + //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 + } + + oldNameMapFName = validParameter.validFile(parameters, "name", true); + if (oldNameMapFName == "not open") { abort = true; } + else if (oldNameMapFName == "not found"){ oldNameMapFName = ""; } + } + + } + catch(exception& e) { + m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand"); + exit(1); + } +} /**************************************************************************************/ int DeconvoluteCommand::execute() { try { - globaldata = GlobalData::getInstance(); - + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + //prepare filenames and open files - filename = globaldata->getFastaFile(); - outputFileName = (getRootName(filename) + "names"); - outFastafile = (getRootName(filename) + "uni_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(); - - //two columns separated by tabs sequence name and then sequence - fastamap->readFastaFile(in); - - //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->print(out); - fastamap->printCondensedFasta(outFasta); + FastaMap fastamap; + if(oldNameMapFName == "") { fastamap.readFastaFile(inFastaName); } + else { fastamap.readFastaFile(inFastaName, oldNameMapFName); } + + 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(); + + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } + } + + itTypes = outputTypes.find("name"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } + } + 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); } }