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

Example 1 with SnpMappingForm

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

the class SnpInteractionAssociationService method createForm.

// Create a form to return to view from Association model object
@Override
public SnpAssociationForm createForm(Association association) {
    // Create form
    SnpAssociationInteractionForm form = new SnpAssociationInteractionForm();
    // Set simple string and boolean values
    form.setAssociationId(association.getId());
    form.setAssociationExtension(association.getAssociationExtension());
    form.setPvalueDescription(association.getPvalueDescription());
    form.setSnpType(association.getSnpType());
    form.setSnpApproved(association.getSnpApproved());
    form.setPvalueMantissa(association.getPvalueMantissa());
    form.setPvalueExponent(association.getPvalueExponent());
    form.setStandardError(association.getStandardError());
    form.setRange(association.getRange());
    form.setDescription(association.getDescription());
    form.setRiskFrequency(association.getRiskFrequency());
    // Set OR/Beta values
    form.setOrPerCopyNum(association.getOrPerCopyNum());
    form.setOrPerCopyRecip(association.getOrPerCopyRecip());
    form.setOrPerCopyRecipRange(association.getOrPerCopyRecipRange());
    form.setBetaNum(association.getBetaNum());
    form.setBetaUnit(association.getBetaUnit());
    form.setBetaDirection(association.getBetaDirection());
    // Add collection of Efo traits
    form.setEfoTraits(association.getEfoTraits());
    // Create form columns
    List<SnpFormColumn> snpFormColumns = new ArrayList<>();
    // For each locus get genes and risk alleles
    Collection<Locus> loci = association.getLoci();
    Collection<GenomicContext> snpGenomicContexts = new ArrayList<GenomicContext>();
    Collection<SingleNucleotidePolymorphism> snps = new ArrayList<SingleNucleotidePolymorphism>();
    List<SnpMappingForm> snpMappingForms = new ArrayList<SnpMappingForm>();
    // Create a column per locus
    if (loci != null && !loci.isEmpty()) {
        for (Locus locus : loci) {
            SnpFormColumn snpFormColumn = new SnpFormColumn();
            // Set genes
            Collection<String> authorReportedGenes = new ArrayList<>();
            for (Gene gene : locus.getAuthorReportedGenes()) {
                authorReportedGenes.add(gene.getGeneName());
            }
            snpFormColumn.setAuthorReportedGenes(authorReportedGenes);
            // Set risk allele
            Collection<RiskAllele> locusRiskAlleles = locus.getStrongestRiskAlleles();
            String strongestRiskAllele = null;
            String snp = null;
            Collection<String> proxySnps = new ArrayList<>();
            Boolean genomeWide = false;
            Boolean limitedList = false;
            String riskFrequency = null;
            // For snp x snp interaction studies should only have one risk allele per locus
            if (locusRiskAlleles != null && locusRiskAlleles.size() == 1) {
                for (RiskAllele riskAllele : locusRiskAlleles) {
                    strongestRiskAllele = riskAllele.getRiskAlleleName();
                    snp = riskAllele.getSnp().getRsId();
                    SingleNucleotidePolymorphism snp_obj = riskAllele.getSnp();
                    snps.add(snp_obj);
                    Collection<Location> locations = snp_obj.getLocations();
                    for (Location location : locations) {
                        SnpMappingForm snpMappingForm = new SnpMappingForm(snp, location);
                        snpMappingForms.add(snpMappingForm);
                    }
                    snpGenomicContexts.addAll(genomicContextRepository.findBySnpId(snp_obj.getId()));
                    // Set proxy
                    if (riskAllele.getProxySnps() != null) {
                        for (SingleNucleotidePolymorphism riskAlleleProxySnp : riskAllele.getProxySnps()) {
                            proxySnps.add(riskAlleleProxySnp.getRsId());
                        }
                    }
                    if (riskAllele.getGenomeWide() != null && riskAllele.getGenomeWide()) {
                        genomeWide = true;
                    }
                    if (riskAllele.getLimitedList() != null && riskAllele.getLimitedList()) {
                        limitedList = true;
                    }
                    riskFrequency = riskAllele.getRiskFrequency();
                }
            } else {
                throw new RuntimeException("More than one risk allele found for locus " + locus.getId() + ", this is not supported yet for SNP interaction associations");
            }
            // Set column attributes
            snpFormColumn.setStrongestRiskAllele(strongestRiskAllele);
            snpFormColumn.setSnp(snp);
            snpFormColumn.setProxySnps(proxySnps);
            snpFormColumn.setGenomeWide(genomeWide);
            snpFormColumn.setLimitedList(limitedList);
            snpFormColumn.setRiskFrequency(riskFrequency);
            snpFormColumns.add(snpFormColumn);
        }
    }
    form.setSnpMappingForms(snpMappingForms);
    form.setGenomicContexts(snpGenomicContexts);
    form.setSnps(snps);
    form.setSnpFormColumns(snpFormColumns);
    form.setNumOfInteractions(snpFormColumns.size());
    return form;
}

Example 2 with SnpMappingForm

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

the class SingleSnpMultiSnpAssociationService method createForm.

// Creates form which we can then return to view for editing etc.
@Override
public SnpAssociationForm createForm(Association association) {
    SnpAssociationStandardMultiForm form = new SnpAssociationStandardMultiForm();
    // Set association ID
    form.setAssociationId(association.getId());
    form.setAssociationExtension(association.getAssociationExtension());
    // Set simple string and float association attributes
    form.setRiskFrequency(association.getRiskFrequency());
    form.setPvalueDescription(association.getPvalueDescription());
    form.setSnpType(association.getSnpType());
    form.setMultiSnpHaplotype(association.getMultiSnpHaplotype());
    form.setSnpApproved(association.getSnpApproved());
    form.setPvalueMantissa(association.getPvalueMantissa());
    form.setPvalueExponent(association.getPvalueExponent());
    form.setStandardError(association.getStandardError());
    form.setRange(association.getRange());
    form.setDescription(association.getDescription());
    // Set OR/Beta values
    form.setOrPerCopyNum(association.getOrPerCopyNum());
    form.setOrPerCopyRecip(association.getOrPerCopyRecip());
    form.setOrPerCopyRecipRange(association.getOrPerCopyRecipRange());
    form.setBetaNum(association.getBetaNum());
    form.setBetaUnit(association.getBetaUnit());
    form.setBetaDirection(association.getBetaDirection());
    // Add collection of Efo traits
    form.setEfoTraits(association.getEfoTraits());
    // For each locus get genes and risk alleles
    Collection<Locus> loci = association.getLoci();
    Collection<Gene> locusGenes = new ArrayList<>();
    Collection<RiskAllele> locusRiskAlleles = new ArrayList<RiskAllele>();
    // For multi-snp and standard snps we assume their is only one locus
    for (Locus locus : loci) {
        locusGenes.addAll(locus.getAuthorReportedGenes());
        locusRiskAlleles.addAll(locus.getStrongestRiskAlleles().stream().sorted((v1, v2) -> Long.compare(v1.getId(), v2.getId())).collect(Collectors.toList()));
        // There should only be one locus thus should be safe to set these here
        form.setMultiSnpHaplotypeNum(locus.getHaplotypeSnpCount());
        form.setMultiSnpHaplotypeDescr(locus.getDescription());
    }
    // Get name of gene and add to form
    Collection<String> authorReportedGenes = new ArrayList<>();
    for (Gene locusGene : locusGenes) {
        authorReportedGenes.add(locusGene.getGeneName());
    }
    form.setAuthorReportedGenes(authorReportedGenes);
    // Handle snp rows
    Collection<GenomicContext> snpGenomicContexts = new ArrayList<GenomicContext>();
    Collection<SingleNucleotidePolymorphism> snps = new ArrayList<>();
    List<SnpFormRow> snpFormRows = new ArrayList<SnpFormRow>();
    List<SnpMappingForm> snpMappingForms = new ArrayList<SnpMappingForm>();
    for (RiskAllele riskAllele : locusRiskAlleles) {
        SnpFormRow snpFormRow = new SnpFormRow();
        snpFormRow.setStrongestRiskAllele(riskAllele.getRiskAlleleName());
        SingleNucleotidePolymorphism snp = riskAllele.getSnp();
        snps.add(snp);
        String rsID = snp.getRsId();
        snpFormRow.setSnp(rsID);
        Collection<Location> locations = snp.getLocations();
        for (Location location : locations) {
            SnpMappingForm snpMappingForm = new SnpMappingForm(rsID, location);
            snpMappingForms.add(snpMappingForm);
        }
        // Set proxy if one is present
        Collection<String> proxySnps = new ArrayList<>();
        if (riskAllele.getProxySnps() != null) {
            for (SingleNucleotidePolymorphism riskAlleleProxySnp : riskAllele.getProxySnps()) {
                proxySnps.add(riskAlleleProxySnp.getRsId());
            }
        }
        snpFormRow.setProxySnps(proxySnps);
        snpGenomicContexts.addAll(genomicContextRepository.findBySnpId(snp.getId()));
        snpFormRows.add(snpFormRow);
    }
    form.setSnpMappingForms(snpMappingForms);
    form.setGenomicContexts(snpGenomicContexts);
    form.setSnps(snps);
    form.setSnpFormRows(snpFormRows);
    return form;
}