X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=degapseqscommand.cpp;h=8687194778d2da8360b3367c3c5ec2bb00108431;hp=7fd2803a4ec6c5e578d7b180a9e08fda1af33385;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677 diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp index 7fd2803..8687194 100644 --- a/degapseqscommand.cpp +++ b/degapseqscommand.cpp @@ -11,49 +11,65 @@ #include "sequence.hpp" //********************************************************************************************************************** -vector DegapSeqsCommand::getValidParameters(){ +vector DegapSeqsCommand::setParameters(){ try { - string Array[] = {"fasta", "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 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, "DegapSeqsCommand", "getValidParameters"); + m->errorOut(e, "DegapSeqsCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -DegapSeqsCommand::DegapSeqsCommand(){ +string DegapSeqsCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; + string helpString = ""; + helpString += "The degap.seqs command reads a fastafile and removes all gap characters.\n"; + helpString += "The degap.seqs command parameter is fasta.\n"; + helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required unless you have a valid current fasta file. \n"; + helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"; + helpString += "The degap.seqs command should be in the following format: \n"; + helpString += "degap.seqs(fasta=yourFastaFile) \n"; + helpString += "Example: degap.seqs(fasta=abrecovery.align) \n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand"); + m->errorOut(e, "DegapSeqsCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector DegapSeqsCommand::getRequiredParameters(){ - try { - string Array[] = {"fasta"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "DegapSeqsCommand", "getRequiredParameters"); - exit(1); - } +string DegapSeqsCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],ng.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, "DegapSeqsCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** -vector DegapSeqsCommand::getRequiredFiles(){ +DegapSeqsCommand::DegapSeqsCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "DegapSeqsCommand", "getRequiredFiles"); + m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand"); exit(1); } } @@ -64,11 +80,10 @@ DegapSeqsCommand::DegapSeqsCommand(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", "outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -92,52 +107,71 @@ DegapSeqsCommand::DegapSeqsCommand(string option) { //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", false); - if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the degap.seqs command."); m->mothurOutEndLine(); abort = true; } + if (fastafile == "not found") { + fastafile = m->getFastaFile(); + if (fastafile != "") { fastaFileNames.push_back(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->splitAtDash(fastafile, fastaFileNames); //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < fastaFileNames.size(); i++) { - if (inputDir != "") { - string path = m->hasPath(fastaFileNames[i]); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; } - } - - ifstream in; - int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror"); - - //if you can't open it, try default location - if (ableToOpen == 1) { - if (m->getDefaultPath() != "") { //default path is set - string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]); - m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - fastaFileNames[i] = tryPath; - } - } - //if you can't open it, try default location - if (ableToOpen == 1) { - if (m->getOutputDir() != "") { //default path is set - string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]); - m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - fastaFileNames[i] = tryPath; + bool ignore = false; + if (fastaFileNames[i] == "current") { + fastaFileNames[i] = m->getFastaFile(); + if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; } } - in.close(); + if (!ignore) { + if (inputDir != "") { + string path = m->hasPath(fastaFileNames[i]); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; } + } + + ifstream in; + int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror"); - if (ableToOpen == 1) { - m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); - //erase from file list - fastaFileNames.erase(fastaFileNames.begin()+i); - i--; + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getDefaultPath() != "") { //default path is set + string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; + } + } + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + fastaFileNames[i] = tryPath; + } + } + + in.close(); + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; + }else { m->setFastaFile(fastaFileNames[i]); } } } @@ -159,32 +193,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option) { exit(1); } } -//********************************************************************************************************************** - -void DegapSeqsCommand::help(){ - try { - m->mothurOut("The degap.seqs command reads a fastafile and removes all gap characters.\n"); - m->mothurOut("The degap.seqs command parameter is fasta.\n"); - m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n"); - m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); - m->mothurOut("The degap.seqs command should be in the following format: \n"); - m->mothurOut("degap.seqs(fasta=yourFastaFile) \n"); - m->mothurOut("Example: degap.seqs(fasta=abrecovery.align) \n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "DegapSeqsCommand", "help"); - exit(1); - } -} - //*************************************************************************************************************** - -DegapSeqsCommand::~DegapSeqsCommand(){ /* do nothing */ } - -//*************************************************************************************************************** - - int DegapSeqsCommand::execute(){ try{ @@ -199,11 +208,13 @@ int DegapSeqsCommand::execute(){ ofstream outFASTA; string tempOutputDir = outputDir; if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); } - string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta"; + map variables; + variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])); + string degapFile = getOutputFileName("fasta", variables); m->openOutputFile(degapFile, outFASTA); while(!inFASTA.eof()){ - if (m->control_pressed) { outputTypes.clear(); inFASTA.close(); outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } + if (m->control_pressed) { outputTypes.clear(); inFASTA.close(); outFASTA.close(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } Sequence currSeq(inFASTA); m->gobble(inFASTA); if (currSeq.getName() != "") { @@ -216,7 +227,7 @@ int DegapSeqsCommand::execute(){ outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile); - if (m->control_pressed) { outputTypes.clear(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } + if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } } //set fasta file as new current fastafile @@ -227,7 +238,7 @@ int DegapSeqsCommand::execute(){ } m->mothurOutEndLine(); - m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine();