X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=dd05afdd0243132497fdab828c384b287ff0b61c;hb=bdb5d82e2a73829b4e1fa42656ad9bcb57e3e948;hp=3ec5f734eebb393c6ff630a1adc8d7e94ab6729f;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp index 3ec5f73..dd05afd 100644 --- a/deconvolutecommand.cpp +++ b/deconvolutecommand.cpp @@ -9,8 +9,57 @@ #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; + //initialize outputTypes + 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 { abort = false; @@ -19,33 +68,67 @@ DeconvoluteCommand::DeconvoluteCommand(string option) { else { //valid paramters for this command - string Array[] = {"fasta"}; + string Array[] = {"fasta", "name","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); map parameters = parser.getParameters(); ValidParameters validParameter; + map::iterator it; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + 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 - 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; } + 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 + } + 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); } } @@ -53,21 +136,17 @@ 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); - } } /**************************************************************************************/ @@ -75,38 +154,36 @@ int DeconvoluteCommand::execute() { try { if (abort == true) { return 0; } - + //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); } }