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

Example 1 with RiskAllele

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

the class AssociationRowProcessor method createLoci.

private Collection<Locus> createLoci(AssociationUploadRow row, Boolean snpInteraction, Boolean multiSnpHaplotype) {
    String delimiter;
    Collection<Locus> loci = new ArrayList<>();
    if (snpInteraction) {
        delimiter = "x";
        // For SNP interaction studies we need to create a locus per risk allele
        // Handle curator entered risk allele
        Collection<RiskAllele> locusRiskAlleles = createLocusRiskAlleles(row.getStrongestAllele(), row.getSnp(), row.getProxy(), row.getRiskFrequency(), row.getSnpStatus(), delimiter);
        // Deal with genes for each interaction which should be
        // separated by 'x'
        String[] separatedGenes = row.getAuthorReportedGene().split(delimiter);
        int geneIndex = 0;
        for (RiskAllele riskAllele : locusRiskAlleles) {
            Locus locus = new Locus();
            // Set risk alleles, assume one locus per risk allele
            Collection<RiskAllele> currentLocusRiskAlleles = new ArrayList<>();
            currentLocusRiskAlleles.add(riskAllele);
            locus.setStrongestRiskAlleles(currentLocusRiskAlleles);
            // Set gene
            String interactionGene = separatedGenes[geneIndex];
            Collection<Gene> locusGenes = associationAttributeService.createLocusGenes(interactionGene, ",");
            locus.setAuthorReportedGenes(locusGenes);
            geneIndex++;
            // Set description
            locus.setDescription("SNP x SNP interaction");
            loci.add(locus);
        }
    } else // Handle multi-snp and standard snp
    {
        delimiter = ";";
        // For multi-snp and standard snps we assume their is only one locus
        Locus locus = new Locus();
        // Handle curator entered genes, for haplotype they are separated by a comma
        if (row.getAuthorReportedGene() != null && !row.getAuthorReportedGene().isEmpty()) {
            Collection<Gene> locusGenes = associationAttributeService.createLocusGenes(row.getAuthorReportedGene(), ",");
            locus.setAuthorReportedGenes(locusGenes);
        }
        // Handle curator entered risk allele
        Collection<RiskAllele> locusRiskAlleles = createLocusRiskAlleles(row.getStrongestAllele(), row.getSnp(), row.getProxy(), row.getRiskFrequency(), row.getSnpStatus(), delimiter);
        // For standard associations set the risk allele frequency to the
        // same value as the overall association frequency
        Collection<RiskAllele> locusRiskAllelesWithRiskFrequencyValues = new ArrayList<>();
        if (!multiSnpHaplotype) {
            for (RiskAllele riskAllele : locusRiskAlleles) {
                riskAllele.setRiskFrequency(row.getAssociationRiskFrequency());
                locusRiskAllelesWithRiskFrequencyValues.add(riskAllele);
            }
            locus.setStrongestRiskAlleles(locusRiskAllelesWithRiskFrequencyValues);
        } else {
            locus.setStrongestRiskAlleles(locusRiskAlleles);
        }
        // Set locus attributes
        Integer haplotypeCount = locusRiskAlleles.size();
        if (haplotypeCount > 1) {
            locus.setHaplotypeSnpCount(haplotypeCount);
            locus.setDescription(String.valueOf(haplotypeCount) + "-SNP haplotype");
        } else {
            locus.setDescription("Single variant");
        }
        loci.add(locus);
    }
    return loci;
}

Example 2 with RiskAllele

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

the class AssociationRowProcessorTest method testCreateAssociationFromUploadRowSnpInteraction.

@Test
public void testCreateAssociationFromUploadRowSnpInteraction() throws Exception {
    // Stubbing mock object behaviour
    when(associationAttributeService.createLocusGenes("PMS1 ", ",")).thenReturn(Arrays.asList(GENE_03));
    when(associationAttributeService.createLocusGenes(" HIBCH", ",")).thenReturn(Arrays.asList(GENE_04));
    when(associationAttributeService.createSnp("rs2562796")).thenReturn(SNP_02);
    when(associationAttributeService.createSnp("rs16832404")).thenReturn(SNP_03);
    when(associationAttributeService.createRiskAllele("rs2562796-T", SNP_02)).thenReturn(RA_02);
    when(associationAttributeService.createRiskAllele("rs16832404-G", SNP_03)).thenReturn(RA_03);
    Association association = associationRowProcessor.createAssociationFromUploadRow(SNP_INTERACTION_ROW);
    verify(associationCalculationService, never()).reverseCI(SNP_INTERACTION_ROW.getRange());
    verify(associationCalculationService, never()).setRange(SNP_INTERACTION_ROW.getStandardError(), SNP_INTERACTION_ROW.getOrPerCopyNum());
    verify(associationAttributeService, never()).getEfoTraitsFromRepository(Collections.EMPTY_LIST);
    verify(associationAttributeService, times(1)).createLocusGenes("PMS1 ", ",");
    verify(associationAttributeService, times(1)).createLocusGenes(" HIBCH", ",");
    verify(associationAttributeService, times(1)).createSnp("rs2562796");
    verify(associationAttributeService, times(1)).createSnp("rs16832404");
    verify(associationAttributeService, times(1)).createRiskAllele("rs2562796-T", SNP_02);
    verify(associationAttributeService, times(1)).createRiskAllele("rs16832404-G", SNP_03);
    assertThat(association).extracting("id", "riskFrequency", "pvalueDescription", "pvalueMantissa", "pvalueExponent", "multiSnpHaplotype", "snpInteraction", "snpApproved", "snpType", "standardError", "range", "description", "orPerCopyNum", "orPerCopyRecip", "orPerCopyRecipRange", "betaNum", "betaUnit", "betaDirection", "study", "associationReport", "lastMappingDate", "lastMappingPerformedBy", "lastUpdateDate").containsExactly(null, "0.52", null, 2, -7, false, true, false, null, (float) 0.6, "[0.82-0.92]", null, (float) 1.22, null, null, null, null, null, null, null, null, null, null);
    assertThat(association.getEfoTraits()).isEmpty();
    assertThat(association.getEvents()).isEmpty();
    assertThat(association.getStudy()).isNull();
    assertThat(association.getLoci()).hasSize(2);
    // Check locus attributes
    Collection<Gene> locusGenes = new ArrayList<>();
    association.getLoci().stream().forEach(locus -> {
        locusGenes.addAll(locus.getAuthorReportedGenes());
    });
    Collection<RiskAllele> locusRiskAlleles = new ArrayList<>();
    association.getLoci().stream().forEach(locus -> {
        locusRiskAlleles.addAll(locus.getStrongestRiskAlleles());
    });
    assertThat(association.getLoci()).extracting(Locus::getDescription).containsOnly("SNP x SNP interaction");
    assertThat(locusGenes).hasSize(2).contains(GENE_03, GENE_04);
    assertThat(locusRiskAlleles).hasSize(2).contains(RA_02, RA_03);
    assertThat(locusRiskAlleles).extracting("riskAlleleName", "riskFrequency", "snp.rsId").contains(tuple("rs2562796-T", "0.3", "rs2562796"), tuple("rs16832404-G", "0.4", "rs16832404"));
    assertThat(locusRiskAlleles).extracting(RiskAllele::getSnp).containsExactly(SNP_02, SNP_03);
}

Example 3 with RiskAllele

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

the class AssociationRowProcessorTest method testCreateAssociationFromUploadRowHaplotype.

@Test
public void testCreateAssociationFromUploadRowHaplotype() throws Exception {
    // Stubbing mock object behaviour
    when(associationAttributeService.createSnp("rs456")).thenReturn(SNP_04);
    when(associationAttributeService.createSnp("rs678")).thenReturn(SNP_05);
    when(associationAttributeService.createRiskAllele("rs456-T", SNP_04)).thenReturn(RA_04);
    when(associationAttributeService.createRiskAllele("rs678-?", SNP_05)).thenReturn(RA_05);
    when(associationCalculationService.reverseCI("[0.87-0.94]")).thenReturn("[1.06-1.15]");
    Association association = associationRowProcessor.createAssociationFromUploadRow(HAPLOTYPE_ROW);
    verify(associationCalculationService, times(1)).reverseCI(Matchers.anyString());
    verify(associationCalculationService, never()).setRange(Matchers.anyDouble(), Matchers.anyDouble());
    verify(associationAttributeService, never()).getEfoTraitsFromRepository(Collections.EMPTY_LIST);
    verify(associationAttributeService, never()).createLocusGenes(Matchers.anyString(), Matchers.anyString());
    verify(associationAttributeService, times(1)).createSnp("rs456");
    verify(associationAttributeService, times(1)).createSnp("rs678");
    verify(associationAttributeService, times(1)).createRiskAllele("rs456-T", SNP_04);
    verify(associationAttributeService, times(1)).createRiskAllele("rs678-?", SNP_05);
    assertThat(association).extracting("id", "riskFrequency", "pvalueDescription", "pvalueMantissa", "pvalueExponent", "multiSnpHaplotype", "snpInteraction", "snpApproved", "snpType", "standardError", "range", "description", "orPerCopyNum", "orPerCopyRecip", "orPerCopyRecipRange", "betaNum", "betaUnit", "betaDirection", "study", "associationReport", "lastMappingDate", "lastMappingPerformedBy", "lastUpdateDate").containsExactly(null, null, "(description)", 2, -7, true, false, false, null, null, "[1.06-1.15]", null, 1.2048193f, 0.83f, "[0.87-0.94]", null, null, null, null, null, null, null, null);
    assertThat(association.getEfoTraits()).isEmpty();
    assertThat(association.getEvents()).isEmpty();
    assertThat(association.getStudy()).isNull();
    assertThat(association.getLoci()).hasSize(1);
    Collection<RiskAllele> locusRiskAlleles = new ArrayList<>();
    association.getLoci().stream().forEach(locus -> {
        locusRiskAlleles.addAll(locus.getStrongestRiskAlleles());
    });
    // Check locus attributes
    Collection<Gene> locusGenes = new ArrayList<>();
    association.getLoci().stream().forEach(locus -> {
        locusGenes.addAll(locus.getAuthorReportedGenes());
    });
    assertThat(association.getLoci()).extracting(Locus::getDescription).containsOnly("2-SNP haplotype");
    assertThat(locusGenes).isEmpty();
    assertThat(locusRiskAlleles).hasSize(2).contains(RA_04, RA_05);
    assertThat(locusRiskAlleles).extracting(RiskAllele::getRiskFrequency).containsNull();
    assertThat(locusRiskAlleles).extracting("riskAlleleName", "riskFrequency", "snp.rsId").contains(tuple("rs456-T", null, "rs456"), tuple("rs678-?", null, "rs678"));
    assertThat(locusRiskAlleles).extracting(RiskAllele::getSnp).containsExactly(SNP_04, SNP_05);
}

Example 4 with RiskAllele

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

the class ValidationChecksBuilder method runLociAttributeChecks.

/**
     * Run loci attributes checks on association
     *
     * @param association association to be checked
     */
public Collection<ValidationError> runLociAttributeChecks(Association association, String eRelease) {
    Collection<ValidationError> validationErrors = new ArrayList<>();
    if (association.getLoci() != null) {
        Set<String> associationGenes = new HashSet<>();
        Collection<ValidationError> geneErrors = new ArrayList<>();
        // Create a unique set of all locus genes
        for (Locus locus : association.getLoci()) {
            Set<String> locusGenes = new HashSet<>();
            if (!locus.getAuthorReportedGenes().isEmpty()) {
                locusGenes = locus.getAuthorReportedGenes().stream().map(Gene::getGeneName).collect(Collectors.toSet());
            }
            associationGenes.addAll(locusGenes);
        }
        // Check genes
        associationGenes.forEach(geneName -> {
            getLog().info("Checking gene: ".concat(geneName));
            ValidationError geneError = errorCreationService.checkGene(geneName, eRelease);
            if (geneError.getError() != null) {
                geneErrors.add(geneError);
            }
        });
        if (!geneErrors.isEmpty()) {
            validationErrors.addAll(geneErrors);
        }
        for (Locus locus : association.getLoci()) {
            Collection<RiskAllele> riskAlleles = locus.getStrongestRiskAlleles();
            // Check risk allele attributes
            riskAlleles.forEach(riskAllele -> {
                ValidationError riskAlleleError = errorCreationService.checkRiskAllele(riskAllele.getRiskAlleleName());
                validationErrors.add(riskAlleleError);
                if (geneErrors.isEmpty()) {
                    Set<String> locusGenes = locus.getAuthorReportedGenes().stream().map(Gene::getGeneName).collect(Collectors.toSet());
                    locusGenes.forEach(geneName -> {
                        getLog().info("Checking snp/gene location: ".concat(geneName).concat(" ").concat(riskAllele.getSnp().getRsId()));
                        ValidationError snpGeneLocationError = errorCreationService.checkSnpGeneLocation(riskAllele.getSnp().getRsId(), geneName, eRelease);
                        validationErrors.add(snpGeneLocationError);
                    });
                } else {
                    ValidationError snpError = errorCreationService.checkSnp(riskAllele.getSnp().getRsId(), eRelease);
                    validationErrors.add(snpError);
                }
            });
        }
    }
    return ErrorProcessingService.checkForValidErrors(validationErrors);
}

Example 5 with RiskAllele

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

the class AssociationAttributeService method createRiskAllele.

public RiskAllele createRiskAllele(String curatorEnteredRiskAllele, SingleNucleotidePolymorphism snp) {
    RiskAllele riskAllele = new RiskAllele();
    riskAllele.setRiskAlleleName(StringProcessingService.tidy_curator_entered_string(curatorEnteredRiskAllele));
    riskAllele.setSnp(snp);
    return riskAllele;
}