Package org.broad.igv.track

Examples of org.broad.igv.track.TrackLoader

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    @Test
    public void basicIOTest() throws Exception {
        String inputPath = TestUtils.DATA_DIR + "vcf/hc_mod.vcf";
        TestUtils.createIndex(inputPath);

        VariantTrack inputTrack = (VariantTrack) (new TrackLoader()).load(new ResourceLocator(inputPath), genome).get(0);

        VCFEncoder encoder = new VCFEncoder();
        Argument arg = new Argument(null, Argument.InputType.VARIANT_TRACK, null, null, null, null, false, null);

        Map<Argument, Object> arguments = new HashMap(1);
        arguments.put(arg, inputTrack);
        encoder.setInputs(null, arguments, arg);

        String chr = "chr20";
        int start = 10499005;
        int end = 10499500;

        String outpath = TestUtils.TMP_OUTPUT_DIR + "hc_mod_out.vcf";
        OutputStream outputStream = new FileOutputStream(outpath);

        List<VCFVariant> infeatures = new ArrayList<VCFVariant>();
        for (Feature feat : inputTrack.getFeatures(chr, start, end)) {
            infeatures.add((VCFVariant) feat);
        }

        encoder.encodeAll(outputStream, infeatures.iterator());

        TestUtils.createIndex(outpath);
        VariantTrack outputTrack = (VariantTrack) (new TrackLoader()).load(new ResourceLocator(inputPath), genome).get(0);

        VCFWriterTest.assertHeadersEquals((VCFHeader) inputTrack.getHeader(), (VCFHeader) outputTrack.getHeader());

        int n = 0;
        for (Feature var1 : inputTrack.getFeatures(chr, start, end)) {
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        LinkedHashMap<Argument, Object> arguments = new LinkedHashMap<Argument, Object>(argumentList.size());

        int argnum = 0;
        arguments.put(argumentList.get(argnum++), "");

        TrackLoader loader = new TrackLoader();
        String[] paths = new String[]{TestUtils.DATA_DIR + "bed/test.bed", TestUtils.DATA_DIR + "bed/testAlternateColor.bed"};
        for (String path : paths) {
            TestUtils.createIndex(path);
            FeatureTrack track = (FeatureTrack) loader.load(new ResourceLocator(path), genome).get(0);
            arguments.put(argumentList.get(argnum++), track);
        }


        List<String> cmd = Arrays.asList(reader.getToolPath(tool), command.cmd);
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            public String get() {
                return path;
            }
        };

        final TrackLoader loader = new TrackLoader();

        Function<String, Void> loadFileFunc = new Function<String, Void>() {
            @Override
            public Void apply(String input) {
                try {
                    List<Track> newTrack = loader.load(new ResourceLocator(path), genome);
                } catch (Exception e) {
                    e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                }
                return null;
            }
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public class UCSCGeneTableCodecTest extends AbstractHeadlessTest {

    @Test
    public void testLoadGenePred() throws Exception {
        String file = TestUtils.DATA_DIR + "gene/EnsembleGenes_sample.genepred";
        TrackLoader loader = new TrackLoader();
        ResourceLocator locator = new ResourceLocator(file);
        Genome genome = TestUtils.loadGenome();
        List<Track> tracks = loader.load(locator, genome);

        assertEquals(1, tracks.size());

        FeatureCodec codec = CodecFactory.getCodec(locator, genome);
        AbstractFeatureReader<Feature, ?> bfs = AbstractFeatureReader.getFeatureReader(locator.getPath(), codec, false);
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    }

    @Test
    public void testLoadUCSC() throws Exception {
        String file = TestUtils.DATA_DIR + "gene/UCSCgenes_sample.gene";
        TrackLoader loader = new TrackLoader();
        ResourceLocator locator = new ResourceLocator(file);
        Genome genome = TestUtils.loadGenome();
        List<Track> tracks = loader.load(locator, genome);

        assertEquals(1, tracks.size());

        FeatureCodec codec = CodecFactory.getCodec(locator.getPath(), genome);
        AbstractFeatureReader<Feature, ?> bfs = AbstractFeatureReader.getFeatureReader(locator.getPath(), codec, false);
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Related Classes of org.broad.igv.track.TrackLoader

  • htsjdk.variant.vcf.VCFHeader
  • org.broad.igv.bbfile.BBFileReader
  • org.broad.igv.bigwig.BigWigDataSource
  • org.broad.igv.cbio.GeneNetworkTest
  • org.broad.igv.cli_plugin.awkPluginTest
  • org.broad.igv.cli_plugin.BEDToolsPluginSourceTest
  • org.broad.igv.cli_plugin.PluginFeatureSourceTest
  • org.broad.igv.cli_plugin.PluginSourceTest
  • org.broad.igv.cli_plugin.VCFEncoderTest
  • org.broad.igv.das.DASFeatureSource
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