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

Example 81 with Taxon

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

the class ProcessedExpressionDataVectorServiceTest method getGeneAssociatedWithEe.

private Collection<Gene> getGeneAssociatedWithEe(ExpressionExperiment ee) {
    Collection<ArrayDesign> ads = this.expressionExperimentService.getArrayDesignsUsed(ee);
    Collection<Gene> genes = new HashSet<>();
    for (ArrayDesign ad : ads) {
        Taxon taxon = this.getTaxon("mouse");
        ad = this.arrayDesignService.thaw(ad);
        for (CompositeSequence cs : ad.getCompositeSequences()) {
            Gene g = this.getTestPersistentGene();
            BlatAssociation blata = BlatAssociation.Factory.newInstance();
            blata.setGeneProduct(g.getProducts().iterator().next());
            BlatResult br = BlatResult.Factory.newInstance();
            BioSequence bs = BioSequence.Factory.newInstance();
            bs.setName(RandomStringUtils.random(10));
            bs.setTaxon(taxon);
            bs = (BioSequence) persisterHelper.persist(bs);
            assertNotNull(bs);
            cs.setBiologicalCharacteristic(bs);
            compositeSequenceService.update(cs);
            cs = compositeSequenceService.load(cs.getId());
            assertNotNull(cs.getBiologicalCharacteristic());
            br.setQuerySequence(bs);
            blata.setBlatResult(br);
            blata.setBioSequence(bs);
            persisterHelper.persist(blata);
            genes.add(g);
        }
    }
    return genes;
}

Example 82 with Taxon

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

the class ExpressionExperimentServiceTest method testGetByTaxon.

@Test
public void testGetByTaxon() {
    ExpressionExperimentService eeService = this.getBean(ExpressionExperimentService.class);
    Taxon taxon = taxonService.findByCommonName("mouse");
    Collection<ExpressionExperiment> list = expressionExperimentService.findByTaxon(taxon);
    assertNotNull(list);
    Taxon checkTaxon = eeService.getTaxon(list.iterator().next());
    assertEquals(taxon, checkTaxon);
}

Example 83 with Taxon

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

the class CompositeSequenceGeneMapperServiceTest method blatCollapsedSequences.

private void blatCollapsedSequences() throws IOException {
    Taxon taxon = taxonService.findByScientificName("Homo sapiens");
    ArrayDesignSequenceAlignmentService aligner = this.getBean(ArrayDesignSequenceAlignmentService.class);
    InputStream blatResultInputStream = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/genome/gpl96.blatresults.psl.gz"));
    Collection<BlatResult> results = blat.processPsl(blatResultInputStream, taxon);
    aligner.processArrayDesign(ad, taxon, results);
    // real stuff.
    ArrayDesignProbeMapperService arrayDesignProbeMapperService = this.getBean(ArrayDesignProbeMapperService.class);
    arrayDesignProbeMapperService.processArrayDesign(ad);
}

Example 84 with Taxon

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

the class ExpressionDataDoubleMatrixTest method setup.

@Before
public void setup() throws Exception {
    Collection<ArrayDesign> ads = new HashSet<>();
    metaData = new SimpleExpressionExperimentMetaData();
    ArrayDesign ad = ArrayDesign.Factory.newInstance();
    ad.setName("new ad");
    ads.add(ad);
    metaData.setArrayDesigns(ads);
    Taxon taxon = Taxon.Factory.newInstance();
    taxon.setCommonName("mouse");
    taxon.setIsGenesUsable(true);
    taxon.setIsSpecies(true);
    metaData.setTaxon(taxon);
    metaData.setName("ee");
    metaData.setQuantitationTypeName("testing");
    metaData.setGeneralType(GeneralType.QUANTITATIVE);
    metaData.setScale(ScaleType.LOG2);
    metaData.setType(StandardQuantitationType.AMOUNT);
    metaData.setIsRatio(true);
    try (InputStream data = this.getClass().getResourceAsStream("/data/loader/aov.results-2-monocyte-data-bytime.bypat.data.sort")) {
        DoubleMatrix<String, String> matrix = simpleExpressionDataLoaderService.parse(data);
        ee = simpleExpressionDataLoaderService.convert(metaData, matrix);
    }
    assertNotNull(ee);
    assertEquals(200, ee.getRawExpressionDataVectors().size());
    assertEquals(59, ee.getBioAssays().size());
}

Example 85 with Taxon

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

the class BioMartEnsemblNcbiObjectGeneratorTest method setUp.

@Before
public void setUp() {
    biomartEnsemblNcbiObjectGenerator = new BiomartEnsemblNcbiObjectGenerator();
    Taxon taxon = Taxon.Factory.newInstance();
    taxon.setIsGenesUsable(true);
    taxon.setNcbiId(10090);
    taxon.setScientificName("Mus musculus");
    taxon.setIsSpecies(true);
    taxa = new ArrayList<>();
    taxa.add(taxon);
    String fileNameBiomartmouse = "/data/loader/protein/biomart/biomartmmusculusShort.txt";
    URL fileNameBiomartmouseURL = this.getClass().getResource(fileNameBiomartmouse);
    taxonBiomartFile = new File(fileNameBiomartmouseURL.getFile());
}