Examples with BioSequence ubic.gemma.model.genome.biosequence.BioSequence used on opensource projects

Example 11 with BioSequence

use of ubic.gemma.model.genome.biosequence.BioSequence in project Gemma by PavlidisLab.

the class SimpleFastaCmdTest method testGetSingle.

@Test
public void testGetSingle() {
    if (this.fastaCmdExecutableNotExists()) {
        return;
    }
    SimpleFastaCmd fastaCmd = new SimpleFastaCmd();
    BioSequence bs = fastaCmd.getByIdentifier(1435867, SimpleFastaCmdTest.TESTBLASTDB, testBlastDbPath);
    assertNotNull(bs);
    String expected = "CCACCTTTCCCTCCACTCCTCACGTTCTCACCTGTAAAGCGTCCCTCCCTCATCCCCATGCCCCCTTACCCTGCAGGGTA" + "GAGTAGGCTAGAAACCAGAGAGCTCCAAGCTCCATCTGTGGAGAGGTGCCATCCTTGGGCTGCAGAGAGAGGAGAATTTG" + "CCCCAAAGCTGCCTGCAGAGCTTCACCACCCTTAGTCTCACAAAGCCTTGAGTTCATAGCATTTCTTGAGTTTTCACCCT" + "GCCCAGCAGGACACTGCAGCACCCAAAGGGCTTCCCAGGAGTAGGGTTGCCCTCAAGAGGCTCTTGGGTCTGATGGCCAC" + "ATCCTGGAATTGTTTTCAAGTTGATGGTCACAGCCCTGAGGCATGTAGGGGCGTGGGGATGCGCTCTGCTCTGCTCTCCT" + "CTCCTGAACCCCTGAACCCTCTGGCTACCCCAGAGCACTTAGAGCCAG";
    assertEquals(expected, bs.getSequence());
}

Example 12 with BioSequence

use of ubic.gemma.model.genome.biosequence.BioSequence in project Gemma by PavlidisLab.

the class SimpleFastaCmdTest method testGetSingleAcc.

@Test
public void testGetSingleAcc() {
    if (this.fastaCmdExecutableNotExists()) {
        return;
    }
    SimpleFastaCmd fastaCmd = new SimpleFastaCmd();
    String accession = "AA000002";
    BioSequence bs = fastaCmd.getByAccession(accession, SimpleFastaCmdTest.TESTBLASTDB, testBlastDbPath);
    assertNotNull("fastacmd failed to find " + accession, bs);
    String expected = "CCACCTTTCCCTCCACTCCTCACGTTCTCACCTGTAAAGCGTCCCTCCCTCATCCCCATGCCCCCTTACCCTGCAGGGTA" + "GAGTAGGCTAGAAACCAGAGAGCTCCAAGCTCCATCTGTGGAGAGGTGCCATCCTTGGGCTGCAGAGAGAGGAGAATTTG" + "CCCCAAAGCTGCCTGCAGAGCTTCACCACCCTTAGTCTCACAAAGCCTTGAGTTCATAGCATTTCTTGAGTTTTCACCCT" + "GCCCAGCAGGACACTGCAGCACCCAAAGGGCTTCCCAGGAGTAGGGTTGCCCTCAAGAGGCTCTTGGGTCTGATGGCCAC" + "ATCCTGGAATTGTTTTCAAGTTGATGGTCACAGCCCTGAGGCATGTAGGGGCGTGGGGATGCGCTCTGCTCTGCTCTCCT" + "CTCCTGAACCCCTGAACCCTCTGGCTACCCCAGAGCACTTAGAGCCAG";
    assertEquals(expected, bs.getSequence());
}

Example 13 with BioSequence

use of ubic.gemma.model.genome.biosequence.BioSequence in project Gemma by PavlidisLab.

the class RepeatScanTest method testFraction.

public final void testFraction() {
    BioSequence b = BioSequence.Factory.newInstance();
    b.setSequence("AAAaaaaAAAAaaa");
    RepeatScan r = new RepeatScan();
    double d = r.computeFractionMasked(b);
    assertEquals(0.5, d, 0.001);
}

Example 14 with BioSequence

use of ubic.gemma.model.genome.biosequence.BioSequence in project Gemma by PavlidisLab.

the class GeoConverterTest method testWithImageNoGenbank.

/*
     * Platform has IMAGE:CCCCC in CLONE_ID column, no genbank accessions anywhere.
     */
@Test
public final void testWithImageNoGenbank() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GPL222_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.setProcessPlatformsOnly(true);
    parser.parse(is);
    GeoPlatform platform = ((GeoParseResult) parser.getResults().iterator().next()).getPlatformMap().get("GPL222");
    Object result = this.gc.convert(platform);
    ArrayDesign ad = (ArrayDesign) result;
    for (CompositeSequence cs : ad.getCompositeSequences()) {
        BioSequence bs = cs.getBiologicalCharacteristic();
        assertTrue(bs.getName().startsWith("IMAGE"));
    }
}

Example 15 with BioSequence

use of ubic.gemma.model.genome.biosequence.BioSequence in project Gemma by PavlidisLab.

the class GeoConverterTest method testImageClones.

/*
     * We should not longer use IMAGE:XXXXX as the sequence name.
     */
@Test
public void testImageClones() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GPL226_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoPlatform platform = ((GeoParseResult) parser.getResults().iterator().next()).getPlatformMap().get("GPL226");
    Object result = this.gc.convert(platform);
    ArrayDesign ad = (ArrayDesign) result;
    assertNotNull(ad);
    for (CompositeSequence cs : ad.getCompositeSequences()) {
        BioSequence bs = cs.getBiologicalCharacteristic();
        assertTrue("Got: " + bs.getName(), !bs.getName().startsWith("IMAGE") || bs.getSequenceDatabaseEntry() == null);
    }
}