Examples with TabixReader htsjdk.tribble.readers.TabixReader used on opensource projects

Example 1 with TabixReader

use of htsjdk.tribble.readers.TabixReader in project ASCIIGenome by dariober.

the class MakeTabixFileTest method canCompressAndIndexHeaderlessVCF.

@Test
public void canCompressAndIndexHeaderlessVCF() throws ClassNotFoundException, IOException, InvalidRecordException, SQLException {
    String infile = "test_data/noheader.vcf";
    File outfile = new File("test_data/noheader.vcf.gz");
    outfile.deleteOnExit();
    File expectedTbi = new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
    expectedTbi.deleteOnExit();
    new MakeTabixIndex(infile, outfile, TabixFormat.VCF);
    assertTrue(outfile.exists());
    assertTrue(outfile.length() > 200);
    assertTrue(expectedTbi.exists());
    assertTrue(expectedTbi.length() > 100);
    TabixReader tbx = new TabixReader(outfile.getAbsolutePath());
    Iterator x = tbx.query("1", 1, 10000000);
    assertTrue(x.next().startsWith("1"));
}

Example 2 with TabixReader

use of htsjdk.tribble.readers.TabixReader in project ASCIIGenome by dariober.

the class MakeTabixFileTest method canCompressAndIndexVCF.

@Test
public void canCompressAndIndexVCF() throws ClassNotFoundException, IOException, InvalidRecordException, SQLException {
    String infile = "test_data/CHD.exon.2010_03.sites.unsorted.vcf";
    File outfile = new File("test_data/tmp6.bed.gz");
    outfile.deleteOnExit();
    File expectedTbi = new File(outfile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
    expectedTbi.deleteOnExit();
    new MakeTabixIndex(infile, outfile, TabixFormat.VCF);
    assertTrue(outfile.exists());
    assertTrue(outfile.length() > 1000);
    assertTrue(expectedTbi.exists());
    assertTrue(expectedTbi.length() > 1000);
    TabixReader tbx = new TabixReader(outfile.getAbsolutePath());
    Iterator x = tbx.query("1", 20000000, 30000000);
    assertTrue(x.next().startsWith("1"));
    // Check you can read ok
    this.vcfTester(outfile.getAbsolutePath());
}

Example 3 with TabixReader

use of htsjdk.tribble.readers.TabixReader in project ASCIIGenome by dariober.

the class Utils method hasTabixIndex.

// public static LinkedHashMap<String, Integer> xterm256ColorCodes(){
// // See http://misc.flogisoft.com/bash/tip_colors_and_formatting
// // From http://jonasjacek.github.io/colors/
// LinkedHashMap<String, Integer> colourCodes= new LinkedHashMap<String, Integer>();
// colourCodes.put("default", 39);
// colourCodes.put("black", 30);
// colourCodes.put("red", 31);
// colourCodes.put("green", 32);
// colourCodes.put("yellow", 33);
// colourCodes.put("blue", 34);
// colourCodes.put("magenta", 35);
// colourCodes.put("cyan", 36);
// colourCodes.put("light_grey", 37);
// colourCodes.put("grey", 90);
// colourCodes.put("light_red", 91);
// colourCodes.put("light_green", 92);
// colourCodes.put("light_yellow", 93);
// colourCodes.put("light_blue", 94);
// colourCodes.put("light_magenta", 95);
// colourCodes.put("light_cyan", 96);
// colourCodes.put("white", 97);
// // To be continued
// return colourCodes;
// }
// public static Color ansiColourToGraphicsColor(int ansiColor) throws InvalidColourException{
// 
// if(!xterm256ColorCodes().entrySet().contains(ansiColor)){
// throw new InvalidColourException();
// }
// if(ansiColor == 30){ return Color.BLACK; }
// if(ansiColor == 31 || ansiColor == 91){ return Color.RED; }
// if(ansiColor == 32 || ansiColor == 92){ return Color.GREEN; }
// if(ansiColor == 33 || ansiColor == 93){ return Color.YELLOW; }
// if(ansiColor == 34 || ansiColor == 94){ return Color.BLUE; }
// if(ansiColor == 35 || ansiColor == 95){ return Color.MAGENTA; }
// if(ansiColor == 36 || ansiColor == 96){ return Color.CYAN; }
// if(ansiColor == 37){ return Color.LIGHT_GRAY; }
// if(ansiColor == 90){ return Color.DARK_GRAY; }
// if(ansiColor == 97){ return Color.WHITE; }
// return Color.BLACK;
// }
/**
 * Return true if fileName has a valid tabix index.
 * @throws IOException
 */
public static boolean hasTabixIndex(String fileName) throws IOException {
    if ((new UrlValidator()).isValid(fileName) && fileName.startsWith("ftp")) {
        // Because of issue #51
        return false;
    }
    try {
        TabixReader tabixReader = new TabixReader(fileName);
        tabixReader.readLine();
        tabixReader.close();
        return true;
    } catch (Exception e) {
        return false;
    }
}

Example 4 with TabixReader

use of htsjdk.tribble.readers.TabixReader in project ASCIIGenome by dariober.

the class TrackWiggles method bedGraphToScores.

/**
 * Get values for bedgraph
 * @throws InvalidRecordException
 * @throws InvalidGenomicCoordsException
 */
private void bedGraphToScores(String fileName) throws IOException, InvalidRecordException, InvalidGenomicCoordsException {
    List<ScreenWiggleLocusInfo> screenWigLocInfoList = new ArrayList<ScreenWiggleLocusInfo>();
    for (int i = 0; i < getGc().getUserWindowSize(); i++) {
        screenWigLocInfoList.add(new ScreenWiggleLocusInfo());
    }
    try {
        TabixReader tabixReader = new TabixReader(fileName);
        Iterator qry = tabixReader.query(this.getGc().getChrom(), this.getGc().getFrom() - 1, this.getGc().getTo());
        while (true) {
            String q = qry.next();
            if (q == null) {
                break;
            }
            if (q.contains("\t__ignore_me__")) {
                // Hack to circumvent issue #38
                continue;
            }
            if (!this.isValidBedGraphLine(q)) {
                continue;
            }
            String[] tokens = q.split("\t");
            int screenFrom = Utils.getIndexOfclosestValue(Integer.valueOf(tokens[1]) + 1, this.getGc().getMapping());
            int screenTo = Utils.getIndexOfclosestValue(Integer.valueOf(tokens[2]), this.getGc().getMapping());
            float value = Float.valueOf(tokens[this.bdgDataColIdx - 1]);
            for (int i = screenFrom; i <= screenTo; i++) {
                screenWigLocInfoList.get(i).increment(value);
            }
        }
    } catch (IOException e) {
        e.printStackTrace();
        System.err.println("Could not open tabix file: " + fileName);
        System.err.println("Is the file sorted and indexed? After sorting by position (sort e.g. -k1,1 -k2,2n), compress with bgzip and index with e.g.:");
        System.err.println("\nbgzip " + fileName);
        System.err.println("tabix -p bed " + fileName + "\n");
    }
    List<Float> screenScores = new ArrayList<Float>();
    for (ScreenWiggleLocusInfo x : screenWigLocInfoList) {
        screenScores.add((float) x.getMeanScore());
    }
    this.setScreenScores(screenScores);
    return;
}

Example 5 with TabixReader

use of htsjdk.tribble.readers.TabixReader in project ASCIIGenome by dariober.

the class TrackBookmark method removeBookmark.

/**
 * Remove the bookmark matching the exact coordinates of the current position.
 * Bookmarks partially overlapping are not removed.
 * @param bookmarkRegion
 * @throws IOException
 * @throws SQLException
 * @throws InvalidRecordException
 * @throws ClassNotFoundException
 * @throws InvalidGenomicCoordsException
 */
public void removeBookmark(GenomicCoords bookmarkRegion) throws IOException, ClassNotFoundException, InvalidRecordException, SQLException, InvalidGenomicCoordsException {
    // To remove a bookmark, iterate through the bgzip file writing records to a tmp file.
    // The record(s) matching this position is not written.
    // 
    File plainNew = new File(this.getWorkFilename() + ".remove");
    plainNew.deleteOnExit();
    BufferedWriter wr = new BufferedWriter(new FileWriter(plainNew));
    InputStream fileStream = new FileInputStream(this.getWorkFilename());
    Reader decoder = new InputStreamReader(new GZIPInputStream(fileStream), "UTF-8");
    BufferedReader br = new BufferedReader(decoder);
    String line;
    while ((line = br.readLine()) != null) {
        if (!line.startsWith("#")) {
            // In case of comment lines
            List<String> pos = Lists.newArrayList(Splitter.on("\t").split(line));
            if (bookmarkRegion.getChrom().equals(pos.get(0)) && bookmarkRegion.getFrom() == Integer.parseInt(pos.get(3)) && bookmarkRegion.getTo() == Integer.parseInt(pos.get(4))) {
                continue;
            }
        }
        wr.write(line + "\n");
    }
    wr.close();
    br.close();
    // Recompress and index replacing the original bgzip file
    new MakeTabixIndex(plainNew.getAbsolutePath(), new File(this.getWorkFilename()), TabixFormat.GFF);
    plainNew.delete();
    this.tabixReader = new TabixReader(this.getWorkFilename());
    // Update track.
    this.update();
}