X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.cpp;fp=degapseqscommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=1d83f3bef00d08574a66d7e5ecf21efa148452a4;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp deleted file mode 100644 index 1d83f3b..0000000 --- a/degapseqscommand.cpp +++ /dev/null @@ -1,239 +0,0 @@ -/* - * degapseqscommand.cpp - * Mothur - * - * Created by westcott on 6/21/10. - * Copyright 2010 Schloss Lab. All rights reserved. - * - */ - -#include "degapseqscommand.h" -#include "sequence.hpp" - -//********************************************************************************************************************** -vector DegapSeqsCommand::setParameters(){ - try { - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,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); - } -} -//********************************************************************************************************************** -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; 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; - - //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->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++) { - - 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--; - } - } - - 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]); } - } - } - - //make sure there is at least one valid file left - if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); 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(fastafile); //if user entered a file with a path then preserve it - } - - } - } - catch(exception& e) { - m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand"); - exit(1); - } -} -//*************************************************************************************************************** -int DegapSeqsCommand::execute(){ - try{ - - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - for (int s = 0; s < fastaFileNames.size(); s++) { - - m->mothurOut("Degapping sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine(); - ifstream inFASTA; - m->openInputFile(fastaFileNames[s], inFASTA); - - ofstream outFASTA; - string tempOutputDir = outputDir; - if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); } - string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta"; - m->openOutputFile(degapFile, outFASTA); - - while(!inFASTA.eof()){ - 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() != "") { - outFASTA << ">" << currSeq.getName() << endl; - outFASTA << currSeq.getUnaligned() << endl; - } - } - inFASTA.close(); - outFASTA.close(); - - outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile); - - 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(); - for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } - m->mothurOutEndLine(); - - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "DegapSeqsCommand", "execute"); - exit(1); - } -} - -//*************************************************************************************************************** -