+++ /dev/null
-/*
- * degapseqscommand.cpp
- * Mothur
- *
- * Created by westcott on 6/21/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "degapseqscommand.h"
-#include "sequence.hpp"
-
-//**********************************************************************************************************************
-vector<string> 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<string> 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<string> 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<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
- map<string,string>::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<string> 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);
- }
-}
-
-//***************************************************************************************************************
-
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