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

Example 6 with SingleNucleotidePolymorphism

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

the class AssociationService method loadAssociatedData.

public void loadAssociatedData(Association association) {
    int traitCount = association.getEfoTraits().size();
    Study study = studyService.fetchOne(association.getStudy());
    AtomicInteger reportedGeneCount = new AtomicInteger();
    Collection<SingleNucleotidePolymorphism> snps = 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 (mappedGeneEntrezIds.containsKey(geneName)) {
                    for (EntrezGene entrezGene : geneEntrezGeneIds) {
                        mappedGeneEntrezIds.get(geneName).add(entrezGene.getEntrezGeneId());
                    }
                } else {
                    Set<String> entrezIds = new HashSet<>();
                    for (EntrezGene entrezGene : geneEntrezGeneIds) {
                        entrezIds.add(entrezGene.getEntrezGeneId());
                    }
                    mappedGeneEntrezIds.put(geneName, entrezIds);
                }
                if (mappedGeneEnsemblIds.containsKey(geneName)) {
                    for (EnsemblGene ensemblGene : geneEnsemblGeneIds) {
                        mappedGeneEnsemblIds.get(geneName).add(ensemblGene.getEnsemblGeneId());
                    }
                } else {
                    Set<String> ensemblIds = new HashSet<>();
                    for (EnsemblGene ensemblGene : geneEnsemblGeneIds) {
                        ensemblIds.add(ensemblGene.getEnsemblGeneId());
                    }
                    mappedGeneEntrezIds.put(geneName, ensemblIds);
                }
            });
            snps.add(snp);
        });
        snps.addAll(locus.getStrongestRiskAlleles().stream().map(RiskAllele::getSnp).collect(Collectors.toList()));
        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 7 with SingleNucleotidePolymorphism

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

the class LociAttributesService method createSnp.

public SingleNucleotidePolymorphism createSnp(String curatorEnteredSNP) {
    // Create new SNP
    SingleNucleotidePolymorphism newSNP = new SingleNucleotidePolymorphism();
    newSNP.setRsId(tidy_curator_entered_string(curatorEnteredSNP));
    return newSNP;
}

Example 8 with SingleNucleotidePolymorphism

use of uk.ac.ebi.spot.goci.model.SingleNucleotidePolymorphism 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());
    // 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;
}

Example 9 with SingleNucleotidePolymorphism

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

the class SnpAssociationTableViewService method createSnpAssociationTableView.

/**
     * Create object, from Association, that will be returned to view
     *
     * @param association Association object
     */
public SnpAssociationTableView createSnpAssociationTableView(Association association) {
    SnpAssociationTableView snpAssociationTableView = new SnpAssociationTableView();
    // For SNP interaction studies snp, proxy snps, risk alleles etc
    // should be separated by an 'x'
    String delimiter = "; ";
    if (association.getSnpInteraction()) {
        delimiter = " x ";
    }
    snpAssociationTableView.setAssociationId(association.getId());
    // For each locus relevant attributes
    Collection<Locus> loci = association.getLoci();
    Collection<String> allLociGenes = new ArrayList<>();
    Collection<String> allLociRiskAlleles = new ArrayList<String>();
    Collection<String> allLociSnps = new ArrayList<String>();
    Collection<String> allLociProxySnps = new ArrayList<String>();
    Collection<String> allLociRiskAlleleFrequencies = new ArrayList<String>();
    Collection<String> allLociSnpStatuses = new ArrayList<String>();
    // By looking at each locus in turn we can keep order in view
    for (Locus locus : loci) {
        // Store gene names, a locus can have a number of genes attached.
        // Per locus create a comma separated list and add to an array.
        // Further processing will then delimit this list
        // either by ; or 'x' depending on association type
        Collection<String> currentlocusGenes = new ArrayList<>();
        String commaSeparatedGenes = "";
        for (Gene gene : locus.getAuthorReportedGenes()) {
            currentlocusGenes.add(gene.getGeneName());
        }
        if (!currentlocusGenes.isEmpty()) {
            commaSeparatedGenes = String.join(", ", currentlocusGenes);
            allLociGenes.add(commaSeparatedGenes);
        } else {
            allLociGenes.add("NR");
        }
        //This sort ensures that haplotype SNPs are displayed in the correct order
        Collection<RiskAllele> ra = locus.getStrongestRiskAlleles().stream().sorted((v1, v2) -> Long.compare(v1.getId(), v2.getId())).collect(Collectors.toList());
        for (RiskAllele riskAllele : ra) {
            allLociRiskAlleles.add(riskAllele.getRiskAlleleName());
            // Based on assumption we only have one locus with a single risk allele attached
            if (!association.getMultiSnpHaplotype() && !association.getSnpInteraction()) {
                if (riskAllele.getRiskFrequency() != null && !riskAllele.getRiskFrequency().isEmpty()) {
                    allLociRiskAlleleFrequencies.add(riskAllele.getRiskFrequency());
                }
            }
            // SNPs attached to risk allele
            SingleNucleotidePolymorphism snp = riskAllele.getSnp();
            allLociSnps.add(snp.getRsId());
            // Set proxies if present
            Collection<String> currentLocusProxies = new ArrayList<>();
            String commaSeparatedProxies = "";
            if (riskAllele.getProxySnps() != null) {
                for (SingleNucleotidePolymorphism proxySnp : riskAllele.getProxySnps()) {
                    currentLocusProxies.add(proxySnp.getRsId());
                }
            }
            // Comma separate proxies in view
            if (!currentLocusProxies.isEmpty()) {
                commaSeparatedProxies = String.join(", ", currentLocusProxies);
                allLociProxySnps.add(commaSeparatedProxies);
            } else {
                allLociProxySnps.add("NR");
            }
            // Only required for SNP interaction studies
            if (association.getSnpInteraction() != null) {
                if (association.getSnpInteraction()) {
                    // Genome wide Vs Limited List
                    Collection<String> snpStatus = new ArrayList<>();
                    String commaSeparatedSnpStatus = "";
                    if (riskAllele.getLimitedList() != null) {
                        if (riskAllele.getLimitedList()) {
                            snpStatus.add("LL");
                        }
                    }
                    if (riskAllele.getGenomeWide() != null) {
                        if (riskAllele.getGenomeWide()) {
                            snpStatus.add("GW");
                        }
                    }
                    if (!snpStatus.isEmpty()) {
                        commaSeparatedSnpStatus = String.join(", ", snpStatus);
                        allLociSnpStatuses.add(commaSeparatedSnpStatus);
                    } else {
                        allLociSnpStatuses.add("NR");
                    }
                    // Allele risk frequency
                    if (riskAllele.getRiskFrequency() != null && !riskAllele.getRiskFrequency().isEmpty()) {
                        allLociRiskAlleleFrequencies.add(riskAllele.getRiskFrequency());
                    } else {
                        allLociRiskAlleleFrequencies.add("NR");
                    }
                }
            }
        }
    }
    // Create delimited strings for view
    String authorReportedGenes = null;
    if (allLociGenes.size() > 1) {
        authorReportedGenes = String.join(delimiter, allLociGenes);
    } else {
        authorReportedGenes = String.join("", allLociGenes);
    }
    snpAssociationTableView.setAuthorReportedGenes(authorReportedGenes);
    String strongestRiskAlleles = null;
    if (allLociRiskAlleles.size() > 1) {
        strongestRiskAlleles = String.join(delimiter, allLociRiskAlleles);
    } else {
        strongestRiskAlleles = String.join("", allLociRiskAlleles);
    }
    snpAssociationTableView.setStrongestRiskAlleles(strongestRiskAlleles);
    String associationSnps = null;
    if (allLociSnps.size() > 1) {
        associationSnps = String.join(delimiter, allLociSnps);
    } else {
        associationSnps = String.join("", allLociSnps);
    }
    snpAssociationTableView.setSnps(associationSnps);
    String associationProxies = null;
    if (allLociProxySnps.size() > 1) {
        associationProxies = String.join(delimiter, allLociProxySnps);
    } else {
        associationProxies = String.join("", allLociProxySnps);
    }
    snpAssociationTableView.setProxySnps(associationProxies);
    // Set both risk frequencies
    String associationRiskAlleleFrequencies = null;
    if (allLociRiskAlleleFrequencies.size() > 1) {
        associationRiskAlleleFrequencies = String.join(delimiter, allLociRiskAlleleFrequencies);
    } else {
        associationRiskAlleleFrequencies = String.join("", allLociRiskAlleleFrequencies);
    }
    snpAssociationTableView.setRiskAlleleFrequencies(associationRiskAlleleFrequencies);
    snpAssociationTableView.setAssociationRiskFrequency(association.getRiskFrequency());
    String associationSnpStatuses = null;
    if (allLociSnpStatuses.size() > 1) {
        associationSnpStatuses = String.join(delimiter, allLociSnpStatuses);
    } else {
        associationSnpStatuses = String.join("", allLociSnpStatuses);
    }
    snpAssociationTableView.setSnpStatuses(associationSnpStatuses);
    snpAssociationTableView.setPvalueMantissa(association.getPvalueMantissa());
    snpAssociationTableView.setPvalueExponent(association.getPvalueExponent());
    snpAssociationTableView.setPvalueDescription(association.getPvalueDescription());
    Collection<String> efoTraits = new ArrayList<>();
    for (EfoTrait efoTrait : association.getEfoTraits()) {
        efoTraits.add(efoTrait.getTrait());
    }
    String associationEfoTraits = null;
    associationEfoTraits = String.join(", ", efoTraits);
    snpAssociationTableView.setEfoTraits(associationEfoTraits);
    // Set OR values
    snpAssociationTableView.setOrPerCopyNum(association.getOrPerCopyNum());
    snpAssociationTableView.setOrPerCopyRecip(association.getOrPerCopyRecip());
    snpAssociationTableView.setOrPerCopyRecipRange(association.getOrPerCopyRecipRange());
    // Set beta values
    snpAssociationTableView.setBetaNum(association.getBetaNum());
    snpAssociationTableView.setBetaDirection(association.getBetaDirection());
    snpAssociationTableView.setBetaUnit(association.getBetaUnit());
    snpAssociationTableView.setRange(association.getRange());
    snpAssociationTableView.setDescription(association.getDescription());
    snpAssociationTableView.setStandardError(association.getStandardError());
    snpAssociationTableView.setAssociationType(association.getSnpType());
    if (association.getMultiSnpHaplotype() != null) {
        if (association.getMultiSnpHaplotype()) {
            snpAssociationTableView.setMultiSnpHaplotype("Yes");
        }
        if (!association.getMultiSnpHaplotype()) {
            snpAssociationTableView.setMultiSnpHaplotype("No");
        }
    }
    if (association.getSnpInteraction() != null) {
        if (association.getSnpInteraction()) {
            snpAssociationTableView.setSnpInteraction("Yes");
        }
        if (!association.getSnpInteraction()) {
            snpAssociationTableView.setSnpInteraction("No");
        }
    }
    if (association.getSnpApproved() != null) {
        if (association.getSnpApproved()) {
            snpAssociationTableView.setSnpApproved("Yes");
        }
        if (!association.getSnpApproved()) {
            snpAssociationTableView.setSnpApproved("No");
        }
    }
    // Get validation warnings
    snpAssociationTableView.setValidationWarnings(associationValidationReportService.getWarningSet(association.getId()));
    // Get mapping details
    if (association.getLastMappingPerformedBy() != null) {
        snpAssociationTableView.setLastMappingPerformedBy(association.getLastMappingPerformedBy());
    }
    snpAssociationTableView.setMappingStatus("false");
    if (association.getLastMappingDate() != null) {
        snpAssociationTableView.setMappingStatus("true");
    }
    if (association.getLastMappingDate() != null) {
        DateFormat df = new SimpleDateFormat("dd-MMM-yyyy HH:mm:ss");
        String dateOfLastMapping = df.format(association.getLastMappingDate());
        snpAssociationTableView.setLastMappingDate(dateOfLastMapping);
    }
    return snpAssociationTableView;
}

Example 10 with SingleNucleotidePolymorphism

use of uk.ac.ebi.spot.goci.model.SingleNucleotidePolymorphism 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.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;
}