X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=reversecommand.cpp;h=a9b297731a346999b155c61d7cab47ff7089063c;hp=9be29152445487dea77a36e62c01812aa617e1ea;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=986663e2220f6b043ee83d1699cfa081dc49cbed diff --git a/reversecommand.cpp b/reversecommand.cpp index 9be2915..a9b2977 100644 --- a/reversecommand.cpp +++ b/reversecommand.cpp @@ -9,59 +9,250 @@ #include "reversecommand.h" #include "sequence.hpp" +#include "qualityscores.h" - -//*************************************************************************************************************** - -ReverseSeqsCommand::ReverseSeqsCommand(){ +//********************************************************************************************************************** +vector ReverseSeqsCommand::setParameters(){ try { - globaldata = GlobalData::getInstance(); - if(globaldata->getFastaFile() == "") { cout << "you need to at least enter a fasta file name" << endl; } + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none","fasta",false,false,true); parameters.push_back(pfasta); + CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none","qfile",false,false,true); parameters.push_back(pqfile); + 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) { - cout << "Standard Error: " << e.what() << " has occurred in the SeqCoordCommand class Function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReverseSeqsCommand", "setParameters"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SeqCoordCommand class function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** +string ReverseSeqsCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The reverse.seqs command reads a fastafile and outputs a fasta file containing the reverse compliment.\n"; + helpString += "The reverse.seqs command parameters fasta or qfile are required.\n"; + helpString += "The reverse.seqs command should be in the following format: \n"; + helpString += "reverse.seqs(fasta=yourFastaFile) \n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "ReverseSeqsCommand", "getHelpString"); exit(1); - } + } +} +//********************************************************************************************************************** +string ReverseSeqsCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],rc,[extension]"; } + else if (type == "qfile") { pattern = "[filename],rc,[extension]"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ReverseSeqsCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +ReverseSeqsCommand::ReverseSeqsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand"); + exit(1); + } } - //*************************************************************************************************************** -ReverseSeqsCommand::~ReverseSeqsCommand(){ /* do nothing */ } +ReverseSeqsCommand::ReverseSeqsCommand(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["qfile"] = 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("qfile"); + //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["qfile"] = inputDir + it->second; } + } + } + //check for required parameters + fastaFileName = validParameter.validFile(parameters, "fasta", true); + if (fastaFileName == "not open") { abort = true; } + else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true; } + else { m->setFastaFile(fastaFileName); } + + qualFileName = validParameter.validFile(parameters, "qfile", true); + if (qualFileName == "not open") { abort = true; } + else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true; } + else { m->setQualFile(qualFileName); } + + if((fastaFileName == "") && (qualFileName == "")){ + fastaFileName = m->getFastaFile(); + if (fastaFileName != "") { m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); } + else { + qualFileName = m->getQualFile(); + if (qualFileName != "") { m->mothurOut("Using " + qualFileName + " as input file for the qfile parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current files for fasta or qfile, and fasta or qfile is a required parameter for the reverse.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 = ""; + } + + } + } + catch(exception& e) { + m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand"); + exit(1); + } +} //*************************************************************************************************************** int ReverseSeqsCommand::execute(){ try{ - ifstream inFASTA; - openInputFile(globaldata->getFastaFile(), inFASTA); + if (abort == true) { if (calledHelp) { return 0; } return 2; } - ofstream outFASTA; - string reverseFile = getRootName(globaldata->getFastaFile()) + "rc" + getExtension(globaldata->getFastaFile()); - openOutputFile(reverseFile, outFASTA); + string fastaReverseFileName; - while(!inFASTA.eof()){ - Sequence currSeq(inFASTA); - currSeq.reverseComplement(); - currSeq.printSequence(outFASTA); + if(fastaFileName != ""){ + ifstream inFASTA; + m->openInputFile(fastaFileName, inFASTA); + + ofstream outFASTA; + string tempOutputDir = outputDir; + if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it + map variables; + variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName)); + variables["[extension]"] = m->getExtension(fastaFileName); + fastaReverseFileName = getOutputFileName("fasta", variables); + m->openOutputFile(fastaReverseFileName, outFASTA); + + while(!inFASTA.eof()){ + if (m->control_pressed) { inFASTA.close(); outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; } + + Sequence currSeq(inFASTA); m->gobble(inFASTA); + if (currSeq.getName() != "") { + currSeq.reverseComplement(); + currSeq.printSequence(outFASTA); + } + } + inFASTA.close(); + outFASTA.close(); + outputNames.push_back(fastaReverseFileName); outputTypes["fasta"].push_back(fastaReverseFileName); } - inFASTA.close(); - outFASTA.close(); - return 0; + string qualReverseFileName; + + if(qualFileName != ""){ + QualityScores currQual; + + ifstream inQual; + m->openInputFile(qualFileName, inQual); + + ofstream outQual; + string tempOutputDir = outputDir; + if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it + map variables; + variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName)); + variables["[extension]"] = m->getExtension(qualFileName); + string qualReverseFileName = getOutputFileName("qfile", variables); + m->openOutputFile(qualReverseFileName, outQual); + + while(!inQual.eof()){ + if (m->control_pressed) { inQual.close(); outQual.close(); m->mothurRemove(qualReverseFileName); return 0; } + currQual = QualityScores(inQual); m->gobble(inQual); + currQual.flipQScores(); + currQual.printQScores(outQual); + } + inQual.close(); + outQual.close(); + outputNames.push_back(qualReverseFileName); outputTypes["qfile"].push_back(qualReverseFileName); + } + + if (m->control_pressed) { m->mothurRemove(qualReverseFileName); m->mothurRemove(fastaReverseFileName); return 0; } + //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("qfile"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); } + } + + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for(int i=0;imothurOut(outputNames[i]); + m->mothurOutEndLine(); + } + + + + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReverseSeqsCommand", "execute"); exit(1); } }