Examples with VcfFilterSequenceOntology com.github.lindenb.jvarkit.tools.vcffilterso.VcfFilterSequenceOntology used on opensource projects

Example 1 with VcfFilterSequenceOntology

use of com.github.lindenb.jvarkit.tools.vcffilterso.VcfFilterSequenceOntology in project jvarkit by lindenb.

the class TestNg01 method testVcfFilterSo.

@Test
public void testVcfFilterSo() throws IOException {
    File output = new File(TEST_RESULTS_DIR, "jeter.filrerso.vcf");
    final AnnPredictionParser parser = new AnnPredictionParserFactory().createDefaultParser();
    final SequenceOntologyTree tree = SequenceOntologyTree.getInstance();
    String acn = "SO:0001583";
    final SequenceOntologyTree.Term term = tree.getTermByAcn(acn);
    final Set<SequenceOntologyTree.Term> terms = term.getAllDescendants();
    Assert.assertNotNull(term);
    Assert.assertTrue(terms.size() > 1);
    Assert.assertTrue(terms.contains(term));
    Assert.assertEquals(0, new VcfFilterSequenceOntology().instanceMain(new String[] { "-o", output.getPath(), "-A", acn, VCF01 }));
    streamVcf(output).forEach(V -> {
        // System.err.println(V.getAttribute("ANN")+" vs "+ terms);
        Assert.assertTrue(parser.getPredictions(V).stream().flatMap(P -> P.getSOTerms().stream()).anyMatch(T -> terms.contains(T)));
    });
    Assert.assertEquals(0, new VcfFilterSequenceOntology().instanceMain(new String[] { "-o", output.getPath(), "-A", acn, "--rmatt", "--invert", VCF01 }));
    streamVcf(output).forEach(V -> {
        Assert.assertFalse(parser.getPredictions(V).stream().flatMap(P -> P.getSOTerms().stream()).anyMatch(T -> terms.contains(T)));
    });
    Assert.assertEquals(0, new VcfFilterSequenceOntology().instanceMain(new String[] { "-o", output.getPath(), "-A", acn, "--rmatt", VCF01 }));
    Assert.assertTrue(streamVcf(output).findAny().isPresent());
    Assert.assertTrue(output.delete());
}