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

Example 1 with SingleNucleotidePolymorphism

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

the class EnsemblMappingPipeline method addGenomicContext.

/**
 * Create GenomicContext objects from the JSONObjects and add them to the class variable "genomic_contexts" (list of
 * "GenomicContext" classes)
 *
 * @param json_gene_list the list of overlapping genes in JSONObject format
 * @param snp_location   an instance of the Location class (chromosome name and position)
 * @param source         the source of the data (Ensembl or NCBI)
 * @param type           the type of genomic context (i.e. overlap, upstream, downstream)
 * @return boolean to indicate whether a closest gene has been found or not (only relevant for upstream and
 * downstream gene)
 */
private boolean addGenomicContext(JSONArray json_gene_list, Location snp_location, String source, String type) {
    String closest_gene = "";
    int closest_distance = 0;
    boolean intergenic = (type.equals("overlap")) ? false : true;
    boolean upstream = (type.equals("upstream")) ? true : false;
    boolean downstream = (type.equals("downstream")) ? true : false;
    Integer position = snp_location.getChromosomePosition();
    SingleNucleotidePolymorphism snp_tmp = new SingleNucleotidePolymorphism();
    snp_tmp.setRsId(getEnsemblMappingResult().getRsId());
    if (getEnsemblMappingResult().getRsId() == null) {
        throw new IllegalArgumentException("error, no RS ID found for location " + snp_location.getId());
    }
    // Get closest gene
    if (intergenic) {
        int pos = position;
        for (int i = 0; i < json_gene_list.length(); ++i) {
            JSONObject json_gene = json_gene_list.getJSONObject(i);
            String gene_name = json_gene.getString("external_name");
            // If the source is NCBI, we parse the ID from the description:
            String gene_id = source.equals(getNcbiSource()) ? parseNCBIid(json_gene.getString("description"), gene_name) : json_gene.getString("id");
            if (source.equals(getNcbiSource())) {
                if ((gene_name != null && getEnsemblMappingResult().getNcbiOverlappingGene().contains(gene_name)) || gene_name == null) {
                    // Skip overlapping genes which also overlap upstream and/or downstream of the variant
                    continue;
                }
            } else {
                if ((gene_name != null && getEnsemblMappingResult().getEnsemblOverlappingGene().contains(gene_name)) || gene_name == null) {
                    // Skip overlapping genes which also overlap upstream and/or downstream of the variant
                    continue;
                }
            }
            int distance = 0;
            if (type.equals("upstream")) {
                distance = pos - json_gene.getInt("end");
            } else if (type.equals("downstream")) {
                distance = json_gene.getInt("start") - pos;
            }
            if ((distance < closest_distance && distance > 0) || closest_distance == 0) {
                closest_gene = gene_id;
                closest_distance = distance;
            }
        }
    }
    for (int i = 0; i < json_gene_list.length(); ++i) {
        JSONObject json_gene = json_gene_list.getJSONObject(i);
        String gene_name = json_gene.getString("external_name");
        // If the source is NCBI, we parse the ID from the description:
        String gene_id = source.equals(getNcbiSource()) ? parseNCBIid(json_gene.getString("description"), gene_name) : json_gene.getString("id");
        String ncbi_id = (source.equals("NCBI")) ? gene_id : null;
        String ensembl_id = (source.equals("Ensembl")) ? gene_id : null;
        int distance = 0;
        if (intergenic) {
            if (source.equals(getNcbiSource())) {
                if ((gene_name != null && getEnsemblMappingResult().getNcbiOverlappingGene().contains(gene_name)) || gene_name == null) {
                    // Skip overlapping genes which also overlap upstream and/or downstream of the variant
                    continue;
                }
            } else {
                if ((gene_name != null && getEnsemblMappingResult().getEnsemblOverlappingGene().contains(gene_name)) || gene_name == null) {
                    // Skip overlapping genes which also overlap upstream and/or downstream of the variant
                    continue;
                }
            }
            int pos = position;
            if (type.equals("upstream")) {
                distance = pos - json_gene.getInt("end");
            } else if (type.equals("downstream")) {
                distance = json_gene.getInt("start") - pos;
            }
        }
        Long dist = (long) distance;
        EntrezGene entrezGene = new EntrezGene();
        entrezGene.setEntrezGeneId(ncbi_id);
        Collection<EntrezGene> entrezGenes = new ArrayList<>();
        entrezGenes.add(entrezGene);
        EnsemblGene ensemblGene = new EnsemblGene();
        ensemblGene.setEnsemblGeneId(ensembl_id);
        Collection<EnsemblGene> ensemblGenes = new ArrayList<>();
        ensemblGenes.add(ensemblGene);
        Gene gene_object = new Gene(gene_name, entrezGenes, ensemblGenes);
        // Check if the gene corresponds to the closest gene
        boolean is_closest_gene = (closest_gene.equals(gene_id) && closest_gene != "") ? true : false;
        GenomicContext gc = new GenomicContext(intergenic, upstream, downstream, dist, snp_tmp, gene_object, snp_location, source, getMappingMethod(), is_closest_gene);
        getEnsemblMappingResult().addGenomicContext(gc);
    }
    return (closest_gene != "") ? true : false;
}

Example 2 with SingleNucleotidePolymorphism

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

the class SnpGenomicContextMappingService method storeSnpGenomicContext.

/**
 * Saves genomic context information to database
 *
 * @param snpToGenomicContextMap map of rs_id and all genomic context details returned from current mapping run
 */
private void storeSnpGenomicContext(Map<String, Set<GenomicContext>> snpToGenomicContextMap) {
    List<SingleNucleotidePolymorphism> updatedSnps = new ArrayList<>();
    // Go through each rs_id and its associated genomic contexts returned from the mapping pipeline
    for (String snpRsId : snpToGenomicContextMap.keySet()) {
        getLog().debug("Storing genomic context for " + snpRsId);
        Set<GenomicContext> genomicContextsFromMapping = snpToGenomicContextMap.get(snpRsId);
        // Check if the SNP exists
        SingleNucleotidePolymorphism snpInDatabase = singleNucleotidePolymorphismRepository.findByRsId(snpRsId);
        if (snpInDatabase == null) {
            snpInDatabase = singleNucleotidePolymorphismQueryService.findByRsIdIgnoreCase(snpRsId);
        }
        if (snpInDatabase != null) {
            Collection<GenomicContext> newSnpGenomicContexts = new ArrayList<>();
            for (GenomicContext genomicContextFromMapping : genomicContextsFromMapping) {
                // Gene should already have been created
                String geneName = genomicContextFromMapping.getGene().getGeneName().trim();
                if (!geneName.equalsIgnoreCase("undefined")) {
                    // Create new genomic context
                    Boolean isIntergenic = genomicContextFromMapping.getIsIntergenic();
                    Boolean isUpstream = genomicContextFromMapping.getIsUpstream();
                    Boolean isDownstream = genomicContextFromMapping.getIsDownstream();
                    Long distance = genomicContextFromMapping.getDistance();
                    String source = genomicContextFromMapping.getSource();
                    String mappingMethod = genomicContextFromMapping.getMappingMethod();
                    Boolean isClosestGene = genomicContextFromMapping.getIsClosestGene();
                    // Location details
                    String chromosomeName = genomicContextFromMapping.getLocation().getChromosomeName();
                    Integer chromosomePosition = genomicContextFromMapping.getLocation().getChromosomePosition();
                    Region regionFromMapping = genomicContextFromMapping.getLocation().getRegion();
                    String regionName = null;
                    if (regionFromMapping.getName() != null) {
                        regionName = regionFromMapping.getName().trim();
                    }
                    // Check if location already exists
                    Location location = locationRepository.findByChromosomeNameAndChromosomePositionAndRegionName(chromosomeName, chromosomePosition, regionName);
                    if (location == null) {
                        location = locationCreationService.createLocation(chromosomeName, chromosomePosition, regionName);
                    }
                    GenomicContext genomicContext = genomicContextCreationService.createGenomicContext(isIntergenic, isUpstream, isDownstream, distance, source, mappingMethod, geneName, snpInDatabase, isClosestGene, location);
                    newSnpGenomicContexts.add(genomicContext);
                } else {
                    getLog().warn("Gene name returned from mapping pipeline is 'undefined' for SNP" + snpInDatabase.getRsId());
                }
            }
            // Save latest mapped information
            snpInDatabase.setGenomicContexts(newSnpGenomicContexts);
            // Update the last update date
            snpInDatabase.setLastUpdateDate(new Date());
            // singleNucleotidePolymorphismRepository.save(snpInDatabase);
            updatedSnps.add(snpInDatabase);
        } else // SNP doesn't exist, this should be extremely rare as SNP value is a copy
        // of the variant entered by the curator which
        // by the time mapping is started should already have been saved
        {
            // TODO WHAT WILL HAPPEN FOR MERGED SNPS
            getLog().error("Adding genomic context for SNP not found in database, RS_ID:" + snpRsId);
            throw new RuntimeException("Adding genomic context for SNP not found in database, RS_ID: " + snpRsId);
        }
    }
    singleNucleotidePolymorphismRepository.save(updatedSnps);
}

Example 3 with SingleNucleotidePolymorphism

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

the class AssociationService method loadAssociatedData.

@Transactional(readOnly = true)
public void loadAssociatedData(Association association) {
    int traitCount = association.getEfoTraits().size();
    // Study study = studyService.fetchOne(association.getStudy());
    Study study = association.getStudy();
    AtomicInteger reportedGeneCount = new AtomicInteger();
    Collection<SingleNucleotidePolymorphism> snps = new HashSet<>();
    Collection<SingleNucleotidePolymorphism> proxySnps = new HashSet<>();
    Collection<Region> regions = new HashSet<>();
    Collection<Gene> mappedGenes = new HashSet<>();
    // Map<String, Set<String>> mappedGeneEntrezIds = new HashMap<>();
    Map<String, Set<String>> mappedGeneEnsemblIds = new HashMap<>();
    association.getLoci().forEach(locus -> {
        locus.getStrongestRiskAlleles().stream().map(RiskAllele::getSnp).forEach(snp -> {
            Collection<Location> snpLocations = snp.getLocations();
            for (Location location : snpLocations) {
                regions.add(location.getRegion());
            }
            snp.getGenomicContexts().forEach(context -> {
                mappedGenes.add(context.getGene());
                String geneName = context.getGene().getGeneName();
                Collection<EntrezGene> geneEntrezGeneIds = context.getGene().getEntrezGeneIds();
                Collection<EnsemblGene> geneEnsemblGeneIds = context.getGene().getEnsemblGeneIds();
                if (mappedGeneEnsemblIds.containsKey(geneName)) {
                    for (EnsemblGene ensemblGene : geneEnsemblGeneIds) {
                        mappedGeneEnsemblIds.get(geneName).add(ensemblGene.getEnsemblGeneId());
                    }
                } else // First time we see a SNP store the location
                {
                    Set<String> ensemblIds = new HashSet<>();
                    for (EnsemblGene ensemblGene : geneEnsemblGeneIds) {
                        ensemblIds.add(ensemblGene.getEnsemblGeneId());
                    }
                    // mappedGeneEntrezIds.put(geneName,
                    // ensemblIds);
                    mappedGeneEnsemblIds.put(geneName, ensemblIds);
                }
            });
            snps.add(snp);
        });
        snps.addAll(locus.getStrongestRiskAlleles().stream().map(RiskAllele::getSnp).collect(Collectors.toList()));
        locus.getStrongestRiskAlleles().forEach(riskAllele -> {
            if (riskAllele.getProxySnps() != null) {
                proxySnps.addAll(riskAllele.getProxySnps());
            }
        });
        reportedGeneCount.addAndGet(locus.getAuthorReportedGenes().size());
        locus.getAuthorReportedGenes().forEach(authorReportedGene -> {
            authorReportedGene.getEnsemblGeneIds().size();
        // authorReportedGene.getEntrezGeneIds().size();
        });
    });
    getLog().trace("Association '" + association.getId() + "' is mapped to " + "" + traitCount + " EFO traits where study id = " + study.getId() + " " + "(author reported " + reportedGeneCount + " gene(s)); " + "this reports on " + snps.size() + " SNPs in " + regions.size() + " regions, " + "mapped to " + mappedGenes.size() + " genes.");
}

Example 4 with SingleNucleotidePolymorphism

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

the class FilteringTest method testFilter.

@Test
public void testFilter() {
    SingleNucleotidePolymorphism template = template(SingleNucleotidePolymorphism.class);
    Filter<SingleNucleotidePolymorphism, String> filter = refine(template).on(template.getRsId()).hasValue("rs123456");
    assertEquals("Filter type does not match expected", SingleNucleotidePolymorphism.class, filter.getFilteredType());
    assertEquals("Filtered method does not match expected", "getRsId", filter.getFilteredMethod().getName());
    assertEquals("Filtered value does not match expected", "rs123456", filter.getFilteredValues().get(0));
    Association template2 = template(Association.class);
    Filter<Association, Float> filter2 = refine(template2).on(template2.getPvalueMantissa()).hasValue(Float.valueOf("10"));
    assertEquals("Filter type does not match expected", Association.class, filter2.getFilteredType());
    assertEquals("Filtered method does not match expected", "getPvalueMantissa", filter2.getFilteredMethod().getName());
    assertEquals(Float.valueOf("10"), filter2.getFilteredValues().get(0), 0.0d);
    DateFormat df1 = new SimpleDateFormat("yyyy-MM-dd");
    DateFormat df2 = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.S");
    Date from = null;
    Date to = null;
    try {
        from = df1.parse("2005-01-01");
        to = df1.parse("2010-01-01");
    } catch (ParseException e) {
        e.printStackTrace();
    }
    String fromValue = df2.format(from).toString();
    String toValue = df2.format(to).toString();
    System.out.println(fromValue);
    System.out.println(toValue);
    Publication publication = template(Publication.class);
    Filter dateFilter = refine(publication).on(publication.getPublicationDate()).hasRange(fromValue, toValue);
    Filter dateFilter2 = refine(publication).on(publication.getPublicationDate()).hasRange(fromValue, toValue);
    assertEquals("Filter type does not match expected", Publication.class, dateFilter.getFilteredType());
    assertEquals("Filtered method does not match expected", "getPublicationDate", dateFilter.getFilteredMethod().getName());
    assertEquals("Filtered value does not match expected", "2010-01-01T00:00:00.0", dateFilter.getFilteredRange().to());
    assertEquals("Hashcodes of the two date filters differ", dateFilter.hashCode(), dateFilter2.hashCode());
}

Example 5 with SingleNucleotidePolymorphism

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

the class AssociationAttributeService method createSnp.

public SingleNucleotidePolymorphism createSnp(String curatorEnteredSNP) {
    curatorEnteredSNP = StringProcessingService.tidy_curator_entered_string(curatorEnteredSNP);
    SingleNucleotidePolymorphism snp = new SingleNucleotidePolymorphism();
    snp.setRsId(curatorEnteredSNP);
    return snp;
}