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/*
* 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","fasta",false,false,true); parameters.push_back(pfasta);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "fastaQual", "none","qfile",false,false,true); 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);
}
}
//**********************************************************************************************************************
string ReverseSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],rc,[extension]"; }
else if (type == "qfile") { pattern = "[filename],rc,[extension]"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "ReverseSeqsCommand", "getOutputPattern");
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
map<string, string> variables;
variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileName));
variables["[extension]"] = m->getExtension(fastaFileName);
fastaReverseFileName = getOutputFileName("fasta", variables);
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
map<string, string> variables;
variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(qualFileName));
variables["[extension]"] = m->getExtension(qualFileName);
string qualReverseFileName = getOutputFileName("qfile", variables);
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 Names: "); 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);
}
}
//***************************************************************************************************************
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