/**
* Test loading a session with spaces in the path and special characters in the file names
*
* @throws Exception
*/
@Test
public void testLoadSessionSpecialChars() throws Exception {
int expTrackCount = 5;
String path = TestUtils.DATA_DIR + "sessions/special_chars.xml";
rewriteRestoreSession(path);
assertEquals(expTrackCount, IGV.getInstance().getVisibleTrackCount());
}
@Test
public void testLoadDataSourceTrack() throws Exception {
String path = TestUtils.DATA_DIR + "sessions/tdf_session.xml";
rewriteRestoreSession(path);
DataSourceTrack track = (DataSourceTrack) IGV.getInstance().getAllTracks().get(0);
assertEquals(true, TestUtils.runMethod(track, "getNormalize"));
assertEquals("NA12878.SLX.egfr.sam.tdf", track.getName());
}
@Test
public void testLoadSessionWithoutLoadedGenome() throws Exception {
GenomeManager.getInstance().setCurrentGenome(null);
assertNull(GenomeManager.getInstance().getGenomeId());
rewriteRestoreSession(EcoliFastaSessionPath);
assertNotNull(GenomeManager.getInstance().getGenomeId());
}
/**
* Very basic test, just makes sure it loads without throwing an exception
*
* @throws Exception
*/
@Test
public void testLoadBedtools_Intersect() throws Exception {
String sessionPath = TestUtils.DATA_DIR + "sessions/GSM_bedtools_intersect.xml";
String toolPath = "/usr/local/bin/bedtools";
boolean haveTool = PluginSpecReader.isToolPathValid(toolPath);
Assume.assumeTrue(haveTool);
rewriteRestoreSession(sessionPath);
}
private void tstLoadVCF(String sessionPath) throws Exception {
rewriteRestoreSession(sessionPath);
VariantTrack vTrack = (VariantTrack) IGV.getInstance().getAllTracks().get(0);
assertEquals(3, vTrack.getAllSamples().size());
assertEquals(8, vTrack.getSquishedHeight());
assertEquals(VariantTrack.ColorMode.ALLELE, vTrack.getColorMode());
}
@Test
public void testLoadSequenceTrackOnlyDiffGenome() throws Exception {
rewriteRestoreSession(EcoliFastaSessionPath);
assertFalse("Gene track exists but it shouldn't", IGV.getInstance().hasGeneTrack());
assertTrue("Sequence track doesn't exist but it should", IGV.getInstance().hasSequenceTrack());
assertNotNull(
"Sequence track doesn't exist but it should", IGV.getInstance().getSequenceTrack());
}
@Test
public void testLoadOverlaySession() throws Exception {
String sessionpath = TestUtils.DATA_DIR + "sessions/hind_gistic_overlay.xml";
rewriteRestoreSession(sessionpath);
// Load the session, check things went well
List<DataTrack> dataTracks = IGV.getInstance().getDataTracks();
assertEquals(3, dataTracks.size());
assertTrue(dataTracks.get(0) instanceof MergedTracks);
}
/**
* Loads path, returns first alignment track
*
* @param sessionPath
* @return
*/
private AlignmentTrack getAlignmentTrack(String sessionPath) throws Exception {
rewriteRestoreSession(sessionPath);
AlignmentTrack alTrack = null;
for (Track tk : IGV.getInstance().getAllTracks()) {
if (tk instanceof AlignmentTrack) {
alTrack = (AlignmentTrack) tk;
}
}
return alTrack;
}
@Test
public void testLoadCoverageTrackSession() throws Exception {
String path = TestUtils.DATA_DIR + "sessions/coverage_snpThreshold_NA06984.xml";
rewriteRestoreSession(path);
// We should have 1 coverage track
CoverageTrack track = (CoverageTrack) IGV.getInstance().getAllTracks().get(0);
assertTrue(track.isShowReference());
assertEquals(0.5, track.getSnpThreshold(), 1e-5);
assertTrue(track.getAutoScale());
}
@Test
public void testGWAS() throws Exception {
String sessionPath = TestUtils.DATA_DIR + "sessions/smallp_session.xml";
rewriteRestoreSession(sessionPath);
boolean haveGWAS = false;
for (Track track : IGV.getInstance().getAllTracks()) {
if (track instanceof GWASTrack) {
haveGWAS = true;
break;
}
}
assertTrue("No GWAS track loaded", haveGWAS);
assertEquals(3, IGV.getInstance().getVisibleTrackCount());
}
/**
* 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
public void testLoadSequenceTrackOnlySameGenome() throws Exception {
String genomePath = TestUtils.DATA_DIR + "fasta/ecoli_out.padded.fasta";
GenomeManager.getInstance().loadGenome(genomePath, null);
genome = GenomeManager.getInstance().getCurrentGenome();
IGV.getInstance().removeTracks(IGV.getInstance().getAllTracks());
assertFalse("Sequence Track exists but it shouldn't", IGV.getInstance().hasSequenceTrack());
String sessionPath = TestUtils.DATA_DIR + "sessions/ecoli_out_seqonly.xml";
rewriteRestoreSession(sessionPath);
assertFalse("Gene track exists but it shouldn't", IGV.getInstance().hasGeneTrack());
assertTrue("Sequence track doesn't exist but it should", IGV.getInstance().hasSequenceTrack());
assertNotNull(
"Sequence track doesn't exist but it should", IGV.getInstance().getSequenceTrack());
}
/** Test creating an analysis track, saving the session, and loading it */
@Ignore("Not ready yet")
@Test
public void testSaveLoadPluginSession() throws Exception {
String toolPath = "/usr/local/bin/bedtools";
boolean haveTool = PluginSpecReader.isToolPathValid(toolPath);
Assume.assumeTrue(haveTool);
String sessionPath = TestUtils.DATA_DIR + "sessions/GSM_beds.xml";
rewriteRestoreSession(sessionPath);
String trackAname = "GSM1004654_100k.bed";
String trackBname = "GSM1004654_10k.bed";
// Generate bedtools subtraction track
PluginSpecReader reader = PluginSpecReader.create(toolPath);
PluginSpecReader.Tool tool = reader.getTools().get(0);
PluginSpecReader.Command command =
AbstractPluginTest.findCommandElementByName(tool, "Subtract");
}
@Test
public void testLoadCombinedDataSourceSession() throws Exception {
String sessionpath = TestUtils.DATA_DIR + "sessions/subtypes_wdiff.xml";
rewriteRestoreSession(sessionpath);
String combPart0 = "TRIBE_p_TCGAaffx_B1_2_GBM_Nsp_GenomeWideSNP_6_E11_155884";
String combPart1 = "TRIGS_p_TCGAaffxB5_sty_GenomeWideSNP_6_D05_223156";
DataTrack track0 =
Iterables.find(IGV.getInstance().getDataTracks(), new ContIdPredicate(combPart0));
DataTrack track1 =
Iterables.find(IGV.getInstance().getDataTracks(), new ContIdPredicate(combPart1));
DataSourceTrack combTrack =
(DataSourceTrack)
Iterables.find(
IGV.getInstance().getDataTracks(),
new ContIdPredicate(new String[] {combPart0, combPart1}));
assertTrue(combTrack.getRenderer() instanceof BarChartRenderer);
assertEquals("Difference", combTrack.getName());
String chr = "chr1";
int start = 0;
int end = 1000;
LocusScore sumScore0 = track0.getSummaryScores(chr, start, end, 0).get(0);
LocusScore sumScore1 = track1.getSummaryScores(chr, start, end, 0).get(0);
LocusScore sumScoreComb = combTrack.getSummaryScores(chr, start, end, 0).get(0);
assertEquals(sumScore0.getStart(), sumScore1.getStart());
assertEquals(sumScore0.getStart(), sumScoreComb.getStart());
assertEquals(sumScore1.getEnd(), sumScoreComb.getEnd());
assertEquals(sumScore0.getScore() - sumScore1.getScore(), sumScoreComb.getScore(), 1e-10);
}