Examples with Gene ubic.gemma.model.genome.Gene used on opensource projects

Example 31 with Gene

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

the class GeneMultifunctionalityPopulationServiceTest method tearDown.

@After
public void tearDown() {
    gene2GoService.removeAll();
    Collection<Gene> genes = geneService.loadAll(testTaxon);
    for (Gene gene : genes) {
        try {
            geneService.remove(gene);
        } catch (Exception ignored) {
        }
    }
}

Example 32 with Gene

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

the class GeneMultifunctionalityPopulationServiceTest method setUp.

@Before
public void setUp() throws Exception {
    if (goService.isRunning()) {
        goService.shutDown();
    }
    gene2GoService.removeAll();
    goService.loadTermsInNameSpace(new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/ontology/molecular-function.test.owl.gz")));
    testTaxon = taxonService.findOrCreate(Taxon.Factory.newInstance("foobly" + RandomStringUtils.randomAlphabetic(2), "doobly" + RandomStringUtils.randomAlphabetic(2), "bar" + RandomStringUtils.randomAlphabetic(2), RandomUtils.nextInt(5000), true, true));
    /*
         * Create genes
         */
    for (int i = 0; i < 120; i++) {
        Gene gene = this.getTestPersistentGene(testTaxon);
        // Some genes get no terms.
        if (i >= 100)
            continue;
        /*
             * Add up to 5 GO terms. Parents mean more will be added.
             */
        for (int j = 0; j <= Math.floor(i / 20); j++) {
            VocabCharacteristic oe = VocabCharacteristic.Factory.newInstance();
            oe.setValueUri(GeneOntologyService.BASE_GO_URI + goTerms[j]);
            oe.setValue(goTerms[j]);
            Gene2GOAssociation g2Go1 = Gene2GOAssociation.Factory.newInstance(gene, oe, GOEvidenceCode.EXP);
            gene2GoService.create(g2Go1);
        }
    }
}

Example 33 with Gene

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

the class GeneMultifunctionalityPopulationServiceTest method test.

@Test
public void test() {
    log.info("Updating multifunctionality");
    s.updateMultifunctionality(testTaxon);
    Collection<Gene> genes = geneService.loadAll(testTaxon);
    genes = geneService.thawLite(genes);
    assertEquals(120, genes.size());
    boolean found = false;
    for (Gene gene : genes) {
        Multifunctionality mf = gene.getMultifunctionality();
        if (mf == null)
            continue;
        if (mf.getNumGoTerms() == 5) {
            // assertEquals( 0.245833, mf.getRank(), 0.001 );
            found = true;
        }
    }
    assertTrue(found);
}

Example 34 with Gene

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

the class StringBiomartGene2GeneProteinLoaderTest method getTestPeristentGenesZebra.

public void getTestPeristentGenesZebra() {
    Gene geneZebraOne = this.makeGene(zebraFish, "zgc.153184", "751652");
    Gene geneZebraTwo = this.makeGene(zebraFish, "appl1", "571540");
    Gene geneZebraThree = this.makeGene(zebraFish, "LOC568371", "568371");
    Gene geneZebraFour = this.makeGene(zebraFish, "TESTGENE", "30425");
    Gene geneZebraFive = this.makeGene(zebraFish, "TESTGENE2", "503936");
    genesZebra.add(this.makeGene(zebraFish, "FOO1", "562059"));
    genesZebra.add(geneZebraOne);
    genesZebra.add(geneZebraTwo);
    genesZebra.add(geneZebraThree);
    genesZebra.add(geneZebraFour);
    genesZebra.add(geneZebraFive);
    Gene2GeneProteinAssociation existingGene2GeneProteinAssociationOne = Gene2GeneProteinAssociation.Factory.newInstance(geneZebraOne, geneZebraThree, null, null, null);
    Gene2GeneProteinAssociation existingGene2GeneProteinAssociationTwo = Gene2GeneProteinAssociation.Factory.newInstance(geneZebraOne, geneZebraTwo, null, null, null);
    // noinspection MismatchedQueryAndUpdateOfCollection
    Collection<Gene2GeneProteinAssociation> geneAssociationZebra = new ArrayList<>();
    geneAssociationZebra.add(existingGene2GeneProteinAssociationTwo);
    geneAssociationZebra.add(existingGene2GeneProteinAssociationOne);
}

Example 35 with Gene

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

the class PhenotypeAssociationManagerServiceImpl method findGenesWithEvidence.

@Override
@Transactional(readOnly = true)
public Collection<GeneEvidenceValueObject> findGenesWithEvidence(String query, Long taxonId) {
    if (query == null || query.length() == 0) {
        throw new IllegalArgumentException("No search query provided");
    }
    // make sure it does an inexact search
    String newQuery = query + "%";
    Taxon taxon = null;
    if (taxonId != null) {
        taxon = this.taxonService.load(taxonId);
    }
    SearchSettings settings = SearchSettingsImpl.geneSearch(newQuery, taxon);
    List<SearchResult> geneSearchResults = this.searchService.search(settings).get(Gene.class);
    Collection<Gene> genes = new HashSet<>();
    if (geneSearchResults == null || geneSearchResults.isEmpty()) {
        return new HashSet<>();
    }
    for (SearchResult sr : geneSearchResults) {
        genes.add((Gene) sr.getResultObject());
    }
    Collection<GeneEvidenceValueObject> geneEvidenceValueObjects = new HashSet<>();
    for (Gene g : genes) {
        GeneEvidenceValueObject geneEvidenceValueObject = new GeneEvidenceValueObject(g, this.convert2ValueObjects(g.getPhenotypeAssociations()));
        geneEvidenceValueObjects.add(geneEvidenceValueObject);
    }
    Collection<GeneEvidenceValueObject> geneValueObjectsFilter = new ArrayList<>();
    for (GeneEvidenceValueObject gene : geneEvidenceValueObjects) {
        if (gene.getEvidence() != null && gene.getEvidence().size() != 0) {
            geneValueObjectsFilter.add(gene);
        }
    }
    return geneValueObjectsFilter;
}