/*
* 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.methyl;
import junit.framework.Assert;
import org.broad.igv.bbfile.BBFileReader;
import org.broad.igv.feature.Strand;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.util.TestUtils;
import org.junit.Test;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import static junit.framework.Assert.assertTrue;
import static org.junit.Assert.assertEquals;
/**
* Test of data source for Michael Ziller's hacked up bigbed format for methylation scores.
*
* @author Jim Robinson
* @date 4/19/12
*/
public class BBMethylDataSourceTest {
@Test
public void testUscQuery() throws Exception {
// Test data
// chr11 10001654 10001656 . 1000 . 100.000 7
// chr11 10001667 10001669 . 833 . 83.333 6
// chr11 10001752 10001754 . 625 . 62.500 8
int[] expectedStarts = {10001654, 10001667, 10001752};
int[] expectedEnds = {10001656, 10001669, 10001754};
float[] expectedPercents = {100.0f, 83.333f, 62.500f};
int[] expectedCounts = {7, 6, 8};
String testFile = TestUtils.DATA_DIR +
"/methylation/usc/jhu-usc.edu_UCEC.IlluminaHiSeq_WGBS.Level_3.1.0.0.hg18.SAMPLE.bb";
Genome genome = null; // Don't need a genome for this test
String chr = "chr11";
int start = 10001654;
int end = 10001754;
BBFileReader reader = new BBFileReader(testFile);
MethylDataSource source = new BBMethylDataSource(reader, BBMethylDataSource.Type.USC, genome);
Iterator<MethylScore> iter = source.query(chr, start, end);
int i = 0;
while (iter.hasNext()) {
MethylScore ms = iter.next();
assertEquals(chr, ms.getChr());
assertEquals(expectedStarts[i], ms.getStart());
assertEquals(expectedEnds[i], ms.getEnd());
assertEquals(expectedPercents[i], ms.getScore(), .000001);
assertEquals(expectedCounts[i], ms.getCount());
assertEquals(Strand.NONE, ms.getStrand());
i++;
}
assertEquals(3, i);
}
//@Test
public void testZillerQuery() throws Exception {
String testFile = "path-to-test-file.bb";
String chr = "chr7";
int start = 26133475;
int end = 27333475;
Genome genome = null;
BBFileReader reader = new BBFileReader(testFile);
MethylDataSource source = new BBMethylDataSource(reader, BBMethylDataSource.Type.ZILLER, genome);
Iterator<MethylScore> iter = source.query(chr, start, end);
// Should find at least 1 score.
assertTrue(iter.hasNext());
while (iter.hasNext()) {
MethylScore score = iter.next();
assertTrue(score.getEnd() >= start && score.getStart() <= end);
assertTrue(score.getScore() >= 0 && score.getScore() <= 100);
}
}
// @Test
public void testCacheQuery() throws Exception {
String testFile = "path-to-test-file.bb";
String chr = "chr7";
int start = 26133475;
int end = 27333475;
Genome genome = null;
BBFileReader reader = new BBFileReader(testFile);
MethylDataSource source = new BBMethylDataSource(reader, BBMethylDataSource.Type.ZILLER, genome);
Iterator<MethylScore> iter = source.query(chr, start, end);
List<MethylScore> nonCachedScores = new ArrayList<MethylScore>();
while (iter.hasNext()) {
nonCachedScores.add(iter.next());
}
int maxTileCount = 100000;
int tileSize = 100;
MethylDataSource cachedSource = new CachingMethylSource(new BBMethylDataSource(reader, BBMethylDataSource.Type.ZILLER, genome),
maxTileCount, tileSize);
Iterator<MethylScore> iter2 = cachedSource.query(chr, start, end);
List<MethylScore> cachedScores = new ArrayList<MethylScore>();
while (iter2.hasNext()) {
cachedScores.add(iter2.next());
}
assertTrue(cachedScores.size() > 0);
Assert.assertEquals(cachedScores.size(), nonCachedScores.size());
for (int i = 0; i < cachedScores.size(); i++) {
MethylScore cScore = cachedScores.get(i);
MethylScore score = nonCachedScores.get(i);
Assert.assertEquals(cScore.getStart(), score.getStart());
Assert.assertEquals(cScore.getChr(), score.getChr());
}
}
}