Examples with GenomicCoords samTextViewer.GenomicCoords used on opensource projects

Example 66 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackWigglesTest method canPrintChromosomeNames.

@Test
public void canPrintChromosomeNames() throws InvalidGenomicCoordsException, IOException, ClassNotFoundException, InvalidRecordException, SQLException {
    GenomicCoords gc = new GenomicCoords("chr7:5540000-5570000", 80, null, null);
    TrackWiggles tw = new TrackWiggles("test_data/hg18_var_sample.wig.v2.1.30.tdf", gc, 4);
    assertTrue(tw.getChromosomeNames().size() > 10);
    tw = new TrackWiggles("test_data/test.bedGraph", gc, 4);
    assertTrue(tw.getChromosomeNames().size() > 0);
    tw = new TrackWiggles("http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsA549Cebpbsc150V0422111RawRep1.bigWig", gc, 4);
    assertTrue(tw.getChromosomeNames().size() > 10);
}

Example 67 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackSet method bookmark.

/**
 * Handle bookmarks by processing cmd line args.
 * @throws InvalidGenomicCoordsException
 * @throws SQLException
 * @throws InvalidRecordException
 * @throws IOException
 * @throws ClassNotFoundException
 * @throws InvalidCommandLineException
 */
public String bookmark(GenomicCoords gc, List<String> cmdInput) throws ClassNotFoundException, IOException, InvalidRecordException, SQLException, InvalidGenomicCoordsException, InvalidCommandLineException {
    String messages = "";
    List<String> args = new ArrayList<String>(cmdInput);
    // Remove command name
    args.remove(0);
    // Get all arguments. What is left is the positional argument
    boolean delete = Utils.argListContainsFlag(args, "-d");
    String name = Utils.getArgForParam(args, "-n", null);
    boolean print = Utils.argListContainsFlag(args, "-print");
    String file = Utils.getArgForParam(args, ">", null);
    GenomicCoords bookmarkRegion = null;
    if (args.size() > 0) {
        List<String> strRegion = Utils.parseStringCoordsToList(args.get(0));
        if (strRegion.get(1) == null) {
            strRegion.set(1, "1");
        }
        if (strRegion.get(2) == null) {
            strRegion.set(2, new Integer(Integer.MAX_VALUE).toString());
        }
        bookmarkRegion = new GenomicCoords(strRegion.get(0) + ":" + strRegion.get(1) + "-" + strRegion.get(2), gc.getUserWindowSize(), gc.getSamSeqDict(), gc.getFastaFile());
    } else {
        bookmarkRegion = new GenomicCoords(gc.toStringRegion(), gc.getUserWindowSize(), gc.getSamSeqDict(), gc.getFastaFile());
    }
    if (print) {
        for (Track tr : this.getTrackList()) {
            if (tr instanceof TrackBookmark) {
                List<String> marks = Utils.tabulateList(((TrackBookmark) tr).asList(), -1);
                messages = Joiner.on("\n").join(marks);
                return messages + "\n";
            }
        }
        return messages;
    }
    if (file != null) {
        for (Track tr : this.getTrackList()) {
            if (tr instanceof TrackBookmark) {
                ((TrackBookmark) tr).save(file, false);
                return messages;
            }
        }
        return messages;
    }
    if (delete) {
        for (Track tr : this.getTrackList()) {
            if (tr instanceof TrackBookmark) {
                ((TrackBookmark) tr).removeBookmark(bookmarkRegion);
                return messages;
            }
        }
        return messages;
    }
    if (name == null) {
        name = ".";
    }
    this.addBookmark(bookmarkRegion, name);
    return messages;
}

Example 68 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackSet method trimTrack.

private GenomicCoords trimTrack(TrackIntervalFeature tr) throws InvalidGenomicCoordsException, IOException {
    GenomicCoords current = tr.getGc();
    TrackIntervalFeature itr = (TrackIntervalFeature) tr;
    List<IntervalFeature> features = itr.getIntervalFeatureList();
    if (features.size() == 0) {
        return current;
    }
    // Get the leftmost and rightmost coordinates of the feature set
    // These might extend beyond the current window.
    int left = Integer.MAX_VALUE;
    int right = 0;
    for (IntervalFeature f : features) {
        if (f.getFrom() < left) {
            left = f.getFrom();
        }
        if (f.getTo() > right) {
            right = f.getTo();
        }
    }
    // See if left and right need to be adjusted by window coordinates
    if (left < current.getFrom()) {
        left = current.getFrom();
    }
    if (right > current.getTo()) {
        right = current.getTo();
    }
    return new GenomicCoords(current.getChrom() + ":" + left + "-" + right, current.getUserWindowSize(), current.getSamSeqDict(), current.getFastaFile());
}

Example 69 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackIntervalFeature method genomicCoordsAllChromMatchInGenome.

/**
 * Execute findAllChromRegexInGenome() and return the extreme coordinates of the matched features
 */
protected GenomicCoords genomicCoordsAllChromMatchInGenome(Pattern pattern, GenomicCoords currentGc) throws IOException, InvalidGenomicCoordsException {
    List<IntervalFeature> matchedFeatures = this.findAllChromMatchInGenome(pattern, currentGc);
    if (matchedFeatures.size() == 0) {
        return currentGc;
    }
    // Now get the coords of the first and last feature matched.
    String chrom = matchedFeatures.get(0).getChrom();
    int startFrom = matchedFeatures.get(0).getFrom();
    int endTo = matchedFeatures.get(matchedFeatures.size() - 1).getTo();
    GenomicCoords allMatchesGc = new GenomicCoords(Utils.coordinatesToString(chrom, startFrom, endTo), currentGc.getUserWindowSize(), currentGc.getSamSeqDict(), currentGc.getFastaFile());
    return allMatchesGc;
}

Example 70 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackIntervalFeature method coordsOfNextFeature.

/**
 *Return the coordinates of the next feature so that the start coincide with the start of the feature and
 * the end is the start + windowSize.
 */
public GenomicCoords coordsOfNextFeature(GenomicCoords currentGc, boolean getPrevious) throws InvalidGenomicCoordsException, IOException {
    IntervalFeature nextFeature;
    if (getPrevious) {
        nextFeature = this.getPreviousFeature(currentGc.getChrom(), currentGc.getFrom());
    } else {
        nextFeature = this.getNextFeature(currentGc.getChrom(), currentGc.getTo());
    }
    if (nextFeature == null) {
        return currentGc;
    }
    GenomicCoords nextGc = new GenomicCoords(Utils.coordinatesToString(nextFeature.getChrom(), nextFeature.getFrom(), nextFeature.getFrom() + currentGc.getGenomicWindowSize() - 1), currentGc.getUserWindowSize(), currentGc.getSamSeqDict(), currentGc.getFastaFile());
    return nextGc;
}