+++ /dev/null
-/*
- * reversecommand.cpp
- * Mothur
- *
- * Created by Pat Schloss on 6/6/09.
- * Copyright 2009 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "reversecommand.h"
-#include "sequence.hpp"
-#include "qualityscores.h"
-
-//**********************************************************************************************************************
-vector<string> ReverseSeqsCommand::setParameters(){
- try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "fastaQual", "none",false,false); parameters.push_back(pfasta);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none",false,false); 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<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ReverseSeqsCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string ReverseSeqsCommand::getHelpString(){
- try {
- 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", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-ReverseSeqsCommand::ReverseSeqsCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["qfile"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-ReverseSeqsCommand::ReverseSeqsCommand(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;
- outputTypes["qfile"] = 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 = ""; }
- else {
- string path;
- it = parameters.find("fasta");
- //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["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; }
- 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 = "";
- }
-
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-
-int ReverseSeqsCommand::execute(){
- try{
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- string fastaReverseFileName;
-
- if(fastaFileName != ""){
- ifstream inFASTA;
- m->openInputFile(fastaFileName, inFASTA);
-
- ofstream outFASTA;
- string tempOutputDir = outputDir;
- if (outputDir == "") { tempOutputDir += m->hasPath(fastaFileName); } //if user entered a file with a path then preserve it
- fastaReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName)) + "rc" + m->getExtension(fastaFileName);
- m->openOutputFile(fastaReverseFileName, outFASTA);
-
- while(!inFASTA.eof()){
- if (m->control_pressed) { inFASTA.close(); outFASTA.close(); m->mothurRemove(fastaReverseFileName); return 0; }
-
- Sequence currSeq(inFASTA); m->gobble(inFASTA);
- if (currSeq.getName() != "") {
- currSeq.reverseComplement();
- currSeq.printSequence(outFASTA);
- }
- }
- inFASTA.close();
- outFASTA.close();
- outputNames.push_back(fastaReverseFileName); outputTypes["fasta"].push_back(fastaReverseFileName);
- }
-
- string qualReverseFileName;
-
- if(qualFileName != ""){
- QualityScores currQual;
-
- ifstream inQual;
- m->openInputFile(qualFileName, inQual);
-
- ofstream outQual;
- string tempOutputDir = outputDir;
- if (outputDir == "") { tempOutputDir += m->hasPath(qualFileName); } //if user entered a file with a path then preserve it
- string qualReverseFileName = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName)) + "rc" + m->getExtension(qualFileName);
- m->openOutputFile(qualReverseFileName, outQual);
-
- while(!inQual.eof()){
- 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); 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();
- for(int i=0;i<outputNames.size();i++){
- m->mothurOut(outputNames[i]);
- m->mothurOutEndLine();
- }
-
-
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "ReverseSeqsCommand", "execute");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
projects / mothur.git / blobdiff