/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.tools.converters;
import org.broad.igv.feature.*;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.tribble.GFFCodec;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import htsjdk.tribble.Feature;
import org.junit.Test;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.List;
import static junit.framework.Assert.assertEquals;
import static junit.framework.Assert.assertTrue;
/**
* @author Jim Robinson
* @date 2/15/12
*/
public class GFFtoBedTest {
@Test
public void testConvert() throws Exception {
File inputFile = new File(TestUtils.DATA_DIR, "gff/gene.unsorted.gff3");
File outputFile = new File(TestUtils.DATA_DIR, "out/gene.bed");
// Convert
GFFtoBed.convert(inputFile, outputFile);
// Now compare features from both files, they should be identical
BufferedReader gffReader = null;
BufferedReader bedReader = null;
try {
Genome genome = null; // Not needed for this test
gffReader = new BufferedReader(new FileReader(inputFile));
GFFParser parser = new GFFParser();
GFFCodec.Version version = inputFile.getPath().endsWith(".gff3") ? GFFCodec.Version.GFF3 : GFFCodec.Version.GFF2;
GFFCodec codec = new GFFCodec(version, null);
List<Feature> gffFeatures = parser.loadFeatures(gffReader, genome, codec);
bedReader = new BufferedReader(new FileReader(outputFile));
FeatureParser bedParser = AbstractFeatureParser.getInstanceFor(new ResourceLocator(outputFile.getAbsolutePath()), null);
List<Feature> bedFeatures = bedParser.loadFeatures(bedReader, genome);
assertTrue(gffFeatures.size() > 0);
assertEquals(gffFeatures.size(), bedFeatures.size());
for (int i = 0; i < gffFeatures.size(); i++) {
BasicFeature gffFeature = (BasicFeature) gffFeatures.get(i);
BasicFeature bedFeature = (BasicFeature) bedFeatures.get(i);
compare(gffFeature, bedFeature);
}
} finally {
gffReader.close();
}
}
private void compare(BasicFeature gffFeature, BasicFeature bedFeature) {
assertEquals(gffFeature.getChr(), bedFeature.getChr());
assertEquals(gffFeature.getStart(), bedFeature.getStart());
assertEquals(gffFeature.getEnd(), bedFeature.getEnd());
assertEquals(gffFeature.getStrand(), bedFeature.getStrand());
assertEquals(gffFeature.getColor(), bedFeature.getColor());
//BED features don't have a type
//assertEquals(gffFeature.getType(), bedFeature.getType());
assertEquals(gffFeature.getStart(), bedFeature.getThickStart());
assertEquals(gffFeature.getThickEnd(), bedFeature.getThickEnd());
if (!Float.isNaN(gffFeature.getScore())) {
assertEquals(gffFeature.getScore(), bedFeature.getScore());
}
assertEquals(gffFeature.getExonCount(), bedFeature.getExonCount());
List<Exon> gffExons = gffFeature.getExons();
List<Exon> bedExons = bedFeature.getExons();
// This is broken for sure, disable for now
// for (int i = 0; i < gffExons.size(); i++) {
//
// Exon gffExon = gffExons.get(i);
// Exon bedExon = bedExons.get(i);
// assertEquals(gffExon.getCdStart(), bedExon.getCdStart());
// assertEquals(gffExon.getCodingLength(), bedExon.getCodingLength());
// assertEquals(gffExon.getCdEnd(), bedExon.getCdEnd());
// assertEquals(gffExon.getReadingShift(), bedExon.getReadingShift());
// }
}
}