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

Example 81 with BioSequence

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

the class FastaParserTest method testParseInputStreamAffyTarget.

public void testParseInputStreamAffyTarget() throws Exception {
    FastaParser p = new FastaParser();
    p.parse(g);
    Collection<BioSequence> actualResult = p.getResults();
    TestCase.assertNotNull(actualResult);
    TestCase.assertEquals(172, actualResult.size());
    for (Object object : actualResult) {
        BioSequence b = (BioSequence) object;
        TestCase.assertTrue(b.getSequenceDatabaseEntry() != null && b.getSequenceDatabaseEntry().getExternalDatabase() != null && b.getSequenceDatabaseEntry().getExternalDatabase().getName().equalsIgnoreCase("genbank"));
        if (FastaParserTest.log.isDebugEnabled())
            FastaParserTest.log.debug("NAME=" + b.getName() + " DESC=" + b.getDescription() + " SEQ=" + b.getSequence() + " GB=" + b.getSequenceDatabaseEntry().getAccession());
    }
}

Example 82 with BioSequence

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

the class FastaParserTest method testParser.

private void testParser(InputStream n) throws java.io.IOException {
    FastaParser p = new FastaParser();
    p.parse(n);
    Collection<BioSequence> actualResult = p.getResults();
    TestCase.assertNotNull(actualResult);
    TestCase.assertEquals(2, actualResult.size());
    for (Object object : actualResult) {
        BioSequence b = (BioSequence) object;
        FastaParserTest.log.debug("NAME=" + b.getName() + " DESC=" + b.getDescription() + " SEQ=" + b.getSequence());
    }
}

Example 83 with BioSequence

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

the class FastaParserTest method testParseMasked.

public void testParseMasked() throws Exception {
    try (InputStream n = FastaParserTest.class.getResourceAsStream("/data/loader/genome/maskedSeq.fa")) {
        FastaParser p = new FastaParser();
        p.parse(n);
        Collection<BioSequence> actualResult = p.getResults();
        TestCase.assertNotNull(actualResult);
        TestCase.assertEquals(7, actualResult.size());
        for (Object object : actualResult) {
            BioSequence b = (BioSequence) object;
            FastaParserTest.log.debug("NAME=" + b.getName() + " DESC=" + b.getDescription() + " SEQ=" + b.getSequence());
        }
    }
}

Example 84 with BioSequence

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

the class SimpleFastaCmdTest method testGetSingleAccNotFound.

@Test
public void testGetSingleAccNotFound() {
    if (this.fastaCmdExecutableNotExists()) {
        return;
    }
    SimpleFastaCmd fastaCmd = new SimpleFastaCmd();
    BioSequence bs = fastaCmd.getByAccession("FAKE.1", SimpleFastaCmdTest.TESTBLASTDB, testBlastDbPath);
    assertNull(bs);
}

Example 85 with BioSequence

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

the class BlatAssociationScorerTest method createBlatResult.

private BlatResult createBlatResult(String name) {
    BlatResult blatResult = BlatResult.Factory.newInstance();
    blatResult.setRepMatches(0);
    blatResult.setMatches(49);
    blatResult.setQueryGapCount(0);
    blatResult.setTargetGapCount(2);
    blatResult.setMismatches(1);
    BioSequence sequence = BioSequence.Factory.newInstance();
    blatResult.setQuerySequence(sequence);
    blatResult.getQuerySequence().setLength(50L);
    Taxon taxon = Taxon.Factory.newInstance();
    taxon.setCommonName("human");
    Chromosome chr = new Chromosome(name, taxon);
    blatResult.setTargetChromosome(chr);
    return blatResult;
}