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* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
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*
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package org.broad.igv.tdf;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.Globals;
import org.broad.igv.data.DatasetDataSource;
import org.broad.igv.data.WiggleDataset;
import org.broad.igv.data.WiggleParser;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.Assume;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestRule;
import org.junit.rules.Timeout;
import java.io.IOException;
import java.util.List;
import static org.junit.Assert.*;
/**
* @author jrobinso
* @date Jul 28, 2010
*/
public class TDFRegressionTests extends AbstractHeadlessTest{
@Rule
public TestRule testTimeout = new Timeout((int) 30e6);
/**
* IGV-1417 and/or IGV-1421 - error reading a version 1 file (error thrown in header)
*/
@Test
public void test_IGV1417() {
String tdfFile = "http://data.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.ewig.tdf";
TDFReader reader = TDFReader.getReader(tdfFile);
assertEquals(1, reader.getVersion());
}
@Test
public void test_v3() {
String tdfFile = "http://data.broadinstitute.org/igvdata/test/tdf/NA12878.pilot2.454.bam.tdf";
TDFReader reader = TDFReader.getReader(tdfFile);
assertEquals(3, reader.getVersion());
}
String[] dm3posChromos = new String[]{"chr2RHet", "chr4", "chrU"};
String[] dm3emptyChromos = new String[]{"chrUextra"};
// NOTE: V3 files for genomes other than hg18, hg19, mm8, or mm9 always fail by definition, so there is nothing to test
// @Test
// public void testChrAlldm3_v3() throws Exception{
// //TODO Put in test dir
// String genPath = "http://igvdata.broadinstitute.org/genomes/dm3.genome"; //"dm3";
//
// String wigPath = TestUtils.DATA_DIR + "wig/dm3_var_sample.wig";
//
// //TDF file generated from wiggle, using IGV 2.1.30 (tdf version 3)
// String tdf3Path = TestUtils.DATA_DIR + "tdf/dm3_var_sample.wig.v2.1.30.tdf";
//
// tstCHR_ALL(genPath, wigPath, tdf3Path, false, dm3posChromos, dm3emptyChromos);
// }
@Test
public void testChrAlldm3_v4() throws Exception{
String genPath = "http://igvdata.broadinstitute.org/genomes/dm3.genome";
String wigPath = TestUtils.DATA_DIR + "wig/dm3_var_sample.wig";
String tdf4Path = TestUtils.DATA_DIR + "tdf/dm3_var_sample.wig.v2.2.1.tdf";
// The chr order test should fail as order for dm3 has been changed with release v2.3
tstCHR_ALL(genPath, wigPath, tdf4Path, false, dm3posChromos, dm3emptyChromos);
}
String[] hg18posChromos = new String[]{"chr6", "chr7", "chr10", "chr11", "chr12"};
String[] hg18emptyChromos = new String[]{"chr1", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chrY"};
@Test
public void testChrAllhg18_v3() throws Exception{
String genPath = TestUtils.DATA_DIR + "genomes/hg18.unittest.genome";
String wigPath = TestUtils.DATA_DIR + "wig/hg18_var_sample.wig";
//TDF file generated from wiggle, using IGV 2.1.30 (tdf version 3)
String tdf3Path = TestUtils.DATA_DIR + "tdf/hg18_var_sample.wig.v2.1.30.tdf";
tstCHR_ALL(genPath, wigPath, tdf3Path, false, hg18posChromos, hg18emptyChromos);
}
//
// @Test
// public void testChrAllhg18_v4() throws Exception{
// String genPath = TestUtils.DATA_DIR + "genomes/hg18.unittest.genome";
//
// String wigPath = TestUtils.DATA_DIR + "wig/hg18_var_sample.wig";
// String tdf4Path = TestUtils.DATA_DIR + "tdf/hg18_var_sample.wig.v2.2.1.tdf";
//
// tstCHR_ALL(genPath, wigPath, tdf4Path, true, hg18posChromos, hg18emptyChromos);
// }
private boolean overlaps(long start, long end, LocusScore score){
return score.getStart() >= start && score.getStart() < end ||
score.getStart() <= end && score.getEnd() > start;
}
/**
* Test that our whole genome view returns valid data, or none at all
*
* @param genPath Path to genome used for tdf
* @param wigPath wig file used as input to tdf TODO Any toTDF file
* @param tdfPath path to outputted tdf file
* @param expHaveChrAll Whether the CHR_ALL call to the datasource is expected to be valid
* @param posChromos Chromosomes for which all values are positive
* @param emptyChromos Chromosomes which have no data
* @throws Exception
*/
public void tstCHR_ALL(String genPath, String wigPath, String tdfPath, boolean expHaveChrAll, String[] posChromos, String[] emptyChromos) throws Exception{
Genome genome = null;
try {
genome = GenomeManager.getInstance().loadGenome(genPath, null);
} catch (Exception e) {
e.printStackTrace();
}
Assume.assumeTrue(genome != null);
WiggleDataset ds = (new WiggleParser(new ResourceLocator(wigPath), genome)).parse();
DatasetDataSource wigSource = new DatasetDataSource(wigPath, ds, genome);
TDFReader tdfReader = TDFReader.getReader(tdfPath);
TDFDataSource tdfSource = new TDFDataSource(tdfReader, 0, tdfPath, genome);
//We can't test for exact equality, so we just look for errors
List<LocusScore> wigScores = wigSource.getSummaryScoresForRange(Globals.CHR_ALL, -1, -1, 0);
List<LocusScore> tdfScores = tdfSource.getSummaryScoresForRange(Globals.CHR_ALL, -1, -1, 0);
assertEquals(expHaveChrAll, tdfSource.isChrOrderValid());
if(!expHaveChrAll){
//Ideally we would recalculate the data, but returning nothing
//is preferable to returning incorrect data
if(tdfScores.size() == 0){
return;
}
}
//TODO This test could be more efficient, and we could be more precise
//about chromosome boundaries
int posChecked = 0;
for(String chromo: posChromos){
//We allow a little slop around chromo boundaries
long range = genome.getChromosome(chromo).getLength() / 1000;
long fudge = Math.max(500, range / 100);
range -= 2 * fudge;
long cMin = genome.getCumulativeOffset(chromo) / 1000 + fudge;
long cMax = cMin + range;
for(int ii= 0; ii < wigScores.size(); ii++){
LocusScore wLocus = wigScores.get(ii);
if(wLocus.getStart() >= cMin && wLocus.getEnd() <= cMax){
float wScore = wigScores.get(ii).getScore();
//Just checking our assumption
assert wScore > 0;
}
LocusScore tLocus = tdfScores.get(ii);
if(overlaps(cMin, cMax, tLocus)){
assertTrue("Found negative value in " + chromo + " at " + tLocus.getStart(), tLocus.getScore() >= 0);
posChecked++;
}
}
}
//assertTrue(posChecked > 0);
System.out.println("# Checked for positive values: " + posChecked);
for(String chromo: emptyChromos){
long range = genome.getChromosome(chromo).getLength() / 1000;
long fudge = Math.max(600, range / 100);
range -= 2 * fudge;
long cMin = (genome.getCumulativeOffset(chromo) / 1000) + fudge;
long cMax = cMin + range;
for(LocusScore wLocus: wigScores){
//Just checking our assumption
assert wLocus.getStart() < cMin || wLocus.getEnd() > cMax;
}
for(LocusScore tdfScore: tdfScores){
boolean hasData = overlaps(cMin, cMax, tdfScore);
hasData &= tdfScore.getScore() != 0.0f;
assertFalse("Found data where none should exist at " + chromo + ":" + tdfScore.getStart() + "-" + tdfScore.getEnd(), hasData);
}
}
}
}