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 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 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); }
/** * 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 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 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)); } }