@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());
}
}
private void loadFromDBProfile(ResourceLocator profileLocator, List<Track> newTracks)
throws IOException {
DBProfile dbProfile = DBProfile.parseProfile(profileLocator.getPath());
for (DBProfile.DBTable table : dbProfile.getTableList()) {
SQLCodecSource source = SQLCodecSource.getFromTable(table);
if (source != null) {
CachingFeatureSource cachingReader = new CachingFeatureSource(source);
FeatureTrack track = new FeatureTrack(profileLocator, cachingReader);
track.setName(source.getTableName());
newTracks.add(track);
} else if (table.getFormat().equals("seg")) {
Genome genome = GenomeManager.getInstance().getCurrentGenome();
SegmentedAsciiDataSet ds =
(new SegmentedReader(table.getDbLocator(), genome)).loadFromDB(table);
loadSegTrack(table.getDbLocator(), newTracks, genome, ds);
} else if (table.getFormat().equals("sample.info")) {
// TODO sampleIdColumnLabel was previously hardcoded as "SAMPLE_ID_ARRAY"
// TODO Basically I'm shoehorning this information into a field usually used for something
// else. Only slightly better
String sampleIdColumnLabel = table.getBinColName();
if (sampleIdColumnLabel == null) {
throw new IllegalArgumentException(
"Profile must have binColName specifying the sample id column label");
}
(new SampleInfoSQLReader(table, sampleIdColumnLabel)).load();
}
}
}
private void loadSMAPFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
List<Feature> features = SMAPParser.parseFeatures(locator, genome);
FeatureCollectionSource src = new FeatureCollectionSource(features, genome);
FeatureTrack track = new FeatureTrack(locator, locator.getName(), src);
track.setRendererClass(SMAPRenderer.class);
track.setDisplayMode(Track.DisplayMode.EXPANDED);
newTracks.add(track);
}
private void loadListFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
try {
FeatureSource source = new FeatureDirSource(locator, genome);
FeatureTrack track = new FeatureTrack(locator, source);
track.setName(locator.getTrackName());
track.setVisibilityWindow(0);
newTracks.add(track);
} catch (IOException ex) {
throw new RuntimeException(ex);
}
}
/**
* Load a mutation file (".mut" or ".maf").
*
* @param locator
* @param newTracks
*/
private void loadMutFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException, TribbleIndexNotFoundException {
MutationTrackLoader loader = new MutationTrackLoader();
List<FeatureTrack> mutationTracks = loader.loadMutationTracks(locator, genome);
for (FeatureTrack track : mutationTracks) {
track.setTrackType(TrackType.MUTATION);
track.setRendererClass(MutationRenderer.class);
newTracks.add(track);
}
}
private void loadSyntentyMapping(ResourceLocator locator, List<Track> newTracks) {
List<BlastMapping> mappings = (new BlastParser()).parse(locator.getPath());
List<htsjdk.tribble.Feature> features = new ArrayList<htsjdk.tribble.Feature>(mappings.size());
features.addAll(mappings);
Genome genome = GenomeManager.getInstance().getCurrentGenome();
FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
track.setName(locator.getTrackName());
// track.setRendererClass(AlignmentBlockRenderer.class);
newTracks.add(track);
}
@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());
}
private void loadDASResource(ResourceLocator locator, List<Track> currentTracks)
throws DataLoadException {
// TODO Connect and get all the attributes of the DAS server, and run the appropriate load
// statements
// TODO Currently we are only going to be doing features
// TODO -- move the source creation to a factory
DASFeatureSource featureSource = null;
try {
featureSource = new DASFeatureSource(locator);
} catch (MalformedURLException e) {
log.error("Malformed URL", e);
throw new DataLoadException("Error: Malformed URL ");
}
FeatureTrack track = new FeatureTrack(locator, featureSource);
// Try to create a sensible name from the path
String name = locator.getName();
if (name == null || name.length() == 0) {
if (locator.getPath().contains("genome.ucsc.edu")) {
name = featureSource.getType();
} else {
name = featureSource.getPath().replace("/das/", "").replace("/features", "");
}
}
track.setName(name);
// A hack until we can notate this some other way
if (locator.getPath().contains("cosmic")) {
track.setRendererClass(CosmicFeatureRenderer.class);
track.setMinimumHeight(2);
track.setHeight(20);
track.setDisplayMode(Track.DisplayMode.EXPANDED);
} else {
track.setRendererClass(IGVFeatureRenderer.class);
track.setMinimumHeight(35);
track.setHeight(45);
}
currentTracks.add(track);
}
/**
* Load the input file as a feature, mutation, or maf (multiple alignment) file.
*
* @param locator
* @param newTracks
*/
private void loadTribbleFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException, TribbleIndexNotFoundException {
String typeString = locator.getTypeString();
// Mutation (mut, maf, vcf) files are handled special. Check here, rather than depend on order
// in giant case statement.
if (MutationTrackLoader.isMutationAnnotationFile(locator)) {
loadMutFile(locator, newTracks, genome); // Must be tried before generic "loadIndexed" below
} else if (VariantTrack.isVCF(typeString)) {
loadVCF(locator, newTracks, genome);
} else {
TribbleFeatureSource tribbleFeatureSource =
TribbleFeatureSource.getFeatureSource(locator, genome);
FeatureSource src =
GFFFeatureSource.isGFF(locator.getPath())
? new GFFFeatureSource(tribbleFeatureSource)
: tribbleFeatureSource;
// Create feature source and track
FeatureTrack t = new FeatureTrack(locator, src);
t.setName(locator.getTrackName());
// t.setRendererClass(BasicTribbleRenderer.class);
// Set track properties from header
Object header = tribbleFeatureSource.getHeader();
if (header != null && header instanceof FeatureFileHeader) {
FeatureFileHeader ffh = (FeatureFileHeader) header;
if (ffh.getTrackType() != null) {
t.setTrackType(ffh.getTrackType());
}
if (ffh.getTrackProperties() != null) {
t.setProperties(ffh.getTrackProperties());
}
if (ffh.getTrackType() == TrackType.REPMASK) {
t.setHeight(15);
}
}
if (locator.getPath().contains(".narrowPeak")
|| locator.getPath().contains(".broadPeak")
|| locator.getPath().contains(".gappedPeak")) {
t.setUseScore(true);
}
newTracks.add(t);
}
}