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

Example 21 with SingleNucleotidePolymorphism

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

the class SingleSnpMultiSnpAssociationService method createAssociation.

public Association createAssociation(SnpAssociationStandardMultiForm form) {
    // Set common string, boolean and float association attributes
    Association association = setCommonAssociationElements(form);
    association.setSnpInteraction(false);
    // Add loci to association, for multi-snp and standard snps we assume their is only one locus
    Collection<Locus> loci = new ArrayList<>();
    Locus locus = new Locus();
    // Set locus description and haplotype count
    // Set this number to the number of rows entered by curator
    Integer numberOfRows = form.getSnpFormRows().size();
    if (numberOfRows > 1) {
        locus.setHaplotypeSnpCount(numberOfRows);
        association.setMultiSnpHaplotype(true);
    }
    if (form.getMultiSnpHaplotypeDescr() != null && !form.getMultiSnpHaplotypeDescr().isEmpty()) {
        locus.setDescription(form.getMultiSnpHaplotypeDescr());
    } else {
        if (numberOfRows > 1) {
            locus.setDescription(numberOfRows + "-SNP haplotype");
        } else {
            locus.setDescription("Single variant");
        }
    }
    // Create gene from each string entered, may sure to check pre-existence
    Collection<String> authorReportedGenes = form.getAuthorReportedGenes();
    Collection<Gene> locusGenes = lociAttributesService.createGene(authorReportedGenes);
    // Set locus genes
    locus.setAuthorReportedGenes(locusGenes);
    // Handle rows entered for haplotype by curator
    Collection<SnpFormRow> rows = form.getSnpFormRows();
    Collection<RiskAllele> locusRiskAlleles = new ArrayList<>();
    for (SnpFormRow row : rows) {
        // Create snps from row information
        String curatorEnteredSNP = row.getSnp();
        SingleNucleotidePolymorphism snp = lociAttributesService.createSnp(curatorEnteredSNP);
        // Get the curator entered risk allele
        String curatorEnteredRiskAllele = row.getStrongestRiskAllele();
        // Create a new risk allele and assign newly created snp
        RiskAllele riskAllele = lociAttributesService.createRiskAllele(curatorEnteredRiskAllele, snp);
        // If association is not a multi-snp haplotype save frequency to risk allele
        if (!form.getMultiSnpHaplotype()) {
            riskAllele.setRiskFrequency(form.getRiskFrequency());
        }
        // Check for proxies and if we have one create a proxy snps
        if (row.getProxySnps() != null && !row.getProxySnps().isEmpty()) {
            Collection<SingleNucleotidePolymorphism> riskAlleleProxySnps = new ArrayList<>();
            for (String curatorEnteredProxySnp : row.getProxySnps()) {
                SingleNucleotidePolymorphism proxySnp = lociAttributesService.createSnp(curatorEnteredProxySnp);
                riskAlleleProxySnps.add(proxySnp);
            }
            riskAllele.setProxySnps(riskAlleleProxySnps);
        }
        locusRiskAlleles.add(riskAllele);
    }
    // Assign all created risk alleles to locus
    locus.setStrongestRiskAlleles(locusRiskAlleles);
    // Add locus to collection and link to our association
    loci.add(locus);
    association.setLoci(loci);
    return association;
}

Example 22 with SingleNucleotidePolymorphism

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

the class SnpInteractionAssociationService method createAssociation.

public Association createAssociation(SnpAssociationInteractionForm form) {
    // Set simple string, boolean and float association attributes
    Association association = setCommonAssociationElements(form);
    // Set multi-snp and snp interaction checkboxes
    association.setMultiSnpHaplotype(false);
    association.setSnpInteraction(true);
    // For each column create a loci
    Collection<Locus> loci = new ArrayList<>();
    for (SnpFormColumn col : form.getSnpFormColumns()) {
        Locus locus = new Locus();
        locus.setDescription("SNP x SNP interaction");
        // Set locus genes
        Collection<String> authorReportedGenes = col.getAuthorReportedGenes();
        Collection<Gene> locusGenes = lociAttributesService.createGene(authorReportedGenes);
        locus.setAuthorReportedGenes(locusGenes);
        // Create SNP
        String curatorEnteredSNP = col.getSnp();
        SingleNucleotidePolymorphism snp = lociAttributesService.createSnp(curatorEnteredSNP);
        // One risk allele per locus
        String curatorEnteredRiskAllele = col.getStrongestRiskAllele();
        RiskAllele riskAllele = lociAttributesService.createRiskAllele(curatorEnteredRiskAllele, snp);
        Collection<RiskAllele> locusRiskAlleles = new ArrayList<>();
        // Set risk allele attributes
        riskAllele.setGenomeWide(col.getGenomeWide());
        riskAllele.setLimitedList(col.getLimitedList());
        riskAllele.setRiskFrequency(col.getRiskFrequency());
        // Check for a proxy and if we have one create a proxy snp
        Collection<String> curatorEnteredProxySnps = col.getProxySnps();
        if (curatorEnteredProxySnps != null && !curatorEnteredProxySnps.isEmpty()) {
            Collection<SingleNucleotidePolymorphism> riskAlleleProxySnps = new ArrayList<>();
            for (String curatorEnteredProxySnp : curatorEnteredProxySnps) {
                SingleNucleotidePolymorphism proxySnp = lociAttributesService.createSnp(curatorEnteredProxySnp);
                riskAlleleProxySnps.add(proxySnp);
            }
            riskAllele.setProxySnps(riskAlleleProxySnps);
        }
        // Link risk allele to locus
        locusRiskAlleles.add(riskAllele);
        locus.setStrongestRiskAlleles(locusRiskAlleles);
        // Add locus to collection and link to our association
        loci.add(locus);
    }
    association.setLoci(loci);
    return association;
}

Example 23 with SingleNucleotidePolymorphism

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

the class AssociationDownloadService method extractGeneticData.

private void extractGeneticData(Association association, StringBuilder line) {
    final StringBuilder strongestAllele = new StringBuilder();
    final StringBuilder reportedGenes = new StringBuilder();
    final StringBuilder rsId = new StringBuilder();
    final StringBuilder proxySnpsRsIds = new StringBuilder();
    final StringBuilder riskAlleleFrequency = new StringBuilder();
    // Set our delimiter for download spreadsheet
    final String delimiter;
    if (association.getSnpInteraction() != null && association.getSnpInteraction()) {
        delimiter = " x ";
    } else {
        delimiter = "; ";
    }
    // Interaction specific values
    if (association.getSnpInteraction() != null && association.getSnpInteraction()) {
        association.getLoci().forEach(locus -> {
            Collection<RiskAllele> ra = locus.getStrongestRiskAlleles().stream().sorted((v1, v2) -> Long.compare(v1.getId(), v2.getId())).collect(Collectors.toList());
            ra.forEach(riskAllele -> {
                if (riskAllele.getRiskFrequency() != null && !riskAllele.getRiskFrequency().isEmpty()) {
                    String frequency = riskAllele.getRiskFrequency();
                    setOrAppend(riskAlleleFrequency, frequency, delimiter);
                } else {
                    setOrAppend(riskAlleleFrequency, "NR", delimiter);
                }
            });
            Collection<String> currentLocusGenes = new ArrayList<>();
            String commaSeparatedGenes = "";
            locus.getAuthorReportedGenes().forEach(gene -> {
                currentLocusGenes.add(gene.getGeneName().trim());
            });
            if (!currentLocusGenes.isEmpty()) {
                commaSeparatedGenes = String.join(", ", currentLocusGenes);
                setOrAppend(reportedGenes, commaSeparatedGenes, delimiter);
            } else {
                setOrAppend(reportedGenes, "NR", delimiter);
            }
        });
    } else {
        // Single study or a haplotype
        association.getLoci().forEach(locus -> {
            Collection<RiskAllele> ra = locus.getStrongestRiskAlleles().stream().sorted((v1, v2) -> Long.compare(v1.getId(), v2.getId())).collect(Collectors.toList());
            ra.forEach(riskAllele -> {
                setOrAppend(riskAlleleFrequency, "", "");
            });
            locus.getAuthorReportedGenes().forEach(gene -> {
                setOrAppend(reportedGenes, gene.getGeneName().trim(), ", ");
            });
        });
    }
    // Set attributes common to all associations
    association.getLoci().forEach(locus -> {
        Collection<RiskAllele> ra = locus.getStrongestRiskAlleles().stream().sorted((v1, v2) -> Long.compare(v1.getId(), v2.getId())).collect(Collectors.toList());
        ra.forEach(riskAllele -> {
            setOrAppend(strongestAllele, riskAllele.getRiskAlleleName(), delimiter);
            SingleNucleotidePolymorphism snp = riskAllele.getSnp();
            setOrAppend(rsId, snp.getRsId(), delimiter);
            Collection<String> currentLocusProxies = new ArrayList<>();
            String colonSeparatedProxies = "";
            if (riskAllele.getProxySnps() != null) {
                for (SingleNucleotidePolymorphism proxySnp : riskAllele.getProxySnps()) {
                    currentLocusProxies.add(proxySnp.getRsId());
                }
            }
            if (!currentLocusProxies.isEmpty()) {
                colonSeparatedProxies = String.join(", ", currentLocusProxies);
                setOrAppend(proxySnpsRsIds, colonSeparatedProxies, delimiter);
            } else {
                setOrAppend(proxySnpsRsIds, "NR", delimiter);
            }
        });
    });
    line.append(reportedGenes.toString());
    line.append("\t");
    line.append(strongestAllele.toString());
    line.append("\t");
    line.append(rsId.toString());
    line.append("\t");
    line.append(proxySnpsRsIds.toString());
    line.append("\t");
    line.append(riskAlleleFrequency.toString());
    line.append("\t");
}

Example 24 with SingleNucleotidePolymorphism

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

the class AssociationEventsViewService method createViews.

@Override
public List<EventView> createViews(Long studyId) {
    List<EventView> views = new ArrayList<>();
    Collection<Association> associations = studyRepository.findOne(studyId).getAssociations();
    if (!associations.isEmpty()) {
        // For each association gather up the events into a collection of views
        associations.forEach(association -> {
            Collection<Event> events = association.getEvents();
            Long associationId = association.getId();
            Collection<SingleNucleotidePolymorphism> snps = singleNucleotidePolymorphismRepository.findByRiskAllelesLociAssociationId(associationId);
            String associationSummary;
            StringJoiner snpJoiner = new StringJoiner(", ");
            snps.forEach(singleNucleotidePolymorphism -> {
                snpJoiner.add(singleNucleotidePolymorphism.getRsId());
            });
            associationSummary = snpJoiner.toString();
            events.forEach(event -> {
                String eventName = eventTypeService.translateEventByEventType(event.getEventType());
                EventView eventView = new AssociationEventView(eventName, event.getEventDate(), associationId, event.getUser().getEmail(), associationSummary);
                views.add(eventView);
            });
        });
    }
    return views;
}