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

Example 6 with PhysicalLocation

use of ubic.gemma.model.genome.PhysicalLocation 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 7 with PhysicalLocation

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

the class NcbiGeneConverter method convert.

public Collection<GeneProduct> convert(NCBIGene2Accession acc, Gene gene) {
    Collection<GeneProduct> geneProducts = new HashSet<>();
    // RNA section
    if (acc.getRnaNucleotideAccession() != null) {
        GeneProduct rna = GeneProduct.Factory.newInstance();
        // set available fields
        rna.setNcbiGi(acc.getRnaNucleotideGI());
        rna.setGene(gene);
        rna.setName(acc.getRnaNucleotideAccession());
        rna.setType(GeneProductType.RNA);
        String description = "Imported from NCBI Gene";
        if (acc.getStatus() != null) {
            description = description + " (Refseq status: " + acc.getStatus() + ").";
        }
        if (acc.getRnaNucleotideAccession() != null) {
            DatabaseEntry accession = DatabaseEntry.Factory.newInstance();
            accession.setAccession(acc.getRnaNucleotideAccession());
            accession.setAccessionVersion(acc.getRnaNucleotideAccessionVersion());
            accession.setExternalDatabase(NcbiGeneConverter.genBank);
            if (rna.getAccessions() == null) {
                rna.setAccessions(new HashSet<DatabaseEntry>());
            }
            rna.getAccessions().add(accession);
        }
        /*
             * Fill in physical location details.
             */
        if (acc.getGenomicNucleotideAccession() != null && gene.getPhysicalLocation() != null) {
            this.getChromosomeDetails(acc, gene);
            PhysicalLocation pl = this.getPhysicalLocation(acc, gene);
            rna.setPhysicalLocation(pl);
        }
        rna.setDescription(description);
        geneProducts.add(rna);
    }
    // Protein section
    if (NcbiGeneConverter.retainProteinInformation && acc.getProteinAccession() != null) {
        GeneProduct protein = GeneProduct.Factory.newInstance();
        // set available fields
        protein.setNcbiGi(acc.getProteinGI());
        protein.setGene(gene);
        protein.setName(acc.getProteinAccession());
        protein.setType(GeneProductType.PROTEIN);
        protein.setDescription("Imported from NCBI Gene" + (acc.getStatus() != null ? " (" + acc.getStatus() + ")" : ""));
        DatabaseEntry accession = DatabaseEntry.Factory.newInstance();
        accession.setAccession(acc.getProteinAccession());
        accession.setAccessionVersion(acc.getProteinAccessionVersion());
        accession.setExternalDatabase(NcbiGeneConverter.genBank);
        Collection<DatabaseEntry> accessions = new HashSet<>();
        accessions.add(accession);
        protein.setAccessions(accessions);
        geneProducts.add(protein);
    }
    return geneProducts;
}

Example 8 with PhysicalLocation

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

the class NcbiGeneConverter method convert.

public Gene convert(NCBIGeneInfo info) {
    Gene gene = Gene.Factory.newInstance();
    gene.setNcbiGeneId(Integer.parseInt(info.getGeneId()));
    gene.setName(info.getDefaultSymbol());
    gene.setOfficialSymbol(info.getDefaultSymbol());
    gene.setOfficialName(info.getDescription());
    gene.setEnsemblId(info.getEnsemblId());
    /*
         * NOTE we allow multiple discontinued or previous ids, separated by commas. This is a hack to account for cases
         * uncovered recently...can be minimized by running this regularly.
         */
    if (info.getHistory() != null) {
        assert info.getHistory().getCurrentId() == null || info.getGeneId().equals(info.getHistory().getCurrentId());
        assert info.getHistory().getPreviousIds() != null;
        if (!info.getHistory().getPreviousIds().isEmpty()) {
            String previousIds = StringUtils.join(info.getHistory().getPreviousIds(), ",");
            gene.setPreviousNcbiId(previousIds);
        }
    } else if (StringUtils.isNotBlank(info.getDiscontinuedId())) {
        if (NcbiGeneConverter.log.isDebugEnabled())
            NcbiGeneConverter.log.debug("Gene matches a gene that was discontinued: " + gene + " matches gene that had id " + info.getDiscontinuedId());
        gene.setPreviousNcbiId(info.getDiscontinuedId());
    }
    gene.setDescription("Imported from NCBI gene; Nomenclature status: " + info.getNomenclatureStatus());
    Taxon t = Taxon.Factory.newInstance();
    t.setNcbiId(info.getTaxId());
    t.setIsGenesUsable(false);
    t.setIsSpecies(true);
    gene.setTaxon(t);
    /*
         * We are going to stop maintaining this information
         */
    PhysicalLocation pl = PhysicalLocation.Factory.newInstance();
    Chromosome chrom = new Chromosome(info.getChromosome(), t);
    pl.setChromosome(chrom);
    gene.setPhysicalLocation(pl);
    Collection<GeneAlias> aliases = gene.getAliases();
    for (String alias : info.getSynonyms()) {
        GeneAlias newAlias = GeneAlias.Factory.newInstance();
        newAlias.setAlias(alias);
        aliases.add(newAlias);
    }
    for (String dbname : info.getDbXrefs().keySet()) {
        if (!dbname.equalsIgnoreCase("Ensembl"))
            continue;
        String identifier = info.getDbXrefs().get(dbname);
        DatabaseEntry crossref = DatabaseEntry.Factory.newInstance();
        crossref.setAccession(identifier);
        crossref.setExternalDatabase(NcbiGeneConverter.getEnsembl());
        gene.getAccessions().add(crossref);
    }
    return gene;
}

Example 9 with PhysicalLocation

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

the class CompositeSequenceDaoImpl method batchGetGenesWithSpecificity.

/**
 * @param batch   of composite sequences to process
 * @param results - adding to this
 */
private void batchGetGenesWithSpecificity(Collection<CompositeSequence> batch, Map<CompositeSequence, Collection<BioSequence2GeneProduct>> results) {
    if (batch.size() == 0) {
        return;
    }
    // language=HQL
    final String queryString = "select cs,bas from CompositeSequence cs, BioSequence2GeneProduct bas inner join cs.biologicalCharacteristic bs " + "inner join fetch bas.geneProduct gp inner join fetch gp.gene gene " + "where bas.bioSequence=bs and cs in (:cs)";
    List<?> qr = this.getHibernateTemplate().findByNamedParam(queryString, "cs", batch);
    for (Object o : qr) {
        Object[] oa = (Object[]) o;
        CompositeSequence csa = (CompositeSequence) oa[0];
        BioSequence2GeneProduct ba = (BioSequence2GeneProduct) oa[1];
        if (ba instanceof BlatAssociation) {
            BlatResult blatResult = ((BlatAssociation) ba).getBlatResult();
            PhysicalLocation pl = blatResult.getTargetAlignedRegion();
            /*
                 * We didn't always used to fill in the targetAlignedRegion ... this is just in case.
                 */
            if (pl == null) {
                pl = PhysicalLocation.Factory.newInstance();
                pl.setChromosome(blatResult.getTargetChromosome());
                pl.setNucleotide(blatResult.getTargetStart());
                pl.setNucleotideLength(blatResult.getTargetEnd().intValue() - blatResult.getTargetStart().intValue());
                pl.setStrand(blatResult.getStrand());
            // Note: not bothering to fill in the bin.
            }
        }
        if (!results.containsKey(csa)) {
            results.put(csa, new HashSet<BioSequence2GeneProduct>());
        }
        results.get(csa).add(ba);
    }
    /*
         * This is kind of important. We ensure we return an empty map for probes that do not have a mapping.
         */
    for (CompositeSequence cs : batch) {
        if (!results.containsKey(cs)) {
            results.put(cs, new HashSet<BioSequence2GeneProduct>());
        }
    }
}

Example 10 with PhysicalLocation

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

the class BlatAssociationScorer method clusterGenes.

/**
 * @param associations assocs.
 * @return map of physical locations for the alignments, and which genes are found there.
 */
private static Map<PhysicalLocation, Collection<Gene>> clusterGenes(Map<Gene, Collection<BlatAssociation>> associations) {
    Map<PhysicalLocation, Collection<Gene>> clusters = new HashMap<>();
    for (Gene gene : associations.keySet()) {
        Collection<BlatAssociation> geneAssoc = associations.get(gene);
        for (BlatAssociation ba : geneAssoc) {
            PhysicalLocation pl = ba.getBlatResult().getTargetAlignedRegion();
            if (!clusters.containsKey(pl)) {
                clusters.put(pl, new HashSet<Gene>());
            }
            clusters.get(pl).add(gene);
        }
    }
    // debugging information about clusters.
    if (BlatAssociationScorer.log.isDebugEnabled()) {
        for (PhysicalLocation pl : clusters.keySet()) {
            if (clusters.get(pl).size() > 1) {
                BlatAssociationScorer.log.debug("Cluster at " + pl + " with " + clusters.get(pl).size() + " members:\n" + StringUtils.join(clusters.get(pl).iterator(), "\n"));
            }
        }
    }
    return clusters;
}