/*
* 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.feature.tribble;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackLoader;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import htsjdk.tribble.AbstractFeatureReader;
import htsjdk.tribble.Feature;
import htsjdk.tribble.FeatureCodec;
import org.junit.Test;
import java.util.List;
import static junit.framework.Assert.assertEquals;
/**
* User: jacob
* Date: 2012/03/08
*/
public class UCSCGeneTableCodecTest extends AbstractHeadlessTest {
@Test
public void testLoadGenePred() throws Exception {
String file = TestUtils.DATA_DIR + "gene/EnsembleGenes_sample.genepred";
TrackLoader loader = new TrackLoader();
ResourceLocator locator = new ResourceLocator(file);
Genome genome = TestUtils.loadGenome();
List<Track> tracks = loader.load(locator, genome);
assertEquals(1, tracks.size());
FeatureCodec codec = CodecFactory.getCodec(locator, genome);
AbstractFeatureReader<Feature, ?> bfs = AbstractFeatureReader.getFeatureReader(locator.getPath(), codec, false);
Iterable<Feature> iter = bfs.iterator();
int count = 0;
for (Feature f : iter) {
if (count == 0) {
assertEquals(67051161, f.getStart());
assertEquals(67163158, f.getEnd());
}
count++;
}
assertEquals(74, count);
}
@Test
public void testLoadUCSC() throws Exception {
String file = TestUtils.DATA_DIR + "gene/UCSCgenes_sample.gene";
TrackLoader loader = new TrackLoader();
ResourceLocator locator = new ResourceLocator(file);
Genome genome = TestUtils.loadGenome();
List<Track> tracks = loader.load(locator, genome);
assertEquals(1, tracks.size());
FeatureCodec codec = CodecFactory.getCodec(locator.getPath(), genome);
AbstractFeatureReader<Feature, ?> bfs = AbstractFeatureReader.getFeatureReader(locator.getPath(), codec, false);
Iterable<Feature> iter = bfs.iterator();
int count = 0;
for (Feature f : iter) {
if (count == 0) {
assertEquals(1115, f.getStart());
assertEquals(4121, f.getEnd());
}
count++;
}
assertEquals(382, count);
}
}