public static void dumpRootAttributes(String ibfFile) { TDFReader reader = TDFReader.getReader(ibfFile); System.out.println("Track line = " + reader.getTrackLine()); TDFGroup group = reader.getGroup("/"); for (Map.Entry<String, String> entries : group.attributes.entrySet()) { System.out.println(entries.getKey() + " = " + entries.getValue()); } System.out.println(reader.getTrackLine()); }
public static void tdfToBedgraph(String tdfFile, String bedGraphFile) throws FileNotFoundException { TDFReader reader = null; PrintStream ps = null; try { reader = TDFReader.getReader(tdfFile); ps = new PrintStream(new BufferedOutputStream(new FileOutputStream(bedGraphFile))); String trackLine = reader.getTrackLine(); if (trackLine != null && trackLine.length() > 0) { ps.println(trackLine); } for (String dsName : reader.getDatasetNames()) { String[] tokens = dsName.split("/"); String chrName = tokens[1]; if (!chrName.equals(Globals.CHR_ALL) && dsName.contains("raw")) { TDFDataset ds = reader.getDataset(dsName); for (int i = 0; i < ds.nTiles; i++) { TDFTile tile = ds.getTile(i); if (tile != null) { dumpTileData(reader, chrName, tile, ps); } } } } } finally { if (reader != null) reader.close(); if (ps != null) ps.close(); } }
private void loadEwigIBFFile(ResourceLocator locator, List<Track> newTracks, Genome genome) { TDFReader reader = TDFReader.getReader(locator.getPath()); TrackProperties props = null; String trackLine = reader.getTrackLine(); if (trackLine != null && trackLine.length() > 0) { props = new TrackProperties(); ParsingUtils.parseTrackLine(trackLine, props); } EWigTrack track = new EWigTrack(locator, genome); if (props != null) { track.setProperties(props); } track.setName(locator.getTrackName()); newTracks.add(track); }
String trackLine = reader.getTrackLine(); if (trackLine != null && trackLine.length() > 0) { props = new TrackProperties();
/** * Test of createDataset method, of class IBFWriter. */ @Test public void testCreateFile() { File testFile = new File("test2.tdf"); testFile.deleteOnExit(); TDFWriter writer = new TDFWriter(testFile, "hg18", type, trackLine, trackNames, wfs, false); writer.closeFile(); TDFReader reader = TDFReader.getReader(testFile.getAbsolutePath()); String[] tn = reader.getTrackNames(); assertEquals(trackNames.length, tn.length); for (int i = 0; i < tn.length; i++) { assertEquals(trackNames[i], tn[i]); } assertEquals(type, reader.getTrackType()); assertEquals(trackLine, reader.getTrackLine()); reader.close(); }