Examples with GenomicCoords samTextViewer.GenomicCoords used on opensource projects

Example 51 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackSetTest method canConstructTrackSetFromURL.

@Test
public void canConstructTrackSetFromURL() throws InvalidGenomicCoordsException, IOException, ClassNotFoundException, BamIndexNotFoundException, InvalidRecordException, SQLException {
    GenomicCoords gc = new GenomicCoords("chr7:5565052-5571960", 80, null, null);
    TrackSet trackSet = new TrackSet();
    trackSet.addTrackFromSource("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqGm12878R2x75Il400SigRep2V2.bigWig", gc, null);
    trackSet.addTrackFromSource("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqGm12878R2x75Il400JunctionsRep2V3.bigBed", gc, null);
    trackSet.addTrackFromSource("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqGm12878R2x75Il400GeneGencV3cRep2V3.gtf.gz", gc, null);
    trackSet.addTrackFromSource("http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqGm12878R2x75Il400SigRep2V2.bigWig", gc, null);
}

Example 52 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackSetTest method canSetVariantReadsFilter.

@Test
public void canSetVariantReadsFilter() throws InvalidCommandLineException, InvalidGenomicCoordsException, IOException, ClassNotFoundException, InvalidRecordException, SQLException {
    GenomicCoords gc = new GenomicCoords("chr7:1-1000", 80, null, "test_data/chr7.fa");
    TrackSet ts = new TrackSet();
    Track t1 = new TrackReads("test_data/ds051.actb.bam", gc);
    ts.addTrack(t1, "x");
    Track t2 = new TrackReads("test_data/ds051.actb.bam", gc);
    ts.addTrack(t2, "x");
    Track t3 = new TrackReads("test_data/ds051.actb.bam", gc);
    ts.addTrack(t3, "x");
    ts.setFilterVariantReads(Utils.tokenize("filterVariantReads -r 1:10", " "));
    assertEquals(1, t1.getFeatureFilter().getVariantFrom());
    assertEquals(10, t1.getFeatureFilter().getVariantTo());
    assertEquals(1, t2.getFeatureFilter().getVariantFrom());
    assertEquals(10, t2.getFeatureFilter().getVariantTo());
    ts.setFilterVariantReads(Utils.tokenize("filterVariantReads -r 1", " "));
    assertEquals(1, t1.getFeatureFilter().getVariantFrom());
    assertEquals(1, t1.getFeatureFilter().getVariantTo());
    // With spaces use single quotes
    ts.setFilterVariantReads(Utils.tokenize("filterVariantReads -r '100 +/- 5'", " "));
    assertEquals(95, t1.getFeatureFilter().getVariantFrom());
    assertEquals(105, t1.getFeatureFilter().getVariantTo());
    ts.setFilterVariantReads(Utils.tokenize("filterVariantReads -r 100+-5", " "));
    assertEquals(95, t1.getFeatureFilter().getVariantFrom());
    assertEquals(105, t1.getFeatureFilter().getVariantTo());
    ts.setFilterVariantReads(Utils.tokenize("filterVariantReads -r 100+5", " "));
    assertEquals(100, t1.getFeatureFilter().getVariantFrom());
    assertEquals(105, t1.getFeatureFilter().getVariantTo());
    ts.setFilterVariantReads(Utils.tokenize("filterVariantReads -r 100-5", " "));
    assertEquals(95, t1.getFeatureFilter().getVariantFrom());
    assertEquals(100, t1.getFeatureFilter().getVariantTo());
    ts.setFilterVariantReads(Utils.tokenize("filterVariantReads -r 100-200", " "));
    assertEquals(1, t1.getFeatureFilter().getVariantFrom());
    assertEquals(100, t1.getFeatureFilter().getVariantTo());
    // Remove filter for this regex track
    ts.setFilterVariantReads(Utils.tokenize("filterVariantReads #1", " "));
    assertEquals(Filter.DEFAULT_VARIANT_CHROM.getValue(), t1.getFeatureFilter().getVariantChrom());
    assertEquals("chr7", t2.getFeatureFilter().getVariantChrom());
}

Example 53 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackSetTest method canSetTrackHeight.

@Test
public void canSetTrackHeight() throws InvalidCommandLineException, IOException, InvalidGenomicCoordsException, ClassNotFoundException, InvalidRecordException, SQLException {
    String intervalFileName = "test_data/bgz_noindex.vcf.bgz";
    GenomicCoords gc = new GenomicCoords("1:1-200000000", 80, null, null);
    TrackSet ts = new TrackSet();
    Track t1 = new TrackIntervalFeature(intervalFileName, gc);
    ts.addTrack(t1, "x");
    Track t2 = new TrackIntervalFeature(intervalFileName, gc);
    ts.addTrack(t2, "x");
    Track t3 = new TrackIntervalFeature(intervalFileName, gc);
    ts.addTrack(t3, "x");
    String cmdInput = "trackHeight 2 #1 #3";
    ts.setTrackHeightForRegex(Utils.tokenize(cmdInput, " "));
    assertEquals(2, ts.getTrack(t1).getyMaxLines());
    assertEquals(10, ts.getTrack(t2).getyMaxLines());
    assertEquals(2, ts.getTrack(t3).getyMaxLines());
    // Defsult regex: All tracks captured
    cmdInput = "trackHeight 99";
    ts.setTrackHeightForRegex(Utils.tokenize(cmdInput, " "));
    assertEquals(99, ts.getTrack(t1).getyMaxLines());
    assertEquals(99, ts.getTrack(t2).getyMaxLines());
    assertEquals(99, ts.getTrack(t3).getyMaxLines());
    // Invert selection
    cmdInput = "trackHeight -v 10 #1";
    ts.setTrackHeightForRegex(Utils.tokenize(cmdInput, " "));
    assertEquals(99, ts.getTrack(t1).getyMaxLines());
    assertEquals(10, ts.getTrack(t2).getyMaxLines());
    assertEquals(10, ts.getTrack(t3).getyMaxLines());
}

Example 54 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackSetTest method canPrintFeaturesToFile.

@Test
public void canPrintFeaturesToFile() throws InvalidGenomicCoordsException, IOException, ClassNotFoundException, BamIndexNotFoundException, InvalidRecordException, SQLException, InvalidCommandLineException, InvalidColourException, ArgumentParserException {
    // --------------------------------------------------------------------
    // Prepare coords and trackSet
    GenomicCoords gc = new GenomicCoords("chr7:5565052-5571960", 80, null, null);
    TrackSet trackSet = new TrackSet();
    trackSet.addTrackFromSource("test_data/hg19_genes.gtf.gz", gc, null);
    trackSet.addTrackFromSource("test_data/hg19_genes.gtf.gz", gc, null);
    // --------------------------------------------------------------------
    // No redirection file: Nothing done
    List<String> cmdInput = Utils.tokenize("print #1 >", " ");
    boolean failed = false;
    try {
        trackSet.setPrintModeAndPrintFeaturesForRegex(cmdInput);
    } catch (InvalidCommandLineException e) {
        failed = true;
    }
    assertTrue(failed);
    // Invalid output: Non existent dir:
    cmdInput = Utils.tokenize("print #1 > test_data/foobar/delete.me", " ");
    failed = false;
    try {
        trackSet.setPrintModeAndPrintFeaturesForRegex(cmdInput);
    } catch (IOException e) {
        failed = true;
    }
    assertTrue(failed);
    // Now give an output file.
    File ff = new File("deleteme.gtf");
    ff.deleteOnExit();
    cmdInput = Utils.tokenize("print #1 > deleteme.gtf", " ");
    trackSet.setPrintModeAndPrintFeaturesForRegex(cmdInput);
    assertTrue(ff.exists());
    assertTrue(ff.length() > 200);
    assertEquals(13, FileUtils.readLines(ff).size());
    // Append to file
    cmdInput = Utils.tokenize("print #1 >> deleteme.gtf", " ");
    trackSet.setPrintModeAndPrintFeaturesForRegex(cmdInput);
    assertEquals(26, FileUtils.readLines(ff).size());
}

Example 55 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackSetTest method canReplaceOverloadedFunctionInAwk.

@Test
public void canReplaceOverloadedFunctionInAwk() throws Exception {
    TrackSet ts = new TrackSet();
    GenomicCoords gc = new GenomicCoords("chr1:1-100", 80, null, null);
    Track t1 = new TrackIntervalFeature("test_data/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf", gc);
    ts.addTrack(t1, "vcf");
    Track t2 = new TrackPileup("test_data/ds051.actb.bam", gc);
    ts.addTrack(t2, "bam");
    Track t3 = new TrackIntervalFeature("test_data/refSeq.bed", gc);
    ts.addTrack(t3, "bed");
    ts.setAwkForTrack(Utils.tokenize("awk 'get(AC) > 2 ||get(GT, 2, 1) && get(INFO/FOO) && get(FMT/BAR)' vcf", " "));
    assertTrue(ts.getTrack(t1).getAwk().endsWith("'"));
    assertTrue(ts.getTrack(t1).getAwk().contains("getInfoTag(\"AC\")"));
    assertTrue(ts.getTrack(t1).getAwk().contains("getFmtTag(\"GT\", 2, 1)"));
    assertTrue(ts.getTrack(t1).getAwk().contains("getInfoTag(\"INFO/FOO\")"));
    assertTrue(ts.getTrack(t1).getAwk().contains("getFmtTag(\"FMT/BAR\")"));
    boolean pass = false;
    try {
        // BAR not qualified by INFO/ or FMT/
        ts.setAwkForTrack(Utils.tokenize("awk 'get(BAR)' vcf", " "));
    } catch (InvalidCommandLineException e) {
        pass = true;
    }
    assertTrue(pass);
    ts.setAwkForTrack(Utils.tokenize("awk 'get( NM ) > 2' bam", " "));
    assertTrue(ts.getTrack(t2).getAwk().contains("getSamTag(\"NM\")"));
    pass = false;
    try {
        // Can't use get() on BED
        ts.setAwkForTrack(Utils.tokenize("awk 'get(NM)' bed", " "));
    } catch (InvalidCommandLineException e) {
        pass = true;
    }
    assertTrue(pass);
    // Nothing to replace
    String awk = "awk 'foo_get() get (bar)' vcf";
    ts.setAwkForTrack(Utils.tokenize(awk, " "));
    assertTrue(ts.getTrack(t1).getAwk().contains("foo_get() get (bar)"));
}