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

Example 46 with Gene

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

the class GeneServiceTest method testFindByAccessionOther.

@Test
public void testFindByAccessionOther() {
    Gene gene = Gene.Factory.newInstance();
    Integer id = Integer.parseInt(RandomStringUtils.randomNumeric(5));
    gene.setNcbiGeneId(id);
    gene.setName(GeneServiceTest.TEST_GENE_NAME);
    ExternalDatabase ensembl = edbs.findByName("Ensembl");
    DatabaseEntry dbe = DatabaseEntry.Factory.newInstance();
    dbe.setAccession("E129458");
    dbe.setExternalDatabase(ensembl);
    gene.getAccessions().add(dbe);
    Taxon human = taxonService.findByCommonName("human");
    gene.setTaxon(human);
    geneDao.create(gene);
    Gene g = geneDao.findByAccession("E129458", ensembl);
    assertNotNull(g);
    assertEquals(g, gene);
    geneDao.remove(gene);
}

Example 47 with Gene

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

the class GeneServiceTest method testGetByGeneAlias.

@Test
public void testGetByGeneAlias() {
    Gene gene = Gene.Factory.newInstance();
    Integer id = Integer.parseInt(RandomStringUtils.randomNumeric(5));
    gene.setNcbiGeneId(id);
    gene.setName(GeneServiceTest.TEST_GENE_NAME);
    Collection<GeneAlias> aliases = new ArrayList<>();
    GeneAlias alias = GeneAlias.Factory.newInstance();
    alias.setId((long) 1);
    alias.setAlias("GRIN1");
    aliases.add(alias);
    gene.setAliases(aliases);
    Collection<Gene> genes = geneDao.findByAlias("GRIN1");
    assertNotNull(genes);
}

Example 48 with Gene

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

the class GeneServiceTest method testFindEvenThoughHaveSameSymbol.

@Test
public void testFindEvenThoughHaveSameSymbol() {
    Gene gene = Gene.Factory.newInstance();
    Integer id = Integer.parseInt(RandomStringUtils.randomNumeric(5));
    gene.setNcbiGeneId(id);
    gene.setName(GeneServiceTest.TEST_GENE_NAME);
    gene.setOfficialName(GeneServiceTest.TEST_GENE_NAME);
    gene.setOfficialSymbol(GeneServiceTest.TEST_GENE_NAME);
    Taxon human = taxonService.findByCommonName("human");
    gene.setTaxon(human);
    PhysicalLocation pl1 = PhysicalLocation.Factory.newInstance();
    Chromosome chromosome = new Chromosome("X", null, this.getTestPersistentBioSequence(), human);
    chromosome = (Chromosome) persisterHelper.persist(chromosome);
    pl1.setChromosome(chromosome);
    pl1.setNucleotide(10000010L);
    pl1.setNucleotideLength(1001);
    pl1.setStrand("-");
    gene.setPhysicalLocation(pl1);
    gene = geneDao.create(gene);
    Long idWeWant = gene.getId();
    Gene gene2 = Gene.Factory.newInstance();
    gene2.setNcbiGeneId(null);
    gene2.setName(GeneServiceTest.TEST_GENE_NAME);
    gene2.setOfficialName(GeneServiceTest.TEST_GENE_NAME);
    gene2.setOfficialSymbol(GeneServiceTest.TEST_GENE_NAME);
    gene2.setTaxon(human);
    PhysicalLocation pl2 = PhysicalLocation.Factory.newInstance();
    Chromosome chromosome2 = new Chromosome("Y", null, this.getTestPersistentBioSequence(), human);
    chromosome2 = (Chromosome) persisterHelper.persist(chromosome2);
    pl2.setChromosome(chromosome2);
    pl2.setChromosome(chromosome);
    pl2.setNucleotide(10000010L);
    pl2.setNucleotideLength(1001);
    pl2.setStrand("-");
    gene2.setPhysicalLocation(pl2);
    gene2 = geneDao.create(gene2);
    gene.setId(null);
    Gene g = geneDao.find(gene);
    assertNotNull(g);
    assertEquals(idWeWant, g.getId());
    geneDao.remove(g);
    geneDao.remove(gene2);
}

Example 49 with Gene

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

the class GeneCoreServiceTest method testSearchGenes.

@Test
public void testSearchGenes() {
    Gene gene = Gene.Factory.newInstance();
    Integer id = Integer.parseInt(RandomStringUtils.randomNumeric(5));
    gene.setNcbiGeneId(id);
    gene.setName("test_search");
    gene.setOfficialName("test_search");
    gene.setOfficialSymbol("test_search");
    Taxon human = taxonService.findByCommonName("human");
    gene.setTaxon(human);
    PhysicalLocation pl1 = PhysicalLocation.Factory.newInstance();
    Chromosome chromosome = new Chromosome("X", null, this.getTestPersistentBioSequence(), human);
    chromosome = (Chromosome) persisterHelper.persist(chromosome);
    pl1.setChromosome(chromosome);
    pl1.setNucleotide(10000010L);
    pl1.setNucleotideLength(1001);
    pl1.setStrand("-");
    gene.setPhysicalLocation(pl1);
    gene = geneDao.create(gene);
    Collection<GeneValueObject> searchResults = geneCoreService.searchGenes("test_search", 1L);
    assertNotNull(searchResults);
    GeneValueObject gvo = searchResults.iterator().next();
    assertNotNull(gvo);
    geneDao.remove(gene);
}

Example 50 with Gene

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

the class ArrayDesignProbeMapperServiceImpl method checkForAlias.

private GeneProduct checkForAlias(GeneProduct geneProduct) {
    Collection<GeneProduct> candidates = geneProductService.findByName(geneProduct.getName(), geneProduct.getGene().getTaxon());
    if (candidates.isEmpty())
        return null;
    Gene gene = geneProduct.getGene();
    for (GeneProduct existing2 : candidates) {
        Collection<GeneAlias> aliases = existing2.getGene().getAliases();
        for (GeneAlias geneAlias : aliases) {
            if (geneAlias.getAlias().equalsIgnoreCase(gene.getOfficialSymbol())) {
                /*
                     * So, our gene products match, and the genes match but via an alias. That's pretty solid.
                     */
                ArrayDesignProbeMapperServiceImpl.log.info("Associated gene product " + geneProduct + " has a match in Gemma through an aliased gene: " + existing2);
                return existing2;
            }
        }
    }
    return null;
}