X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniqueseqscommand.cpp;h=f72a7c9c7e1264265d4d28e1072e087cf501c288;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=a4395a700e26d27ebd36d1151f48129f6bef045d;hpb=f09bacac01a842a74c1c1b69070852cc969ff506;p=mothur.git diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp index a4395a7..f72a7c9 100644 --- a/deuniqueseqscommand.cpp +++ b/deuniqueseqscommand.cpp @@ -11,64 +11,78 @@ #include "sequence.hpp" //********************************************************************************************************************** -vector DeUniqueSeqsCommand::getValidParameters(){ +vector DeUniqueSeqsCommand::setParameters(){ try { - string Array[] = {"fasta", "name","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); 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, "DeUniqueSeqsCommand", "getValidParameters"); + m->errorOut(e, "DeUniqueSeqsCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -DeUniqueSeqsCommand::DeUniqueSeqsCommand(){ +string DeUniqueSeqsCommand::getHelpString(){ try { - //initialize outputTypes - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; + string helpString = ""; + helpString += "The deunique.seqs command reads a fastafile and namefile, and creates a fastafile containing all the sequences.\n"; + helpString += "The deunique.seqs command parameters are fasta and name, both are required, unless you have valid current name and fasta files.\n"; + helpString += "The deunique.seqs command should be in the following format: \n"; + helpString += "deunique.seqs(fasta=yourFastaFile, name=yourNameFile) \n"; + helpString += "Example deunique.seqs(fasta=abrecovery.unique.fasta, name=abrecovery.names).\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "DeUniqueSeqsCommand", "DeconvoluteCommand"); + m->errorOut(e, "DeUniqueSeqsCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector DeUniqueSeqsCommand::getRequiredParameters(){ - try { - string Array[] = {"fasta","name"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "DeUniqueSeqsCommand", "getRequiredParameters"); - exit(1); - } +string DeUniqueSeqsCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],redundant.fasta"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "DeUniqueSeqsCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** -vector DeUniqueSeqsCommand::getRequiredFiles(){ +DeUniqueSeqsCommand::DeUniqueSeqsCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "DeUniqueSeqsCommand", "getRequiredFiles"); + m->errorOut(e, "DeUniqueSeqsCommand", "DeconvoluteCommand"); exit(1); } } /**************************************************************************************/ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option) { try { - 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 if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"fasta", "name","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -111,7 +125,11 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option) { //check for required parameters fastaFile = validParameter.validFile(parameters, "fasta", true); if (fastaFile == "not open") { abort = true; } - else if (fastaFile == "not found") { fastaFile = ""; m->mothurOut("fasta is a required parameter for the deunique.seqs command."); m->mothurOutEndLine(); abort = true; } + else if (fastaFile == "not found") { + fastaFile = m->getFastaFile(); + if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " 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->setFastaFile(fastaFile); } //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"){ @@ -121,7 +139,11 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option) { nameFile = validParameter.validFile(parameters, "name", true); if (nameFile == "not open") { abort = true; } - else if (nameFile == "not found"){ nameFile = ""; m->mothurOut("name is a required parameter for the deunique.seqs command."); m->mothurOutEndLine(); abort = true; } + else if (nameFile == "not found"){ + nameFile = m->getNameFile(); + if (nameFile != "") { m->mothurOut("Using " + nameFile + " as input file for the name parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setNameFile(nameFile); } } } @@ -130,50 +152,32 @@ DeUniqueSeqsCommand::DeUniqueSeqsCommand(string option) { exit(1); } } -//********************************************************************************************************************** - -void DeUniqueSeqsCommand::help(){ - try { - m->mothurOut("The deunique.seqs command reads a fastafile and namefile, and creates a fastafile containing all the sequences.\n"); - m->mothurOut("The deunique.seqs command parameters are fasta and name, both are required.\n"); - m->mothurOut("The deunique.seqs command should be in the following format: \n"); - m->mothurOut("deunique.seqs(fasta=yourFastaFile, name=yourNameFile) \n"); - m->mothurOut("Example deunique.seqs(fasta=abrecovery.unique.fasta, name=abrecovery.names).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); - - } - catch(exception& e) { - m->errorOut(e, "DeUniqueSeqsCommand", "help"); - exit(1); - } -} - /**************************************************************************************/ int DeUniqueSeqsCommand::execute() { try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } //prepare filenames and open files ofstream out; string outFastaFile = m->getRootName(m->getSimpleName(fastaFile)); int pos = outFastaFile.find("unique"); - if (pos != string::npos) { - outFastaFile = outputDir + outFastaFile.substr(0, pos) + "redundant" + m->getExtension(fastaFile); - }else{ - outFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "redundant" + m->getExtension(fastaFile); - } + if (pos != string::npos) { outFastaFile = outputDir + outFastaFile.substr(0, pos); } + else { outFastaFile = outputDir + outFastaFile; } + map variables; + variables["[filename]"] = outFastaFile; + outFastaFile = getOutputFileName("fasta", variables); m->openOutputFile(outFastaFile, out); readNamesFile(); - if (m->control_pressed) { out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; } + if (m->control_pressed) { out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; } ifstream in; m->openInputFile(fastaFile, in); while (!in.eof()) { - if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); remove(outFastaFile.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; } Sequence seq(in); m->gobble(in); @@ -207,7 +211,7 @@ int DeUniqueSeqsCommand::execute() { } } - if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -215,6 +219,13 @@ int DeUniqueSeqsCommand::execute() { outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile); 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); } + } + return 0; } catch(exception& e) {