X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=reversecommand.cpp;h=a9b297731a346999b155c61d7cab47ff7089063c;hp=5eceb3049f0d6cbc41025c875843adce306a745c;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=74d3aaf0f85080ea3cfb1f1871e706bab9f48392 diff --git a/reversecommand.cpp b/reversecommand.cpp index 5eceb30..a9b2977 100644 --- a/reversecommand.cpp +++ b/reversecommand.cpp @@ -12,56 +12,68 @@ #include "qualityscores.h" //********************************************************************************************************************** -vector ReverseSeqsCommand::getValidParameters(){ +vector ReverseSeqsCommand::setParameters(){ try { - string Array[] = {"fasta", "qfile", "outputdir", "inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + 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) { - m->errorOut(e, "ReverseSeqsCommand", "getValidParameters"); + m->errorOut(e, "ReverseSeqsCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -ReverseSeqsCommand::ReverseSeqsCommand(){ +string ReverseSeqsCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["qfile"] = tempOutNames; + 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", "ReverseSeqsCommand"); + m->errorOut(e, "ReverseSeqsCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** - -vector ReverseSeqsCommand::getRequiredParameters(){ - try { - string Array[] = {"fasta", "qfile"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "ReverseSeqsCommand", "getRequiredParameters"); - 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); + } } - //********************************************************************************************************************** - -vector ReverseSeqsCommand::getRequiredFiles(){ +ReverseSeqsCommand::ReverseSeqsCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "ReverseSeqsCommand", "getRequiredFiles"); + m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand"); exit(1); } -}//*************************************************************************************************************** +} +//*************************************************************************************************************** ReverseSeqsCommand::ReverseSeqsCommand(string option) { try { @@ -69,11 +81,10 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option) { //allow user to run help 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", "qfile", "outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -103,27 +114,43 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option) { //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; } - - if(fastaFileName == "not open" && qualFileName == "not open"){ - m->mothurOut("fasta or qfile 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 = ""; - outputDir += m->hasPath(fastaFileName); //if user entered a file with a path then preserve it } } @@ -133,25 +160,6 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option) { exit(1); } } -//********************************************************************************************************************** - -void ReverseSeqsCommand::help(){ - try { - 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 parameters fasta or qfile are 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) { - m->errorOut(e, "ReverseSeqsCommand", "help"); - exit(1); - } -} - -//*************************************************************************************************************** - -ReverseSeqsCommand::~ReverseSeqsCommand(){ /* do nothing */ } - //*************************************************************************************************************** @@ -167,11 +175,16 @@ int ReverseSeqsCommand::execute(){ m->openInputFile(fastaFileName, inFASTA); ofstream outFASTA; - fastaReverseFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName); + 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(); remove(fastaReverseFileName.c_str()); return 0; } + if (m->control_pressed) { inFASTA.close(); outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; } Sequence currSeq(inFASTA); m->gobble(inFASTA); if (currSeq.getName() != "") { @@ -181,7 +194,7 @@ int ReverseSeqsCommand::execute(){ } inFASTA.close(); outFASTA.close(); - outputNames.push_back(fastaReverseFileName); + outputNames.push_back(fastaReverseFileName); outputTypes["fasta"].push_back(fastaReverseFileName); } string qualReverseFileName; @@ -193,27 +206,49 @@ int ReverseSeqsCommand::execute(){ m->openInputFile(qualFileName, inQual); ofstream outQual; - string qualReverseFileName = outputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName); - m->openOutputFile(qualReverseFileName, 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(); remove(qualReverseFileName.c_str()); return 0; } + 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); + 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 Name: "); m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for(int i=0;imothurOut(outputNames[i]); m->mothurOutEndLine(); } + + return 0; } catch(exception& e) {