X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=reversecommand.cpp;fp=reversecommand.cpp;h=c664ad7548b52f8966c799749f382d31169f564d;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/reversecommand.cpp b/reversecommand.cpp
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+++ b/reversecommand.cpp
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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",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);
+	}
+}
+
+//***************************************************************************************************************