X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=degapseqscommand.cpp;h=8687194778d2da8360b3367c3c5ec2bb00108431;hp=e475727cb68dd0a28c27ffb64f699a9e633229f8;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=15bc21bb4281af0f3ea7b29d9b9363f4635ef939 diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp index e475727..8687194 100644 --- a/degapseqscommand.cpp +++ b/degapseqscommand.cpp @@ -10,19 +10,80 @@ #include "degapseqscommand.h" #include "sequence.hpp" +//********************************************************************************************************************** +vector DegapSeqsCommand::setParameters(){ + try { + 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", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string DegapSeqsCommand::getHelpString(){ + try { + 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", "getHelpString"); + 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); + } +} +//********************************************************************************************************************** +DegapSeqsCommand::DegapSeqsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand"); + exit(1); + } +} //*************************************************************************************************************** - DegapSeqsCommand::DegapSeqsCommand(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", "outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -35,43 +96,82 @@ DegapSeqsCommand::DegapSeqsCommand(string option) { 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 = ""; } //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(); - ableToOpen = m->openInputFile(tryPath, in, "noerror"); - 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 (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 (!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 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]); } } } @@ -93,36 +193,11 @@ 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{ - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } for (int s = 0; s < fastaFileNames.size(); s++) { @@ -133,11 +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) { 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() != "") { @@ -148,13 +225,20 @@ int DegapSeqsCommand::execute(){ inFASTA.close(); outFASTA.close(); - outputNames.push_back(degapFile); + outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile); - if (m->control_pressed) { 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 + string current = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } } 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();