Examples with Config coloring.Config used on opensource projects

Example 1 with Config

use of coloring.Config in project ASCIIGenome by dariober.

the class TrackProcessorTest method canProcessTracks.

@Test
public void canProcessTracks() throws InvalidGenomicCoordsException, IOException, ClassNotFoundException, BamIndexNotFoundException, InvalidRecordException, SQLException, InvalidConfigException, InvalidCommandLineException, DocumentException, InvalidColourException {
    new Config(null);
    GenomicCoords gc = new GenomicCoords("chr7:1-100", 80, null, null);
    List<String> genome = new ArrayList<String>();
    genome.add("test_data/ear045.oxBS.actb.bam");
    gc.setGenome(genome, true);
    GenomicCoordsHistory gch = new GenomicCoordsHistory();
    gch.add(gc);
    TrackSet trackSet = new TrackSet();
    trackSet.addTrackFromSource("test_data/hg19_genes.gtf.gz", gc, null);
    trackSet.addTrackFromSource("test_data/ear045.oxBS.actb.bam", gc, null);
    trackSet.addTrackFromSource("test_data/ear045.oxBS.actb.tdf", gc, null);
    TrackProcessor tp = new TrackProcessor(trackSet, gch);
// tp.iterateTracks();
}

Example 2 with Config

use of coloring.Config in project ASCIIGenome by dariober.

the class TrackSetTest method canAddBookmarkTrack.

@Test
public void canAddBookmarkTrack() throws InvalidGenomicCoordsException, IOException, ClassNotFoundException, InvalidRecordException, SQLException, InvalidColourException, InvalidCommandLineException, InvalidConfigException {
    new Config(null);
    List<String> cmdInput = new ArrayList<String>();
    cmdInput.add("bookmark");
    cmdInput.add("bookmark_1");
    TrackSet ts = new TrackSet();
    GenomicCoords gc = new GenomicCoords("chr1:1-100", 80, null, null);
    ts.bookmark(gc, cmdInput);
    assertTrue(ts.getTrackList().size() == 1);
    ts.getTrackList().get(0).setNoFormat(true);
    GenomicCoords gc2 = new GenomicCoords("chr1:1-1000", 80, null, null);
    ts.bookmark(gc2, cmdInput);
    TrackBookmark bm = (TrackBookmark) ts.getTrackList().get(0);
    assertEquals(2, bm.getIntervalFeatureList().size());
    bm.setPrintMode(PrintRawLine.CLIP);
    // NB: it prints twice the same gc becouse the position is nt changed
    System.out.println(bm.printLines());
}

Example 3 with Config

use of coloring.Config in project ASCIIGenome by dariober.

the class TrackTest method canPrintBamWithClippedSeq.

@Test
public void canPrintBamWithClippedSeq() throws InvalidGenomicCoordsException, IOException, InvalidColourException, InvalidCommandLineException, ClassNotFoundException, InvalidRecordException, SQLException, InvalidConfigException {
    new Config(null);
    GenomicCoords gc = new GenomicCoords("chr7:5566733-5566903", 160, null, null);
    TrackReads tif = new TrackReads("test_data/ds051.actb.bam", gc);
    tif.setNoFormat(true);
    tif.setPrintMode(PrintRawLine.CLIP);
    assertTrue(tif.printLines().contains(" CTCAT[+"));
    assertTrue(tif.printLines().contains(" CCCFF[+"));
}

Example 4 with Config

use of coloring.Config in project ASCIIGenome by dariober.

the class TrackTest method printIsNotResetAfterExec.

@Test
public void printIsNotResetAfterExec() throws InvalidGenomicCoordsException, IOException, InvalidColourException, InvalidCommandLineException, ClassNotFoundException, InvalidRecordException, SQLException, InvalidConfigException {
    new Config(null);
    // BAM
    GenomicCoords gc = new GenomicCoords("chr7:5566733-5566903", 80, null, null);
    TrackReads tif = new TrackReads("test_data/ds051.short.bam", gc);
    tif.setNoFormat(true);
    tif.setPrintMode(PrintRawLine.FULL);
    tif.setSystemCommandForPrint("grep NCNNTCCC");
    assertEquals(2, tif.printLines().split("\n").length);
    // Call printLines again on new coordinates:
    // The sys command is still on
    gc = new GenomicCoords("chr7:5566733-5566904", 80, null, null);
    tif.setGc(gc);
    System.err.println(tif.printLines());
    assertEquals(2, tif.printLines().split("\n").length);
    // Now turn it off:
    tif.setSystemCommandForPrint("");
    assertEquals(22, tif.printLines().split("\n").length);
}

Example 5 with Config

use of coloring.Config in project ASCIIGenome by dariober.

the class TrackTest method canConcatTitleAndTrack.

// @Test
// public void canSetVariantReadsFilterBasedOnScreenPercent() throws InvalidCommandLineException, InvalidGenomicCoordsException, IOException, ClassNotFoundException, InvalidRecordException, SQLException{
// 
// GenomicCoords gc= new GenomicCoords("chr7:3-101", 1000, null, "test_data/chr7.fa");
// 
// Track t1= new TrackReads("test_data/ds051.actb.bam", gc);
// 
// t1.setVariantReadInInterval("0.0", true);
// assertEquals(3, t1.getFeatureFilter().getVariantFrom());
// assertEquals(3, t1.getFeatureFilter().getVariantTo());
// 
// t1.setVariantReadInInterval("1.0", true);
// assertEquals(101, t1.getFeatureFilter().getVariantFrom());
// assertEquals(101, t1.getFeatureFilter().getVariantTo());
// 
// //     (101-3+1) * 0.5 = 49.5
// // We round to 49.5 to 50. So:
// //     3 + 50 - 1 = 52
// t1.setVariantReadInInterval("0.5", true);
// assertEquals(52, t1.getFeatureFilter().getVariantFrom());
// 
// gc= new GenomicCoords("chr7:3-102", 1000, null, "test_data/chr7.fa");
// t1= new TrackReads("test_data/ds051.actb.bam", gc);
// t1.setVariantReadInInterval("0.5", true);
// assertEquals(52, t1.getFeatureFilter().getVariantFrom());
// 
// // Must fail
// boolean pass= false;
// try{
// t1.setVariantReadInInterval("foo", true);
// } catch(NumberFormatException e){
// pass= true;
// }
// assertTrue(pass);
// }
@Test
public void canConcatTitleAndTrack() throws ClassNotFoundException, IOException, InvalidGenomicCoordsException, InvalidRecordException, SQLException, InvalidConfigException, InvalidColourException {
    new Config(null);
    GenomicCoords gc = new GenomicCoords("1:735171-2045891", 80, null, null);
    TrackIntervalFeature tif = new TrackIntervalFeature("test_data/CHD.exon.2010_03.sites.vcf", gc);
    tif.setNoFormat(true);
    tif.setTrackTag("title.bed");
    String[] lines = tif.concatTitleAndTrack().split("\n");
    assertEquals(3, lines.length);
    assertTrue(lines[0].startsWith("title.bed"));
    assertTrue(lines[0].trim().endsWith("A"));
    System.err.println(tif.concatTitleAndTrack());
    // Do not put on different lines
    tif.setTrackTag("LoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooongTitle.bed");
    lines = tif.concatTitleAndTrack().split("\n");
    assertEquals(4, lines.length);
    System.err.println(tif.concatTitleAndTrack());
}