Examples with GenomicCoords samTextViewer.GenomicCoords used on opensource projects

Example 61 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackTest method canHighlightFormatInVcfLines.

@Test
public void canHighlightFormatInVcfLines() throws ClassNotFoundException, IOException, InvalidGenomicCoordsException, InvalidRecordException, SQLException, InvalidColourException, InvalidCommandLineException {
    GenomicCoords gc = new GenomicCoords("1:1-20000000", 80, null, null);
    TrackIntervalFeature tif = new TrackIntervalFeature("test_data/info_formats.vcf.gz", gc);
    tif.setPrintMode(PrintRawLine.FULL);
    // Highlight FORMAT tag and associated values
    tif.setHighlightPattern(Pattern.compile("GT"));
    String out = tif.printLines();
    assertTrue(out.contains("\033[7mGT\033[27m"));
    assertTrue(out.contains("\033[7m1/0\033[27m"));
    assertTrue(out.contains("\033[7m1|2\033[27m"));
    // // Tag GTFF is not highlighted because the match is partial
    // assertTrue(out.contains("\033[7m1|2\033[27m:100:0,0"));
    // 
    // // This should match both:
    // tif.setHighlightPattern(Pattern.compile("GT|GTFF"));
    // // TODO: assertTrue(out.contains("\033[7m1|2\033[27m:100:0,0"));
    // Turn the string-table to back to a list and ensure that all fields are there
    List<String> xlist = Splitter.on("\t").omitEmptyStrings().splitToList(out.replaceAll(" +|\n", "\t"));
    assertEquals(33, xlist.size());
}

Example 62 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackTest method canPrintVcfWithClippedSeq.

@Test
public void canPrintVcfWithClippedSeq() throws InvalidGenomicCoordsException, IOException, InvalidColourException, InvalidCommandLineException, ClassNotFoundException, InvalidRecordException, SQLException, InvalidConfigException {
    new Config(null);
    GenomicCoords gc = new GenomicCoords("1:1019492-1019672", 160, null, null);
    TrackIntervalFeature tif = new TrackIntervalFeature("test_data/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf", gc);
    tif.setNoFormat(true);
    tif.setPrintMode(PrintRawLine.CLIP);
    assertTrue(tif.printLines().contains(" GTCAC["));
}

Example 63 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackTest method canHighlightPrintableLines.

@Test
public void canHighlightPrintableLines() throws ClassNotFoundException, IOException, InvalidGenomicCoordsException, InvalidRecordException, SQLException, InvalidColourException, InvalidCommandLineException {
    GenomicCoords gc = new GenomicCoords("1:1-400000", 80, null, null);
    TrackIntervalFeature tif = new TrackIntervalFeature("test_data/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf", gc);
    tif.setPrintMode(PrintRawLine.FULL);
    tif.setHighlightPattern(Pattern.compile("200000"));
    String out = tif.printLines();
    assertTrue(out.contains("\033[7m200000\033[27m"));
    // Multiple patterns
    tif.setHighlightPattern(Pattern.compile("ALU"));
    out = tif.printLines();
    assertTrue(out.contains("\033[7mALU\033[27m"));
    // Pattern start of line
    tif.setHighlightPattern(Pattern.compile("1"));
    tif.setPrintMode(PrintRawLine.FULL);
    out = tif.printLines();
    assertTrue(out.startsWith("\033[38;5;0;48;5;231m\033[7m1"));
    // Pattern EOL
    tif.setHighlightPattern(Pattern.compile("1\\|1"));
    out = tif.printLines();
    assertTrue(out.trim().endsWith("1|1\033[27m"));
    // No pattern
    tif.setHighlightPattern(Pattern.compile("FOOBAR"));
    out = tif.printLines();
    assertTrue(!out.contains("\033[7m"));
    // Reset
    tif.setHighlightPattern(Pattern.compile(""));
    out = tif.printLines();
    assertTrue(!out.contains("\033[7m"));
    // Highlight FORMAT tag and associated values
    tif.setHighlightPattern(Pattern.compile("GT"));
    out = tif.printLines();
    assertTrue(out.contains("\033[7mGT\033[27m"));
    assertTrue(out.contains("\033[7m.|.\033[27m"));
    assertTrue(out.contains("\033[7m0|0\033[27m"));
    // Turn the string-table to back to a list and ensure that all fields are there
    List<String> xlist = Splitter.on("\t").omitEmptyStrings().splitToList(out.replaceAll(" +|\n", "\t"));
    assertEquals(24, xlist.size());
}

Example 64 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackTest method canParsePrintableLinesWithInvalidCommand.

@Test
public void canParsePrintableLinesWithInvalidCommand() throws ClassNotFoundException, IOException, InvalidGenomicCoordsException, InvalidRecordException, SQLException, InvalidColourException, InvalidCommandLineException {
    // Invalid command: Empty output. But note that no exception is thrown!
    GenomicCoords gc = new GenomicCoords("chr1:1-100000", 80, null, null);
    TrackIntervalFeature tif = new TrackIntervalFeature("test_data/hg19_genes_head.gtf", gc);
    tif.setSystemCommandForPrint("foo");
    assertEquals("", tif.printLines());
}

Example 65 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackWigglesTest method invalidBedgraphRecordAsNaN.

@Test
public void invalidBedgraphRecordAsNaN() throws IOException, NoSuchAlgorithmException, InvalidGenomicCoordsException, InvalidRecordException, ClassNotFoundException, SQLException {
    GenomicCoords gc = new GenomicCoords("chr1:1-10", 10, null, null);
    TrackWiggles tw = new TrackWiggles("test_data/invalid-1.bedgraph", gc, 4);
    assertEquals(tw.getScreenScores().get(0), Float.NaN, 0.0001);
    assertEquals(tw.getScreenScores().get(1), 10, 0.0001);
}