Examples with EntrezGene uk.ac.ebi.spot.goci.model.EntrezGene used on opensource projects

Example 6 with EntrezGene

use of uk.ac.ebi.spot.goci.model.EntrezGene in project goci by EBISPOT.

the class SnpGenomicContextMappingService method storeGenes.

/**
 * Create/update genes with latest mapping information
 *
 * @param geneToExternalIdMap map of a gene name and all external database IDs from current mapping run
 * @param source              the source of mapping, either Ensembl or Entrez
 */
private void storeGenes(Map<String, Set<String>> geneToExternalIdMap, String source) {
    List<Gene> genesToUpdate = new ArrayList<>();
    List<Gene> genesToCreate = new ArrayList<>();
    List<EntrezGene> entrezGenesToDelete = new ArrayList<>();
    List<EnsemblGene> ensemblGenesToDelete = new ArrayList<>();
    for (String geneName : geneToExternalIdMap.keySet()) {
        Set<String> externalIds = geneToExternalIdMap.get(geneName);
        // Find any existing database genes that match the gene name
        // IgnoreCase query is not used here as we want
        // the exact gene name returned from mapping
        Gene existingGeneInDatabase = geneQueryService.findByGeneName(geneName);
        // If gene is not found in database then create one
        if (existingGeneInDatabase == null) {
            Gene newGene = createGene(geneName, externalIds, source);
            genesToCreate.add(newGene);
        } else // Update gene
        {
            if (source.equalsIgnoreCase("Ensembl")) {
                // Get a list of current Ensembl IDs linked to existing gene
                Collection<EnsemblGene> oldEnsemblGenesLinkedToGene = existingGeneInDatabase.getEnsemblGeneIds();
                Collection<Long> oldEnsemblIdsLinkedToGene = new ArrayList<>();
                for (EnsemblGene oldEnsemblGeneLinkedToGene : oldEnsemblGenesLinkedToGene) {
                    oldEnsemblIdsLinkedToGene.add(oldEnsemblGeneLinkedToGene.getId());
                }
                Collection<EnsemblGene> newEnsemblGenes = new ArrayList<>();
                for (String id : externalIds) {
                    EnsemblGene ensemblGene = createOrRetrieveEnsemblExternalId(id, geneName);
                    newEnsemblGenes.add(ensemblGene);
                }
                // Set latest IDs from mapping run
                existingGeneInDatabase.setEnsemblGeneIds(newEnsemblGenes);
                // Save changes
                // geneRepository.save(existingGeneInDatabase);
                genesToUpdate.add(existingGeneInDatabase);
                // Clean-up any Ensembl IDs that may now be left without a gene linked
                for (Long oldEnsemblIdLinkedToGene : oldEnsemblIdsLinkedToGene) {
                    cleanUpEnsemblGenes(oldEnsemblIdLinkedToGene, ensemblGenesToDelete);
                }
            }
            if (source.equalsIgnoreCase("Entrez")) {
                // Get a list of of current Entrez IDs linked to existing gene
                Collection<EntrezGene> oldEntrezGenesLinkedToGene = existingGeneInDatabase.getEntrezGeneIds();
                Collection<Long> oldEntrezGenesIdsLinkedToGene = new ArrayList<>();
                for (EntrezGene oldEntrezGeneLinkedToGene : oldEntrezGenesLinkedToGene) {
                    oldEntrezGenesIdsLinkedToGene.add(oldEntrezGeneLinkedToGene.getId());
                }
                Collection<EntrezGene> newEntrezGenes = new ArrayList<>();
                for (String id : externalIds) {
                    EntrezGene entrezGene = createOrRetrieveEntrezExternalId(id, geneName);
                    newEntrezGenes.add(entrezGene);
                }
                // Set latest IDs from mapping run
                existingGeneInDatabase.setEntrezGeneIds(newEntrezGenes);
                // Save changes
                // geneRepository.save(existingGeneInDatabase);
                genesToUpdate.add(existingGeneInDatabase);
                // Clean-up any Entrez IDs that may now be left without a gene linked
                for (Long oldEntrezGenesIdLinkedToGene : oldEntrezGenesIdsLinkedToGene) {
                    cleanUpEntrezGenes(oldEntrezGenesIdLinkedToGene, entrezGenesToDelete);
                }
            }
        }
    }
    ensemblGeneRepository.delete(ensemblGenesToDelete);
    entrezGeneRepository.delete(entrezGenesToDelete);
    geneRepository.save(genesToCreate);
    geneRepository.save(genesToUpdate);
}

Example 7 with EntrezGene

use of uk.ac.ebi.spot.goci.model.EntrezGene in project goci by EBISPOT.

the class SnpGenomicContextMappingService method createOrRetrieveEntrezExternalId.

/**
 * Method to create an Entrez gene, this database table holds entrez gene IDs
 *
 * @param id       Entrez gene ID
 * @param geneName Gene name allows method to check if this id is actually already linked to another gene
 */
private EntrezGene createOrRetrieveEntrezExternalId(String id, String geneName) {
    EntrezGene entrezGene = entrezGeneQueryService.findByEntrezGeneId(id);
    // Create new entry in ENTREZ_GENE table for this ID
    if (entrezGene == null) {
        entrezGene = new EntrezGene();
        entrezGene.setEntrezGeneId(id);
        entrezGeneRepository.save(entrezGene);
    } else // Check this ID is not linked to a gene with a different name
    {
        Gene existingGeneLinkedToId = entrezGene.getGene();
        if (existingGeneLinkedToId != null) {
            if (!Objects.equals(existingGeneLinkedToId.getGeneName(), geneName)) {
                getLog().warn("Entrez ID: " + id + ", is already used in database by a different gene(s): " + existingGeneLinkedToId.getGeneName() + ". Will update so links to " + geneName);
                // For gene already linked to this entrez ID remove the entrez ID
                existingGeneLinkedToId.getEntrezGeneIds().remove(entrezGene);
                geneRepository.save(existingGeneLinkedToId);
            }
        }
    }
    return entrezGene;
}