/*
* 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.
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package org.broad.igv.track;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.feature.FeatureDB;
import org.broad.igv.feature.IGVFeature;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.tools.IgvTools;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.broad.igv.variant.VariantTrack;
import htsjdk.tribble.Feature;
import org.junit.Before;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestRule;
import org.junit.rules.Timeout;
import java.io.File;
import java.util.*;
import static junit.framework.Assert.*;
/**
* @author Jim Robinson
* @date 10/3/11
*/
public class TrackLoaderTest extends AbstractHeadlessTest {
TrackLoader trackLoader;
@Rule
public TestRule testTimeout = new Timeout((int) (500 * 60e3));
@Before
public void setUp() throws Exception {
super.setUp();
trackLoader = new TrackLoader();
}
@Test
public void testLoadBEDIndexed() throws Exception {
String filepath = TestUtils.DATA_DIR + "bed/intervalTest.bed";
TestUtils.createIndex(filepath);
tstLoadFi(filepath, 1, true);
}
@Test
public void testLoadBEDtxt() throws Exception {
String filepath = TestUtils.DATA_DIR + "bed/intervalTest.bed.txt";
TestUtils.createIndex(filepath);
tstLoadFi(filepath, 1, true);
}
@Test
public void testLoadBEDNotIndexed() throws Exception {
String filepath = TestUtils.DATA_DIR + "bed/intervalTest.bed";
if (TrackLoader.isIndexed(new ResourceLocator(filepath), null)) {
File f = new File(filepath + ".idx");
f.delete();
}
tstLoadFi(filepath, 1, false);
}
@Test
public void testBEDCodec1() throws Exception {
// This file has an extra tab in the second to last line. Should have no effect, but earlier versions
// of IGV would split on tabs only and throw a runtime exception.
String filepath = TestUtils.DATA_DIR + "bed/multi_tab.bed";
tstLoadFi(filepath, null, false);
}
/**
* Make sure we throw an exception when parsing a bad file
* @throws Exception
*/
@Test(expected = RuntimeException.class)
public void testBEDCodec2() throws Exception {
String filepath = TestUtils.DATA_DIR + "bed/bad_file.bed";
tstLoadFi(filepath, null, false);
}
@Test
public void testLoadSIF() throws Exception {
String filepath = TestUtils.DATA_DIR + "sample/BRCA_sif.txt";
List<String> expectedAttributeNames = Arrays.asList("TCGA_EXPERIMENT", "TCGA_BATCH", "TUMOR_NORMAL",
"BIRDSEED_GENDER", "LEVEL2_NOISE", "LEVEL3_SEGMENT_COUNT", "PURITY PLOIDY", "DELTA",
"CANCER_DNA_FRACTION", "SUBCLONAL_GENOME_FRACTION");
tstLoadFi(filepath, 0, false); //Sample information file, shouldn't have tracks.
Set<String> attrNames = new HashSet<String>(AttributeManager.getInstance().getAttributeNames());
assertTrue(attrNames.size() >= expectedAttributeNames.size()); // Can be larger because of default attributes
for (String name : expectedAttributeNames) {
assertTrue(expectedAttributeNames.contains(name));
}
}
@Test
public void testLoadGFF() throws Exception {
String filepath = TestUtils.DATA_DIR + "gff/simfeatures.gff3";
List<Track> tracks = trackLoader.load(new ResourceLocator(filepath), genome);
assertEquals(1, tracks.size());
FeatureTrack track = (FeatureTrack) tracks.get(0);
assertEquals("notmeaningful", track.getName());
List<Feature> features = track.getFeatures("chr1", 0, Integer.MAX_VALUE);
assertEquals(2, features.size());
IGVFeature feat0 = (IGVFeature) features.get(0);
IGVFeature feat1 = (IGVFeature) features.get(1);
assertEquals(707 - 1, feat0.getStart());
assertEquals(943, feat0.getEnd());
assertEquals(7563 - 1, feat1.getStart());
assertEquals(7938, feat1.getEnd());
}
@Test
public void testLoadGFFAliasedChrs() throws Exception {
String filepath = TestUtils.DATA_DIR + "gff/aliased.unsorted.gff";
Genome genome = IgvTools.loadGenome(TestUtils.DATA_DIR + "genomes/hg18_truncated_aliased.genome");
List<Track> tracks = trackLoader.load(new ResourceLocator(filepath), genome);
assertEquals(1, tracks.size());
FeatureTrack track = (FeatureTrack) tracks.get(0);
assertEquals("aliased.unsorted.gff", track.getName());
List<Feature> features = track.getFeatures("chr1", 0, Integer.MAX_VALUE);
assertEquals(56, features.size());
features = track.getFeatures("chr5", 0, Integer.MAX_VALUE);
assertEquals(16, features.size());
//Non-aliased
features = track.getFeatures("NC_007072.3", 0, Integer.MAX_VALUE);
assertEquals(30, features.size());
}
/**
* Test that we properly load a vcf file, even though the
* extension is upper-case. IGV-2012
*
* @throws Exception
*/
@Test
public void testLoadVCFUpperCase() throws Exception {
String filepath = TestUtils.DATA_DIR + "vcf/HC_MOD_CAPS.VCF";
ResourceLocator locator = new ResourceLocator(filepath);
TestUtils.createIndex(filepath);
List<Track> tracks = trackLoader.load(locator, genome);
assertEquals(1, tracks.size());
assertTrue("VCF file loaded incorrect track type", tracks.get(0) instanceof VariantTrack);
}
private List<Track> tstLoadFi(String filepath, Integer expected_tracks, boolean makeIndex) throws Exception {
Genome genome = TestUtils.loadGenome();
return tstLoadFi(filepath, expected_tracks, genome, makeIndex);
}
private List<Track> tstLoadFi(String filepath, Integer expected_tracks, Genome genome, boolean makeIndex) throws Exception {
return tstLoadFi(this.trackLoader, filepath, expected_tracks, genome, makeIndex);
}
static List<Track> tstLoadFi(TrackLoader trackLoader, String filepath, Integer expected_tracks, Genome genome, boolean makeIndex) throws Exception {
ResourceLocator locator = new ResourceLocator(filepath);
//Try creating an index
//UI would ask for confirmation
if (makeIndex) {
try {
TestUtils.createIndex(filepath);
} catch (Exception e) {
}
}
List<Track> tracks = trackLoader.load(locator, genome);
if (expected_tracks != null) {
assertEquals(expected_tracks.intValue(), tracks.size());
if (expected_tracks == 0) {
return tracks;
}
}
Track track = tracks.get(0);
assertEquals(locator, track.getResourceLocator());
return tracks;
}
@Test
public void testBEDLoadsAliases() throws Exception {
tstLoadFi(TestUtils.DATA_DIR + "bed/canFam2_alias.bed", 1, false);
String[] aliases = new String[]{"AAAA", "BBB", "CCC"};
for (String alias : aliases) {
Feature feat = FeatureDB.getFeature(alias);
assertNotNull(feat);
}
}
static String[] filenamesNoIndex = new String[]{"cufflinks/sample_genes.fpkm_tracking", "cufflinks/sample_gene_exp.diff", "/bb/chr21.refseq.bb", "/bed/MT_test.bed", "/bed/Unigene.sample.bed",
"/bed/test.bed", "/cn/HindForGISTIC.hg16.cn", "/folder with spaces/test.wig",
"/gct/igv_test2.gct", "/gct/affy_human_mod.gct", "/gff/gene.unsorted.gff3", "/igv/MIP_44.cn",
"/maf/TCGA_GBM_Level3_Somatic_Mutations_08.28.2008.maf.gz",
"/psl/fishBlat.psl", "/seg/canFam2_hg18.seg", "/wig/test.wig"};
private static ArrayList<String> tmp = new ArrayList<String>(filenamesNoIndex.length);
static String[] filenamesTryIndex;
static {
tmp.add("/sam/test_2.sam");
filenamesTryIndex = tmp.toArray(new String[tmp.size()]);
}
public void tstFilesHeadless(String[] filenames, boolean tryIndex) throws Exception {
Genome genome = TestUtils.loadGenome();
for (String finame : filenames) {
tstLoadFi(TestUtils.DATA_DIR + finame, null, genome, tryIndex);
}
}
@Test
public void testFilesHeadlessTryIndex() throws Exception {
tstFilesHeadless(filenamesTryIndex, true);
}
@Test
public void testFilesHeadlessNoIndex() throws Exception {
tstFilesHeadless(filenamesNoIndex, false);
}
@Test
public void testWigAndBigWig() throws Exception {
String wigPath = TestUtils.DATA_DIR + "wig/test_fixedStep.wig";
String bigWigPath = TestUtils.DATA_DIR + "wig/test_fixedStep.bigwig";
List<Track> wigtracks = tstLoadFi(wigPath, 1, false);
List<Track> bigWigtracks = tstLoadFi(bigWigPath, 1, false);
String chr = "chr19";
int start = 5930725;
int end = 5930764;
int zoom = 21;
DataSourceTrack wigTrack = (DataSourceTrack) wigtracks.get(0);
DataSourceTrack bigWigTrack = (DataSourceTrack) bigWigtracks.get(0);
int trials = 10;
for (int ii = 0; ii < trials; ii++) {
int strt = start + ii;
List<LocusScore> wigScores = wigTrack.getSummaryScores(chr, strt, end, zoom).getFeatures();
List<LocusScore> bigWigScores = bigWigTrack.getSummaryScores(chr, strt, end, zoom).getFeatures();
assertEquals(wigScores.size(), bigWigScores.size());
int ind = 0;
for (LocusScore ws : wigScores) {
LocusScore bws = bigWigScores.get(ind);
assertEquals(ws.getScore(), bws.getScore());
ind++;
}
}
}
@Test
public void testBedAndBigBed() throws Exception {
String bedPath = TestUtils.DATA_DIR + "bed/Unigene.sample.nolong.bed";
String bigBedPath = TestUtils.DATA_DIR + "bed/Unigene.sample.nolong.bigbed";
File bigBedFile = new File(bigBedPath);
//Need to index so query of bed file is accurate
TestUtils.createIndex(bedPath);
List<Track> bedtracks = tstLoadFi(bedPath, 1, false);
List<Track> bigBedtracks = tstLoadFi(bigBedPath, 1, false);
String chr = "chr2";
int start = 178711404 - 1;
int end = 179189619 + 1;
FeatureTrack bedTrack = (FeatureTrack) bedtracks.get(0);
FeatureTrack bigBedTrack = (FeatureTrack) bigBedtracks.get(0);
//Multiple trials because we're concerned about file open/close issues
int trials = 10;
for (int ii = 0; ii < trials; ii++) {
int strt = start + ii;
List<Feature> bedFeatures = bedTrack.getFeatures(chr, strt, end);
List<Feature> bigBedFeatures = bigBedTrack.getFeatures(chr, strt, end);
TestUtils.assertFeatureListsEqual(bedFeatures.iterator(), bigBedFeatures.iterator());
//NOT FOOLPROOF
assertTrue(bigBedFile.canWrite());
}
}
/**
* Test loading segmented data file from a sql database, using a profile
*
* @throws Exception
*/
@Test
public void testLoadSegProfile() throws Exception {
String path = TestUtils.DATA_DIR + "sql/seg_canFam2_profile.dbxml";
int expectedTracks = 6;
List<Track> tracks = trackLoader.load(new ResourceLocator(path), genome);
assertEquals(expectedTracks, tracks.size());
Set<String> expSampleIds = new HashSet<String>(Arrays.asList("0123-A", "0123-B-1", "0123-C-1", "0123-C-2", "0123-C-3"));
Set<String> actSampleIds = new HashSet<String>(5);
for (Track track : tracks) {
if (track instanceof DataSourceTrack) {
actSampleIds.add(track.getName());
}
}
assertEquals(expSampleIds, actSampleIds);
}
/**
* Test loading sample information file from a sql database, using a profile
*
* @throws Exception
*/
@Test
public void testLoadSampleInfoProfile() throws Exception {
AttributeManager.getInstance().clearAllAttributes();
String path = TestUtils.DATA_DIR + "sql/sampleinfo_brca_sif_profile.dbxml";
int expectedTracks = 0;
List<Track> tracks = trackLoader.load(new ResourceLocator(path), genome);
assertEquals(expectedTracks, tracks.size());
String[] attrNames = "TCGA_EXPERIMENT TCGA_BATCH TUMOR_NORMAL BIRDSEED_GENDER LEVEL2_NOISE LEVEL3_SEGMENT_COUNT PURITY PLOIDY DELTA CANCER_DNA_FRACTION SUBCLONAL_GENOME_FRACTION".split("\\s+");
Set<String> expAttrNames = new HashSet<String>(Arrays.asList(attrNames));
List<String> actAttrNames = AttributeManager.getInstance().getAttributeNames();
actAttrNames.remove("NAME");
actAttrNames.remove("DATA TYPE");
actAttrNames.remove("DATA FILE");
assertEquals(actAttrNames.size(), expAttrNames.size());
for (String attrName : actAttrNames) {
assertTrue(expAttrNames.contains(attrName));
}
}
//@Test
public void testLoadScratch() throws Exception {
String path = "http://data.broadinstitute.org/igvdata/annotations/hg19/EnsemblGenes.ensGene";
tstLoadFi(path, 1, genome, false);
}
}