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

Example 21 with Gene

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

the class Gene2GeneCoexpressionServiceTest method setup.

@Before
public void setup() {
    Taxon mouseTaxon = taxonS.findByCommonName("mouse");
    firstGene = Gene.Factory.newInstance();
    firstGene.setName("test_gene2geneCoexpression");
    firstGene.setTaxon(mouseTaxon);
    firstGene = geneS.create(firstGene);
    Gene secondGene = Gene.Factory.newInstance();
    secondGene.setName("test_gene2geneCoexpression2");
    secondGene.setTaxon(mouseTaxon);
    secondGene = geneS.create(secondGene);
    List<NonPersistentNonOrderedCoexpLink> links = new ArrayList<>();
    links.add(new NonPersistentNonOrderedCoexpLink(MouseGeneCoExpression.Factory.newInstance(0.9, secondGene.getId(), firstGene.getId())));
    ee = this.getTestPersistentBasicExpressionExperiment();
    Set<Gene> genesTested = new HashSet<>();
    genesTested.add(firstGene);
    genesTested.add(secondGene);
    g2gCoexpressionService.createOrUpdate(ee, links, new LinkCreator(mouseTaxon), genesTested);
}

Example 22 with Gene

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

the class CompositeSequenceGeneMapperServiceTest method cleanup.

@After
public void cleanup() {
    ad = arrayDesignService.findByShortName(arrayAccession);
    if (ad != null) {
        for (ExpressionExperiment ee : arrayDesignService.getExpressionExperiments(ad)) {
            eeService.remove(ee);
        }
        arrayDesignService.remove(ad);
    }
    Collection<Gene> genes = geneService.loadAll();
    for (Gene gene : genes) {
        try {
            geneService.remove(gene);
        } catch (Exception ignored) {
        }
    }
}

Example 23 with Gene

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

the class CompositeSequenceGeneMapperServiceTest method testGetCompositeSequencesByGeneId.

/**
 * Tests finding the composite sequences for a given gene id.
 */
@Test
public void testGetCompositeSequencesByGeneId() {
    Collection<Gene> genes = geneService.findByOfficialSymbol(geneOfficialSymbol);
    if (genes == null || genes.isEmpty())
        return;
    Gene g = genes.iterator().next();
    Collection<CompositeSequence> compositeSequences = geneService.getCompositeSequencesById(g.getId());
    assertNotNull(compositeSequences);
    assertEquals(compositeSequences.size(), 1);
    assertEquals((compositeSequences.iterator().next()).getName(), csName);
}

Example 24 with Gene

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

the class ExternalFileGeneLoaderServiceTest method testLoad.

/*
     * Test method for
     * {@link ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceImpl#load(java.lang.String, java.lang.String)}.
     * Tests that 2 genes are loaded sucessfully into Gemma.
     */
@Test
public void testLoad() throws Exception {
    int numbersGeneLoaded = externalFileGeneLoaderService.load(geneFile, TAXON_NAME);
    assertEquals(2, numbersGeneLoaded);
    Collection<Gene> geneCollection = geneService.findByOfficialSymbol("ZYXMMMM");
    Gene gene = geneCollection.iterator().next();
    gene = geneService.thaw(gene);
    Collection<GeneProduct> geneProducts = gene.getProducts();
    assertEquals(TAXON_NAME, gene.getTaxon().getCommonName());
    // same as the symbol
    assertEquals("ZYXMMMM", gene.getName());
    assertEquals("ZYXMMMM", gene.getOfficialSymbol());
    assertEquals("zyxin", gene.getOfficialName());
    assertEquals(1, geneProducts.size());
    GeneProduct prod = geneProducts.iterator().next();
    assertEquals("Gene product placeholder", prod.getDescription());
    // should not involve any updates if we try loading it again.
    numbersGeneLoaded = externalFileGeneLoaderService.load(geneFile, TAXON_NAME);
    assertEquals(0, numbersGeneLoaded);
    // show that we add a product if the gene exists, but is missing one.
    GeneProduct gp = gene.getProducts().iterator().next();
    gene.getProducts().clear();
    geneProductService.remove(gp);
    geneService.update(gene);
    assertEquals(0, geneService.getProducts(gene.getId()).size());
    numbersGeneLoaded = externalFileGeneLoaderService.load(geneFile, TAXON_NAME);
    assertEquals(1, numbersGeneLoaded);
    assertEquals(1, geneService.getProducts(gene.getId()).size());
    // should not involve any updates if we try loading it again as it is now complete.
    numbersGeneLoaded = externalFileGeneLoaderService.load(geneFile, TAXON_NAME);
    assertEquals(0, numbersGeneLoaded);
}

Example 25 with Gene

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

the class LinearModelAnalyzer method getProbeToGeneMap.

/**
 * Needed to compute the number of genes tested/detected.
 */
private Map<CompositeSequence, Collection<Gene>> getProbeToGeneMap(Map<String, ? extends Collection<DifferentialExpressionAnalysisResult>> resultLists) {
    Map<CompositeSequence, Collection<Gene>> result = new HashMap<>();
    for (Collection<DifferentialExpressionAnalysisResult> resultList : resultLists.values()) {
        for (DifferentialExpressionAnalysisResult d : resultList) {
            CompositeSequence probe = d.getProbe();
            result.put(probe, new HashSet<Gene>());
        }
    }
    // testing environment, etc.
    if (result.isEmpty()) {
        return new HashMap<>();
    }
    return compositeSequenceService.getGenes(result.keySet());
}