X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.cpp;h=663a6bf81d0fbbda91052e6cc0433df8e2d7fb4a;hb=f54925b51425c714502e90dd40b621a80fe1f583;hp=fba2d27ebf470c968f50f64c71c54917f0e8f5df;hpb=163b300cfd7d4ca4e70c454be20f07b1d8346650;p=mothur.git diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp index fba2d27..663a6bf 100644 --- a/deconvolutecommand.cpp +++ b/deconvolutecommand.cpp @@ -10,7 +10,7 @@ #include "deconvolutecommand.h" /**************************************************************************************/ -DeconvoluteCommand::DeconvoluteCommand(string option) { +DeconvoluteCommand::DeconvoluteCommand(string option) { try { abort = false; @@ -19,23 +19,53 @@ DeconvoluteCommand::DeconvoluteCommand(string option) { else { //valid paramters for this command - string Array[] = {"fasta", "name"}; + 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; } } + //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 = 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 = 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 = ""; cout << "fasta is a required parameter for the unique.seqs command." << endl; 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 += 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; } @@ -44,11 +74,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option) { } 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); } } @@ -56,21 +82,17 @@ 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); - } } /**************************************************************************************/ @@ -80,25 +102,33 @@ int DeconvoluteCommand::execute() { if (abort == true) { return 0; } //prepare filenames and open files - string outNameFile = (getRootName(inFastaName) + "names"); - string outFastaFile = (getRootName(inFastaName) + "unique" + getExtension(inFastaName)); + string outNameFile = outputDir + getRootName(getSimpleName(inFastaName)) + "names"; + string outFastaFile = outputDir + getRootName(getSimpleName(inFastaName)) + "unique" + getExtension(inFastaName); 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) { 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(); + m->mothurOutEndLine(); + + + 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); } }