X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=reversecommand.cpp;h=7b58162d20d8ac1910323c2946f7f8b4c05299af;hb=6d12ed0ba66fb35e9e2781fe3ca361e2293f2476;hp=b8ccc0747d54300f4fbc655729d9ce58b6f2d112;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git diff --git a/reversecommand.cpp b/reversecommand.cpp index b8ccc07..7b58162 100644 --- a/reversecommand.cpp +++ b/reversecommand.cpp @@ -10,12 +10,58 @@ #include "reversecommand.h" #include "sequence.hpp" - +//********************************************************************************************************************** +vector ReverseSeqsCommand::getValidParameters(){ + try { + string Array[] = {"fasta", "outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ReverseSeqsCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +ReverseSeqsCommand::ReverseSeqsCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector ReverseSeqsCommand::getRequiredParameters(){ + try { + string Array[] = {"fasta"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ReverseSeqsCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ReverseSeqsCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles"); + exit(1); + } +} //*************************************************************************************************************** -ReverseSeqsCommand::ReverseSeqsCommand(string option){ +ReverseSeqsCommand::ReverseSeqsCommand(string option) { try { - globaldata = GlobalData::getInstance(); abort = false; //allow user to run help @@ -23,54 +69,69 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){ else { //valid paramters for this command - string Array[] = {"fasta"}; + string Array[] = {"fasta", "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; + map::iterator it; - ValidParameters* validParameter = new ValidParameters(); - //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; + + //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; } + } + } + //check for required parameters - fasta = validParameter->validFile(parameters, "fasta", true); + fasta = validParameter.validFile(parameters, "fasta", true); if (fasta == "not open") { abort = true; } - else if (fasta == "not found") { fasta = ""; cout << "fasta is a required parameter for the reverse.seqs command." << endl; abort = true; } - else { globaldata->setFastaFile(fasta); globaldata->setFormat("fasta"); } + else if (fasta == "not found") { fasta = ""; m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true; } - delete validParameter; + //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(fasta); //if user entered a file with a path then preserve it + } + } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the ReverseSeqsCommand class function ReverseSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** void ReverseSeqsCommand::help(){ try { - cout << "The reverse.seqs command reads a fastafile and ...." << "\n"; - cout << "The reverse.seqs command parameter is fasta and it is required." << "\n"; - cout << "The reverse.seqs command should be in the following format: " << "\n"; - cout << "reverse.seqs(fasta=yourFastaFile) " << "\n"; + m->mothurOut("The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n"); + m->mothurOut("The reverse.seqs command parameter is fasta and it is required.\n"); + m->mothurOut("The reverse.seqs command should be in the following format: \n"); + m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n"); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReverseSeqsCommand", "help"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the ReverseSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //*************************************************************************************************************** @@ -86,29 +147,37 @@ int ReverseSeqsCommand::execute(){ if (abort == true) { return 0; } ifstream inFASTA; - openInputFile(fasta, inFASTA); + m->openInputFile(fasta, inFASTA); ofstream outFASTA; - string reverseFile = getRootName(fasta) + "rc" + getExtension(fasta); - openOutputFile(reverseFile, outFASTA); + string reverseFile = outputDir + m->getRootName(m->getSimpleName(fasta)) + "rc" + m->getExtension(fasta); + m->openOutputFile(reverseFile, outFASTA); while(!inFASTA.eof()){ - Sequence currSeq(inFASTA); - currSeq.reverseComplement(); - currSeq.printSequence(outFASTA); + if (m->control_pressed) { inFASTA.close(); outFASTA.close(); remove(reverseFile.c_str()); return 0; } + + Sequence currSeq(inFASTA); m->gobble(inFASTA); + if (currSeq.getName() != "") { + currSeq.reverseComplement(); + currSeq.printSequence(outFASTA); + } } inFASTA.close(); outFASTA.close(); + if (m->control_pressed) { remove(reverseFile.c_str()); return 0; } + + m->mothurOutEndLine(); + m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut(reverseFile); m->mothurOutEndLine(); outputNames.push_back(reverseFile); outputTypes["fasta"].push_back(reverseFile); + m->mothurOutEndLine(); + + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReverseSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ReverseSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReverseSeqsCommand", "execute"); exit(1); } }