/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package gff;

import java.util.*;
import java.io.*;

import org.biojava.bio.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.seq.impl.*;
import org.biojava.bio.program.gff.*;

/**
 * Converts a Genbank file into a fasta file for the sequence and a GFF file for
 * the features.
 * <P>
 * This program demonstrates how to read in a Genbank file, how to write a fasta
 * file and how to write GFF.
 * <P>
 * Use:<br>
 * <code>java GenbankToGffFasta genbankFile fastaOut gffOut</code>
 * <P>
 * Based heavily off of EmblToGffFasta by Matthew Pocock.  It was pretty much a
 * global replace of 'embl' with 'genbank'.
 *
 * @author Greg Cox
 */
public class GenbankToGffFasta
{
	public static void main(String [] args) throws Exception
	{
		if(args.length != 3)
		{
			throw new Exception("Use: GenbankToGffFasta genbankFile fastaOut gffOut");
		}

		try
		{
			// make the files early to get exceptions about stupid file names
			File genbankFile = new File(args[0]);
			File fastaFile = new File(args[1]);
			File gffFile = new File(args[2]);

			// reading Genbank stuff
			SequenceFormat gFormat = new GenbankFormat();
			BufferedReader gReader = new BufferedReader(
				new InputStreamReader(new FileInputStream(genbankFile)));
			SequenceBuilderFactory sFact = new GenbankProcessor.Factory(SimpleSequenceBuilder.FACTORY);
			Alphabet alpha = DNATools.getDNA();
			SymbolTokenization rParser = alpha.getTokenization("token");

			// fasta stuff
			SequenceFormat fFormat = new FastaFormat();
			OutputStream fastaOut = new FileOutputStream(fastaFile);

			// gff stuff
			GFFWriter writer = new GFFWriter(
				new PrintWriter(new OutputStreamWriter(new FileOutputStream(gffFile))));
			SequencesAsGFF seqsAsGFF = new SequencesAsGFF();

			// Loop over each sequence in the genbank file.
			// Write the sequence to a fasta file
			// Write the features to a .gff file
			SequenceIterator seqI =
				new StreamReader(gReader, gFormat, rParser, sFact);

			while(seqI.hasNext())
			{
				Sequence seq = seqI.nextSequence();
				fFormat.writeSequence(seq, new PrintStream(fastaOut));
				seqsAsGFF.processSequence(seq, writer);
			}
		}
		catch (Throwable t)
		{
			t.printStackTrace();
			System.exit(1);
		}
	}
}