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

Example 16 with SingleNucleotidePolymorphism

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

the class AssociationRowProcessor method createLocusRiskAlleles.

private Collection<RiskAllele> createLocusRiskAlleles(String strongestAllele, String snp, String proxy, String riskFrequency, String snpStatus, String delimiter) {
    Collection<RiskAllele> locusRiskAlleles = new ArrayList<>();
    // For our list of snps, proxies and risk alleles separate by delimiter
    List<String> snps = new ArrayList<>();
    String[] separatedSnps = snp.split(delimiter);
    for (String separatedSnp : separatedSnps) {
        //            if(separatedSnp != null & separatedSnp.trim().equals("")) {
        snps.add(separatedSnp.trim());
    //            }
    }
    List<String> riskAlleles = new ArrayList<>();
    String[] separatedRiskAlleles = strongestAllele.split(delimiter);
    for (String separatedRiskAllele : separatedRiskAlleles) {
        //            if(separatedRiskAllele != null & separatedRiskAllele.trim().equals("")) {
        riskAlleles.add(separatedRiskAllele.trim());
    //            }
    }
    List<String> proxies = new ArrayList<>();
    if (proxy != null) {
        String[] separatedProxies = proxy.split(delimiter);
        for (String separatedProxy : separatedProxies) {
            //                if(separatedProxy != null & separatedProxy.trim().equals("")) {
            proxies.add(separatedProxy.trim());
        //                }
        }
    }
    // Value is only recorded for SNP interaction associations
    List<String> riskFrequencies = new ArrayList<>();
    Iterator<String> riskFrequencyIterator = null;
    if (riskFrequency != null) {
        String[] separatedRiskFrequencies = riskFrequency.split(delimiter);
        for (String separatedRiskFrequency : separatedRiskFrequencies) {
            riskFrequencies.add(separatedRiskFrequency.trim());
        }
        riskFrequencyIterator = riskFrequencies.iterator();
    }
    // Snp status
    List<String> snpStatuses = new ArrayList<>();
    Iterator<String> snpStatusIterator = null;
    if (snpStatus != null) {
        String[] separatedSnpStatuses = snpStatus.split(delimiter);
        for (String separatedSnpStatus : separatedSnpStatuses) {
            snpStatuses.add(separatedSnpStatus.trim());
        }
        snpStatusIterator = snpStatuses.iterator();
    }
    Iterator<String> riskAlleleIterator = riskAlleles.iterator();
    Iterator<String> snpIterator = snps.iterator();
    Iterator<String> proxyIterator = proxies.iterator();
    // Loop through our risk alleles
    if (riskAlleles.size() == snps.size()) {
        while (riskAlleleIterator.hasNext()) {
            String snpValue = snpIterator.next().trim();
            String riskAlleleValue = riskAlleleIterator.next().trim();
            SingleNucleotidePolymorphism newSnp = associationAttributeService.createSnp(snpValue);
            // Create a new risk allele and assign newly created snp
            RiskAllele newRiskAllele = associationAttributeService.createRiskAllele(riskAlleleValue, newSnp);
            // Check for proxies and if we have one create a proxy snp
            if (proxies.size() != 0) {
                if (proxies.size() == snps.size()) {
                    String proxyValue = proxyIterator.next().trim();
                    Collection<SingleNucleotidePolymorphism> newRiskAlleleProxies = new ArrayList<>();
                    //                        else
                    if (proxyValue.contains(",")) {
                        String[] splitProxyValues = proxyValue.split(",");
                        for (String splitProxyValue : splitProxyValues) {
                            SingleNucleotidePolymorphism proxySnp = associationAttributeService.createSnp(splitProxyValue.trim());
                            newRiskAlleleProxies.add(proxySnp);
                        }
                    } else {
                        SingleNucleotidePolymorphism proxySnp = associationAttributeService.createSnp(proxyValue);
                        newRiskAlleleProxies.add(proxySnp);
                    }
                    newRiskAllele.setProxySnps(newRiskAlleleProxies);
                } else {
                    getLog().error("Proxy SNP number and SNP number do not match");
                }
            }
            // If there is no curator entered value for risk allele frequency don't save
            String riskFrequencyValue = null;
            if (riskFrequencyIterator != null) {
                riskFrequencyValue = riskFrequencyIterator.next().trim();
            }
            if (riskFrequencyValue != null) {
                newRiskAllele.setRiskFrequency(riskFrequencyValue);
            }
            // Handle snp statuses, these should only apply to SNP interaction associations
            String snpStatusValue = null;
            if (snpStatusIterator != null) {
                snpStatusValue = snpStatusIterator.next().trim();
            }
            if (snpStatus != null && !snpStatus.equalsIgnoreCase("NR")) {
                if (snpStatusValue.contains("GW") || snpStatusValue.contains("gw")) {
                    newRiskAllele.setGenomeWide(true);
                }
                if (snpStatusValue.contains("LL") || snpStatusValue.contains("ll")) {
                    newRiskAllele.setLimitedList(true);
                }
            }
            locusRiskAlleles.add(newRiskAllele);
        }
    } else {
        getLog().error("Mismatched number of snps and risk alleles");
    }
    return locusRiskAlleles;
}

Example 17 with SingleNucleotidePolymorphism

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

the class PussycatGOCIController method renderSNP.

@RequestMapping(value = "/snps/{rsID}")
@ResponseBody
public String renderSNP(@PathVariable String rsID, HttpSession session) throws PussycatSessionNotReadyException, NoRenderableDataException {
    SingleNucleotidePolymorphism snp = template(SingleNucleotidePolymorphism.class);
    Filter filter = refine(snp).on(snp.getRsId()).hasValue(rsID);
    return getPussycatSession(session).performRendering(getRenderletNexus(session), filter);
}

Example 18 with SingleNucleotidePolymorphism

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

the class SnpGetter method getSnpRsIdList.

public Collection<String> getSnpRsIdList() {
    Collection<String> rsIds = new ArrayList<>();
    SingleNucleotidePolymorphismService snpService = getSingleNucleotidePolymorphismService();
    List<SingleNucleotidePolymorphism> snps = snpService.findAll();
    for (SingleNucleotidePolymorphism snp : snps) {
        rsIds.add(snp.getRsId());
    }
    return rsIds;
}

Example 19 with SingleNucleotidePolymorphism

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

the class TestFiltering 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);
    Study study = template(Study.class);
    Filter dateFilter = refine(study).on(study.getPublicationDate()).hasRange(fromValue, toValue);
    Filter dateFilter2 = refine(study).on(study.getPublicationDate()).hasRange(fromValue, toValue);
    assertEquals("Filter type does not match expected", Study.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 20 with SingleNucleotidePolymorphism

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

the class LociAttributesService method saveRiskAlleles.

public Collection<RiskAllele> saveRiskAlleles(Collection<RiskAllele> strongestRiskAlleles) {
    //Create new risk allele, at present we always create a new risk allele for each locus within an association
    Collection<RiskAllele> riskAlleles = new ArrayList<RiskAllele>();
    strongestRiskAlleles.forEach(riskAllele -> {
        getLog().info("Saving " + riskAllele.getRiskAlleleName());
        SingleNucleotidePolymorphism savedSnp = saveSnp(riskAllele.getSnp());
        riskAllele.setSnp(savedSnp);
        Collection<SingleNucleotidePolymorphism> savedProxySnps = new ArrayList<SingleNucleotidePolymorphism>();
        if (riskAllele.getProxySnps() != null && !riskAllele.getProxySnps().isEmpty()) {
            riskAllele.getProxySnps().forEach(singleNucleotidePolymorphism -> {
                savedProxySnps.add(saveSnp(singleNucleotidePolymorphism));
            });
        }
        riskAllele.setProxySnps(savedProxySnps);
        riskAlleleRepository.save(riskAllele);
        riskAlleles.add(riskAllele);
    });
    return riskAlleles;
}