Package org.broad.igv.feature.genome

Examples of org.broad.igv.feature.genome.Genome

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        String indexFile = infile + ".idx";
        File idxFi = new File(indexFile);
        assertTrue(idxFi.exists());
        idxFi.deleteOnExit();

        Genome genome = IgvTools.loadGenome(fasta_file);
        FeatureCodec codec = CodecFactory.getCodec(infile, genome);
        AbstractFeatureReader<Feature, ?> reader = AbstractFeatureReader.getFeatureReader(infile, codec, true);
        String chr = "NC_000913_bb";
        Iterator<Feature> features = reader.query(chr, 5085, 5091);
        int count = 0;
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    }

    @Test
    public void testLoadGFFAliasedChrs() throws Exception {
        String filepath = TestUtils.DATA_DIR + "gff/aliased.unsorted.gff";
        Genome genome = IgvTools.loadGenome(TestUtils.DATA_DIR + "genomes/hg18_truncated_aliased.genome");
        List<Track> tracks = trackLoader.load(new ResourceLocator(filepath), genome);
        assertEquals(1, tracks.size());
        FeatureTrack track = (FeatureTrack) tracks.get(0);

        assertEquals("aliased.unsorted.gff", track.getName());
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        assertTrue("VCF file loaded incorrect track type", tracks.get(0) instanceof VariantTrack);

    }

    private List<Track> tstLoadFi(String filepath, Integer expected_tracks, boolean makeIndex) throws Exception {
        Genome genome = TestUtils.loadGenome();
        return tstLoadFi(filepath, expected_tracks, genome, makeIndex);
    }
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        tmp.add("/sam/test_2.sam");
        filenamesTryIndex = tmp.toArray(new String[tmp.size()]);
    }

    public void tstFilesHeadless(String[] filenames, boolean tryIndex) throws Exception {
        Genome genome = TestUtils.loadGenome();
        for (String finame : filenames) {
            tstLoadFi(TestUtils.DATA_DIR + finame, null, genome, tryIndex);
        }
    }
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*/
public class EQTLCodecTest {
    @Test
    public void testDecode() throws Exception {

        Genome genome = null;  // Genome not needed for this test

        EQTLCodec codec = new EQTLCodec(genome);

        String line = "rs4700772\t5\t180341845\tENSG00000168903.7\tBTNL3\t180415845\t129.858921455635\t1.61918925670937e-27";

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    @Test
    public void testGetSummaryScoresForSNPs() throws Exception {

        ResourceLocator locator = new ResourceLocator(TestUtils.DATA_DIR + "cn/multi_snp.cn");
        Genome genome = TestUtils.loadGenome();
        IGVDataset ds = new IGVDataset(locator, genome);
        DatasetDataSource dataSource = new DatasetDataSource("Sample1", ds, genome);
        String chr = "chr10";

        dataSource.cacheSummaryTiles = false;
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public class FreqDataTest extends AbstractHeadlessTest {

    @Test
    public void test() throws IOException {

        Genome genome = TestUtils.loadGenome();

        String segfile = TestUtils.DATA_DIR + "seg/canFam2_hg18.seg";


        SegmentedDataSet sd = new SegmentedAsciiDataSet(new ResourceLocator(segfile), genome);
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    }

    @Test
    public void testFeatureLookupInSmallVCF() throws IOException {
        String vcfFile = TestUtils.DATA_DIR + "vcf/example4-last-gsnap-2_fixed.vcf";
        Genome genome = null; // <= Don't do chromosome conversion
        FeatureCodec codec = CodecFactory.getCodec(vcfFile, genome);
        boolean isVCF = codec.getClass().isAssignableFrom(VCFCodec.class);

        TestUtils.createIndex(vcfFile);
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        int[] expectedCounts = {7, 6, 8};

        String testFile = TestUtils.DATA_DIR +
                "/methylation/usc/jhu-usc.edu_UCEC.IlluminaHiSeq_WGBS.Level_3.1.0.0.hg18.SAMPLE.bb";

        Genome genome = null;  // Don't need a genome for this test

        String chr = "chr11";
        int start = 10001654;
        int end = 10001754;
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        String testFile = "path-to-test-file.bb";
        String chr = "chr7";
        int start = 26133475;
        int end = 27333475;
        Genome genome = null;

        BBFileReader reader = new BBFileReader(testFile);
        MethylDataSource source = new BBMethylDataSource(reader, BBMethylDataSource.Type.ZILLER, genome);
        Iterator<MethylScore> iter = source.query(chr, start, end);
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Related Classes of org.broad.igv.feature.genome.Genome

  • org.broad.igv.data.AbstractDataSourceTest
  • org.broad.igv.data.HostedDataTest
  • org.broad.igv.data.seg.FreqDataTest
  • org.broad.igv.feature.Chromosome
  • org.broad.igv.feature.exome.ExomeReferenceFrame
  • org.broad.igv.feature.FeatureDB
  • org.broad.igv.feature.FeatureUtils
  • org.broad.igv.feature.FeatureUtilsTest
  • org.broad.igv.feature.GisticFileParser
  • org.broad.igv.feature.tribble.CachingFeatureReaderTest
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