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 loading a session with a bedtools analysis track
*
* @throws Exception
*/
@Test
public void testLoadBedtools_Subtract() throws Exception {
String toolPath = "/usr/local/bin/bedtools";
boolean haveTool = PluginSpecReader.isToolPathValid(toolPath);
Assume.assumeTrue(haveTool);
String sessionPath = TestUtils.DATA_DIR + "sessions/GSM_bedtools_subtract.xml";
rewriteRestoreSession(sessionPath);
String trackAname = "GSM1004654_100k.bed";
String trackBname = "GSM1004654_10k.bed";
String analId = "BEDTools Remove/Subtract";
FeatureTrack analTrack = null, trackA = null, trackB = null;
for (Track track : IGV.getInstance().getAllTracks()) {
if (track.getId().equals(analId)) {
analTrack = (FeatureTrack) track;
} else if (track.getName().equals(trackAname)) {
trackA = (FeatureTrack) track;
} else if (track.getName().equals(trackBname)) {
trackB = (FeatureTrack) track;
}
}
String chr = "chr2";
int start = 177932002;
int end = 180561093;
List<Feature> aFeatures = trackA.getFeatures(chr, start, end);
List<Feature> bFeatures = trackB.getFeatures(chr, start, end);
List<Feature> analFeatures = analTrack.getFeatures(chr, start, end);
// Fairly coarse check, these actually might not exactly be true
// due to splitting of exons
int checked = 0;
for (Feature afeat : analFeatures) {
if (afeat.getStart() < start || afeat.getStart() > end) continue;
// This particular feature splits funny, it's not a bug, at least not with IGV
if (afeat.getStart() == 178625608) continue;
assertTrue(listContainsFeature(aFeatures, afeat));
assertFalse(listContainsFeature(bFeatures, afeat));
checked++;
}
assert checked > 0;
}
/**
* 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);
}
@Override
public boolean apply(Track input) {
boolean contains = true;
for (String contId : contIds) {
contains &= input.getId().contains(contId);
if (!contains) break;
}
return contains;
}