/*
* 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.BasicFeature;
import org.broad.igv.track.FeatureSource;
import org.broad.igv.track.GFFFeatureSource;
import org.broad.igv.track.TribbleFeatureSource;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import htsjdk.tribble.Feature;
import org.junit.Test;
import java.util.Iterator;
import static junit.framework.Assert.assertEquals;
/**
* User: jacob
* Date: 2013-Mar-21
*/
public class GFFCodecTest extends AbstractHeadlessTest {
/**
* Make sure we parse the attributes to get the name of this feature
* GTF has a bunch of different ones
*
* @throws Exception
*/
@Test
public void testGetNameGTF() throws Exception {
String path = TestUtils.DATA_DIR + "gtf/transcript_id.gtf";
String expName = "YAL069W";
GFFFeatureSource src = new GFFFeatureSource(TribbleFeatureSource.getFeatureSource(new ResourceLocator(path), null));
Iterator<Feature> iter = src.getFeatures("I", 0, Integer.MAX_VALUE);
while (iter.hasNext()) {
BasicFeature bf = (BasicFeature) iter.next();
assertEquals(expName, bf.getName());
}
}
/**
* Insure we can parse a GFF file that includes a fasta section.
*
* @throws Exception
*/
@Test
public void testGFFWithFasta() throws Exception {
String path = TestUtils.DATA_DIR + "gff/gffWithFasta.gff";
final ResourceLocator locator = new ResourceLocator(path);
TribbleFeatureSource tribbleFeatureSource = TribbleFeatureSource.getFeatureSource(locator, genome);
FeatureSource source = new GFFFeatureSource(tribbleFeatureSource);
int featureCount = 0;
Iterator<Feature> iter = source.getFeatures("chr7", 0, Integer.MAX_VALUE);
while (iter.hasNext()) {
BasicFeature bf = (BasicFeature) iter.next();
featureCount++;
}
assertEquals(2, featureCount);
}
}