private ClinVar parseClinvar(EvidenceEntry evidenceEntry) { String clinicalSignificance = getAdditionalProperty(evidenceEntry, CLINICAL_SIGNIFICANCE_IN_SOURCE_FILE); List<String> traitList = null; if (evidenceEntry.getHeritableTraits() != null) { traitList = evidenceEntry .getHeritableTraits() .stream() .map((heritableTrait) -> heritableTrait.getTrait()) .collect(Collectors.toList()); } List<String> geneNameList = null; if (evidenceEntry.getGenomicFeatures() != null) { geneNameList = evidenceEntry .getGenomicFeatures() .stream() .map((genomicFeature) -> genomicFeature.getXrefs().get(SYMBOL)) .collect(Collectors.toList()); } String reviewStatus = getAdditionalProperty(evidenceEntry, REVIEW_STATUS_IN_SOURCE_FILE); return new ClinVar(evidenceEntry.getId(), clinicalSignificance, traitList, geneNameList, reviewStatus); }
public EvidenceEntry fromClinVar(ClinVar clinVar) { EvidenceSource evidenceSource = new EvidenceSource(CLINVAR, null, null); String url = clinVar.getAccession().startsWith("RCV") ? "https://www.ncbi.nlm.nih.gov/clinvar/" + clinVar.getAccession() : null; List<HeritableTrait> heritableTraits = null; if (CollectionUtils.isNotEmpty(clinVar.getTraits())) { heritableTraits = clinVar.getTraits() .stream() .map(trait -> new HeritableTrait(trait, ModeOfInheritance.NA)) if (CollectionUtils.isNotEmpty(clinVar.getGeneNames())) { genomicFeatures = clinVar.getGeneNames() .stream() .map(geneName -> new GenomicFeature(FeatureTypes.gene, null, Collections.singletonMap(SYMBOL, geneName))) if (StringUtils.isNotEmpty(clinVar.getReviewStatus())) { additionalProperties.add( new Property(null, REVIEW_STATUS_IN_SOURCE_FILE, clinVar.getReviewStatus())); if (StringUtils.isNotEmpty(clinVar.getClinicalSignificance())) { additionalProperties.add( new Property(null, CLINICAL_SIGNIFICANCE_IN_SOURCE_FILE, clinVar.getClinicalSignificance())); VariantClassification variantClassification = getVariantClassification(clinVar.getClinicalSignificance().toLowerCase()); ConsistencyStatus consistencyStatus = getConsistencyStatus(clinVar.getReviewStatus().toLowerCase()); return new EvidenceEntry( evidenceSource, Collections.emptyList(), null, url, clinVar.getAccession(), null, null, heritableTraits, genomicFeatures,
variantAnnotation.getVariantTraitAssociation().getClinvar() .forEach(cv -> { xrefs.add(cv.getAccession()); cv.getTraits().forEach(cvt -> traits.add("CV" + FIELD_SEP + cv.getAccession() + FIELD_SEP + cvt + FIELD_SEP + "cs:" + cv.getClinicalSignificance())); });
addNotNull(xrefs, clinVar.getAccession());
private ClinVar parseClinvar(EvidenceEntry evidenceEntry) { String clinicalSignificance = getAdditionalProperty(evidenceEntry, CLINICAL_SIGNIFICANCE_IN_SOURCE_FILE); List<String> traitList = null; if (evidenceEntry.getHeritableTraits() != null) { traitList = evidenceEntry .getHeritableTraits() .stream() .map((heritableTrait) -> heritableTrait.getTrait()) .collect(Collectors.toList()); } List<String> geneNameList = null; if (evidenceEntry.getGenomicFeatures() != null) { geneNameList = evidenceEntry .getGenomicFeatures() .stream() .map((genomicFeature) -> genomicFeature.getXrefs().get(SYMBOL)) .collect(Collectors.toList()); } String reviewStatus = getAdditionalProperty(evidenceEntry, REVIEW_STATUS_IN_SOURCE_FILE); return new ClinVar(evidenceEntry.getId(), clinicalSignificance, traitList, geneNameList, reviewStatus); }
return new ClinVar(acc, clinicalSignificanceName, traitNames, geneNameList, reviewStatus);
return new ClinVar(acc, clinicalSignificanceName, traitNames, geneNameList, reviewStatus);
@Override public ClinVar build() { try { ClinVar record = new ClinVar(); record.accession = fieldSetFlags()[0] ? this.accession : (java.lang.String) defaultValue(fields()[0]); record.clinicalSignificance = fieldSetFlags()[1] ? this.clinicalSignificance : (java.lang.String) defaultValue(fields()[1]); record.traits = fieldSetFlags()[2] ? this.traits : (java.util.List<java.lang.String>) defaultValue(fields()[2]); record.geneNames = fieldSetFlags()[3] ? this.geneNames : (java.util.List<java.lang.String>) defaultValue(fields()[3]); record.reviewStatus = fieldSetFlags()[4] ? this.reviewStatus : (java.lang.String) defaultValue(fields()[4]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }