Examples with GeneProduct ubic.gemma.model.genome.gene.GeneProduct used on opensource projects

Example 36 with GeneProduct

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

the class GenericGenelistDesignGenerator method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception exception = super.processCommandLine(args);
    if (exception != null) {
        return exception;
    }
    ExternalDatabase genbank = externalDatabaseService.findByName("Genbank");
    ExternalDatabase ensembl = externalDatabaseService.findByName("Ensembl");
    assert genbank != null;
    assert ensembl != null;
    /*
         * Create the stub array design for the organism. The name and etc. are generated automatically. If the design
         * exists, we update it.
         */
    String shortName = this.generateShortName();
    ArrayDesign arrayDesign = ArrayDesign.Factory.newInstance();
    arrayDesign.setShortName(shortName);
    // common name
    arrayDesign.setPrimaryTaxon(taxon);
    String nameExt = useNCBIIds ? ", indexed by NCBI IDs" : useEnsemblIds ? ", indexed by Ensembl IDs" : "";
    arrayDesign.setName("Generic platform for " + taxon.getScientificName() + nameExt);
    arrayDesign.setDescription("Created by Gemma");
    // this is key
    arrayDesign.setTechnologyType(TechnologyType.NONE);
    if (arrayDesignService.find(arrayDesign) != null) {
        AbstractCLI.log.info("Platform for " + taxon + " already exists, will update");
        arrayDesign = arrayDesignService.find(arrayDesign);
        arrayDesignService.deleteGeneProductAssociations(arrayDesign);
        arrayDesign = arrayDesignService.load(arrayDesign.getId());
    } else {
        AbstractCLI.log.info("Creating new 'generic' platform");
        arrayDesign = arrayDesignService.create(arrayDesign);
    }
    arrayDesign = arrayDesignService.thaw(arrayDesign);
    // temporary: making sure we set it, as it is new.
    arrayDesign.setTechnologyType(TechnologyType.NONE);
    /*
         * Load up the genes for the organism.
         */
    Collection<Gene> knownGenes = geneService.loadAll(taxon);
    AbstractCLI.log.info("Taxon has " + knownGenes.size() + " genes");
    // this would be good for cases where the identifier we are using has changed.
    Map<Gene, CompositeSequence> existingGeneMap = new HashMap<>();
    if (!useNCBIIds && !useEnsemblIds) {
        // only using this for symbol changes.
        existingGeneMap = this.getExistingGeneMap(arrayDesign);
    }
    Map<String, CompositeSequence> existingSymbolMap = this.getExistingProbeNameMap(arrayDesign);
    int count = 0;
    int numWithNoTranscript = 0;
    // int hasGeneAlready = 0;
    // int numNewGenes = 0;
    int numNewElements = 0;
    int numUpdatedElements = 0;
    for (Gene gene : knownGenes) {
        gene = geneService.thaw(gene);
        Collection<GeneProduct> products = gene.getProducts();
        if (products.isEmpty()) {
            numWithNoTranscript++;
            AbstractCLI.log.debug("No transcript for " + gene);
            continue;
        }
        count++;
        CompositeSequence csForGene = null;
        if (useNCBIIds) {
            if (gene.getNcbiGeneId() == null) {
                AbstractCLI.log.debug("No NCBI ID for " + gene + ", skipping");
                continue;
            }
            if (existingSymbolMap.containsKey(gene.getNcbiGeneId().toString())) {
                csForGene = existingSymbolMap.get(gene.getNcbiGeneId().toString());
            }
        } else if (useEnsemblIds) {
            if (gene.getEnsemblId() == null) {
                AbstractCLI.log.debug("No Ensembl ID for " + gene + ", skipping");
                continue;
            }
            if (existingSymbolMap.containsKey(gene.getEnsemblId())) {
                csForGene = existingSymbolMap.get(gene.getEnsemblId());
            }
        } else {
            /*
                 * detect when the symbol has changed
                 */
            if (existingSymbolMap.containsKey(gene.getOfficialSymbol())) {
                csForGene = existingSymbolMap.get(gene.getOfficialSymbol());
            } else if (existingGeneMap.containsKey(gene)) {
                csForGene = existingGeneMap.get(gene);
                AbstractCLI.log.debug("Gene symbol has changed for: " + gene + "? Current element has name=" + csForGene.getName());
                csForGene.setName(gene.getOfficialSymbol());
            }
        }
        assert csForGene == null || csForGene.getId() != null : "Null id for " + csForGene;
        /*
             * We arbitrarily link the "probe" to one of the gene's RNA transcripts. We could consider other strategies
             * to pick the representative, but it generally doesn't matter.
             */
        for (GeneProduct geneProduct : products) {
            if (!GeneProductType.RNA.equals(geneProduct.getType())) {
                continue;
            }
            /*
                 * Name is usually the genbank or ensembl accession
                 */
            String name = geneProduct.getName();
            BioSequence bioSequence = BioSequence.Factory.newInstance();
            Collection<DatabaseEntry> accessions = geneProduct.getAccessions();
            bioSequence.setName(name);
            bioSequence.setTaxon(taxon);
            bioSequence.setPolymerType(PolymerType.RNA);
            bioSequence.setType(SequenceType.mRNA);
            BioSequence existing = null;
            if (accessions.isEmpty()) {
                // this should not be hit.
                AbstractCLI.log.warn("No accession for " + name);
                DatabaseEntry de = DatabaseEntry.Factory.newInstance();
                de.setAccession(name);
                if (name.startsWith("ENS") && name.length() > 10) {
                    de.setExternalDatabase(ensembl);
                } else {
                    if (name.matches("^[A-Z]{1,2}(_?)[0-9]+(\\.[0-9]+)?$")) {
                        de.setExternalDatabase(genbank);
                    } else {
                        AbstractCLI.log.info("Name doesn't look like genbank or ensembl, skipping: " + name);
                        continue;
                    }
                }
                bioSequence.setSequenceDatabaseEntry(de);
            } else {
                bioSequence.setSequenceDatabaseEntry(accessions.iterator().next());
                existing = bioSequenceService.findByAccession(accessions.iterator().next());
            // FIXME It is possible that this sequence will have been aligned to the genome, which is a bit
            // confusing. So it will map to a gene. Worse case: it maps to more than one gene ...
            }
            if (existing == null) {
                bioSequence = (BioSequence) this.getPersisterHelper().persist(bioSequence);
            } else {
                bioSequence = existing;
            }
            assert bioSequence != null && bioSequence.getId() != null;
            if (bioSequence.getSequenceDatabaseEntry() == null) {
                AbstractCLI.log.info("No DB entry for " + bioSequence + "(" + gene + "), will look for a better sequence to use ...");
                continue;
            }
            if (csForGene == null) {
                if (AbstractCLI.log.isDebugEnabled())
                    AbstractCLI.log.debug("New element " + " with " + bioSequence + " for " + gene);
                csForGene = CompositeSequence.Factory.newInstance();
                if (useNCBIIds) {
                    if (gene.getNcbiGeneId() == null) {
                        continue;
                    }
                    csForGene.setName(gene.getNcbiGeneId().toString());
                } else if (useEnsemblIds) {
                    if (gene.getEnsemblId() == null) {
                        continue;
                    }
                    csForGene.setName(gene.getEnsemblId());
                } else {
                    csForGene.setName(gene.getOfficialSymbol());
                }
                csForGene.setArrayDesign(arrayDesign);
                csForGene.setBiologicalCharacteristic(bioSequence);
                csForGene.setDescription("Generic expression element for " + gene);
                csForGene = compositeSequenceService.create(csForGene);
                assert csForGene.getId() != null : "No id for " + csForGene + " for " + gene;
                arrayDesign.getCompositeSequences().add(csForGene);
                numNewElements++;
            } else {
                if (AbstractCLI.log.isDebugEnabled())
                    AbstractCLI.log.debug("Updating existing element: " + csForGene + " with " + bioSequence + " for " + gene);
                csForGene.setArrayDesign(arrayDesign);
                csForGene.setBiologicalCharacteristic(bioSequence);
                csForGene.setDescription("Generic expression element for " + gene);
                assert csForGene.getId() != null : "No id for " + csForGene + " for " + gene;
                compositeSequenceService.update(csForGene);
                // making sure ...
                csForGene = compositeSequenceService.load(csForGene.getId());
                assert csForGene.getId() != null;
                arrayDesign.getCompositeSequences().add(csForGene);
                numUpdatedElements++;
            }
            assert bioSequence.getId() != null;
            assert geneProduct.getId() != null;
            assert csForGene.getBiologicalCharacteristic() != null && csForGene.getBiologicalCharacteristic().getId() != null;
            AnnotationAssociation aa = AnnotationAssociation.Factory.newInstance();
            aa.setGeneProduct(geneProduct);
            aa.setBioSequence(bioSequence);
            annotationAssociationService.create(aa);
            break;
        }
        if (count % 100 == 0)
            AbstractCLI.log.info(count + " genes processed; " + numNewElements + " new elements; " + numUpdatedElements + " updated elements; " + numWithNoTranscript + " genes had no transcript and were skipped.");
    }
    // is this necessary? causes an error sometimes.
    // arrayDesignService.update( arrayDesign );
    AbstractCLI.log.info("Array design has " + arrayDesignService.numCompositeSequenceWithGenes(arrayDesign) + " 'probes' associated with genes.");
    arrayDesignReportService.generateArrayDesignReport(arrayDesign.getId());
    auditTrailService.addUpdateEvent(arrayDesign, AnnotationBasedGeneMappingEvent.Factory.newInstance(), count + " genes processed; " + numNewElements + " new elements; " + numUpdatedElements + " updated elements; " + numWithNoTranscript + " genes had no transcript and were skipped.");
    arrayDesignAnnotationService.deleteExistingFiles(arrayDesign);
    AbstractCLI.log.info("Don't forget to update the annotation files");
    return null;
}

Example 37 with GeneProduct

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

the class BlatAssociationServiceTest method setup.

@Before
public void setup() {
    int numSequencesToCreate = 20;
    for (int i = 0; i < numSequencesToCreate; i++) {
        BioSequence bs = this.getTestPersistentBioSequence();
        if (i == 11) {
            bs.setSequence(testSequence);
            bs.setName(testSequenceName);
            this.bioSequenceService.update(bs);
        }
        BlatResult br = this.getTestPersistentBlatResult(bs);
        br.setQuerySequence(bs);
        blatResultService.update(br);
        BlatAssociation ba = BlatAssociation.Factory.newInstance();
        Gene g = this.getTestPersistentGene();
        GeneProduct gp = this.getTestPersistentGeneProduct(g);
        if (i == 10) {
            g.setOfficialName(testGeneIdentifier);
            gp.setGene(g);
            gp.setName(testGeneIdentifier);
            this.geneProductService.update(gp);
        }
        ba.setGeneProduct(gp);
        ba.setBlatResult(br);
        ba.setBioSequence(bs);
        blatAssociationService.create(ba);
    }
}

Example 38 with GeneProduct

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

the class BlatAssociationServiceTest method testFindGene.

@Test
public final void testFindGene() {
    Gene g = Gene.Factory.newInstance();
    g.setOfficialName(testGeneIdentifier);
    GeneProduct gp = GeneProduct.Factory.newInstance();
    gp.setName(testGeneIdentifier);
    g.getProducts().add(gp);
    gp.setGene(g);
    Collection<BlatAssociation> res = this.blatAssociationService.find(g);
    assertEquals(1, res.size());
}

Example 39 with GeneProduct

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

the class GenomePersisterTest method testPersistGeneProduct.

/*
     * Going the opposite way as the other test.
     *
     */
@Test
public void testPersistGeneProduct() {
    Gene gene = Gene.Factory.newInstance();
    gene.setName(RandomStringUtils.randomAlphabetic(10));
    gene.setNcbiGeneId(Integer.parseInt(RandomStringUtils.randomNumeric(8)));
    GeneProduct gp = GeneProduct.Factory.newInstance();
    gp.setName(RandomStringUtils.randomAlphabetic(10));
    gp.setGene(gene);
    gp.setNcbiGi(RandomStringUtils.randomAlphabetic(10));
    gene.getProducts().add(gp);
    gp = (GeneProduct) this.persisterHelper.persist(gp);
    assertNotNull(gp.getId());
    assertNotNull(gp.getGene().getId());
}

Example 40 with GeneProduct

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

the class GenomePersisterTest method testPersistGene.

@Test
public void testPersistGene() {
    Gene gene = Gene.Factory.newInstance();
    gene.setName(RandomStringUtils.randomAlphabetic(10));
    gene.setNcbiGeneId(Integer.parseInt(RandomStringUtils.randomNumeric(8)));
    Collection<GeneProduct> gps = new HashSet<>();
    for (int i = 0; i < 10; i++) {
        GeneProduct gp = GeneProduct.Factory.newInstance();
        gp.setName(RandomStringUtils.randomAlphabetic(10));
        gp.setGene(gene);
        gp.setNcbiGi(RandomStringUtils.randomAlphabetic(10));
        gps.add(gp);
    }
    gene.setProducts(gps);
    gene = (Gene) this.persisterHelper.persistOrUpdate(gene);
    assertNotNull(gene.getId());
    assertNotNull(gene.getName());
    assertNotNull(gene.getProducts());
    for (GeneProduct product : gene.getProducts()) {
        assertNotNull(product.getId());
        assertNotNull(product.getName());
    }
}