/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.tools.converters;
import org.broad.igv.feature.BasicFeature;
import org.broad.igv.feature.GFFParser;
import org.broad.igv.feature.tribble.GFFCodec;
import org.broad.igv.feature.tribble.IGVBEDCodec;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.Feature;
import java.io.*;
import java.util.List;
/**
* Convert a GFF to a BED file, keeping the column 9 attribute tags.
*
* @author Jim Robinson
* @date 2/5/12
*/
public class GFFtoBed {
public static void convert(File inputFile, File outputFile) {
GFFParser parser = new GFFParser();
BufferedReader reader = null;
PrintWriter pw = null;
try {
GFFCodec.Version version = inputFile.getPath().endsWith(".gff3") ? GFFCodec.Version.GFF3 : GFFCodec.Version.GFF2;
GFFCodec gffCodec = new GFFCodec(version, null);
reader = ParsingUtils.openBufferedReader(new ResourceLocator(inputFile.getAbsolutePath()));
List<Feature> features = parser.loadFeatures(reader, null, gffCodec);
IGVBEDCodec codec = new IGVBEDCodec();
codec.setGffTags(true);
pw = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));
pw.println("#gffTags");
for(Feature feature : features) {
BasicFeature bf = (BasicFeature) feature;
String line = codec.encode(bf);
pw.println(line);
}
} catch (IOException e) {
e.printStackTrace();
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException e) {
}
}
try {
if (pw != null) pw.close();
} catch (Exception e) {
}
}
}
public static void main(String [] args) {
File gffFile = new File("/Users/jrobinso/projects/igv-js/igv/assets/hg19/gencode.v18.transcripts.patched_contigs.gtf");
File bedFile = new File("/Users/jrobinso/projects/igv-js/igv/assets/hg19/gencode.v18.transcripts.patched_contigs.bed");
convert(gffFile, bedFile);
}
}