private ProteinVariantAnnotation getProteinAnnotation(ConsequenceType consequenceType) { if (consequenceType.getProteinVariantAnnotation() != null) { QueryResult<ProteinVariantAnnotation> proteinVariantAnnotation = proteinDBAdaptor.getVariantAnnotation( consequenceType.getEnsemblTranscriptId(), consequenceType.getProteinVariantAnnotation().getPosition(), consequenceType.getProteinVariantAnnotation().getReference(), consequenceType.getProteinVariantAnnotation().getAlternate(), new QueryOptions()); if (proteinVariantAnnotation.getNumResults() > 0) { return proteinVariantAnnotation.getResult().get(0); } } return null; }
private ConsequenceType findCodingOverlappingConsequenceType(ConsequenceType consequenceType, List<ConsequenceType> consequenceTypeList) { for (ConsequenceType consequenceType1 : consequenceTypeList) { if (isCoding(consequenceType1) && consequenceType.getEnsemblTranscriptId().equals(consequenceType1.getEnsemblTranscriptId()) && consequenceType.getProteinVariantAnnotation().getPosition() .equals(consequenceType1.getProteinVariantAnnotation().getPosition())) { return consequenceType1; } } return null; }
private ConsequenceType findCodingOverlappingConsequenceType(ConsequenceType consequenceType, List<ConsequenceType> consequenceTypeList) { for (ConsequenceType consequenceType1 : consequenceTypeList) { if (isCoding(consequenceType1) && consequenceType.getEnsemblTranscriptId().equals(consequenceType1.getEnsemblTranscriptId()) && consequenceType.getProteinVariantAnnotation().getPosition() .equals(consequenceType1.getProteinVariantAnnotation().getPosition())) { return consequenceType1; } } return null; }
private ProteinVariantAnnotation getProteinAnnotation(ConsequenceType consequenceType) { if (consequenceType.getProteinVariantAnnotation() != null) { QueryResult<ProteinVariantAnnotation> proteinVariantAnnotation = proteinDBAdaptor.getVariantAnnotation( consequenceType.getEnsemblTranscriptId(), consequenceType.getProteinVariantAnnotation().getPosition(), consequenceType.getProteinVariantAnnotation().getReference(), consequenceType.getProteinVariantAnnotation().getAlternate(), new QueryOptions()); if (proteinVariantAnnotation.getNumResults() > 0) { return proteinVariantAnnotation.getResult().get(0); } } return null; }
private void addProteinSubstitutionScore(ConsequenceType consequenceType, Score score) { ProteinVariantAnnotation proteinVariantAnnotation = consequenceType.getProteinVariantAnnotation(); List<Score> proteinSubstitionScores; if(proteinVariantAnnotation==null) { proteinVariantAnnotation = new ProteinVariantAnnotation(); consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation); proteinSubstitionScores = new ArrayList<>(); proteinVariantAnnotation.setSubstitutionScores(proteinSubstitionScores); } else { proteinSubstitionScores = proteinVariantAnnotation.getSubstitutionScores(); } proteinSubstitionScores.add(score); }
protected boolean setInsertionAlleleAminoacidChange(String referenceCodon, char[] modifiedCodonArray, char[] formattedReferenceCodonArray, char[] formattedModifiedCodonArray, boolean useMitochondrialCode, boolean firstCodon) { // Set codon str, protein ref and protein alt ONLY for the first codon mofified by the insertion if (firstCodon) { firstCodon = false; // Only the exact codon where the deletion starts is set consequenceType.setCodon(String.valueOf(formattedReferenceCodonArray) + "/" + String.valueOf(formattedModifiedCodonArray)); // Assumes proteinVariantAnnotation attribute is already initialized consequenceType .getProteinVariantAnnotation() .setReference(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, referenceCodon)); consequenceType .getProteinVariantAnnotation() .setAlternate(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, String.valueOf(modifiedCodonArray))); } return firstCodon; }
protected boolean setInsertionAlleleAminoacidChange(String referenceCodon, char[] modifiedCodonArray, char[] formattedReferenceCodonArray, char[] formattedModifiedCodonArray, boolean useMitochondrialCode, boolean firstCodon) { // Set codon str, protein ref and protein alt ONLY for the first codon mofified by the insertion if (firstCodon) { firstCodon = false; // Only the exact codon where the deletion starts is set consequenceType.setCodon(String.valueOf(formattedReferenceCodonArray) + "/" + String.valueOf(formattedModifiedCodonArray)); // Assumes proteinVariantAnnotation attribute is already initialized consequenceType .getProteinVariantAnnotation() .setReference(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, referenceCodon)); consequenceType .getProteinVariantAnnotation() .setAlternate(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, String.valueOf(modifiedCodonArray))); } return firstCodon; }
.getProteinVariantAnnotation() .setReference(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, referenceCodon1)); consequenceType .getProteinVariantAnnotation() .setAlternate(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, modifiedCodon));
.getProteinVariantAnnotation() .setReference(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, referenceCodon1)); consequenceType .getProteinVariantAnnotation() .setAlternate(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, modifiedCodon));
if (consequenceType.getProteinVariantAnnotation() != null) { stringBuilder.append(consequenceType.getProteinVariantAnnotation().getPosition()); stringBuilder.append(FIELD_SEPARATOR); stringBuilder.append(consequenceType.getProteinVariantAnnotation().getReference()) .append("/") .append(consequenceType.getProteinVariantAnnotation().getAlternate()); stringBuilder.append(FIELD_SEPARATOR); if (consequenceType.getProteinVariantAnnotation().getSubstitutionScores() != null) { List<String> sift = consequenceType.getProteinVariantAnnotation().getSubstitutionScores().stream() .filter(t -> t.getSource().equalsIgnoreCase("sift")) .map(Score::getDescription) List<String> polyphen = consequenceType.getProteinVariantAnnotation().getSubstitutionScores().stream() .filter(t -> t.getSource().equalsIgnoreCase("polyphen")) .map(Score::getDescription)
.getProteinVariantAnnotation() .setReference(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, referenceCodon1)); consequenceType .getProteinVariantAnnotation() .setAlternate(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, modifiedCodon));
consequenceType.getProteinVariantAnnotation().setReference(referenceA); consequenceType.getProteinVariantAnnotation().setAlternate(alternativeA);
consequenceType.getProteinVariantAnnotation().setReference(referenceA); consequenceType.getProteinVariantAnnotation().setAlternate(alternativeA);
consequenceType.getProteinVariantAnnotation().setReference(referenceA); consequenceType.getProteinVariantAnnotation().setAlternate(alternativeA);
.getProteinVariantAnnotation() .setReference(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, referenceCodon1)); consequenceType .getProteinVariantAnnotation() .setAlternate(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, modifiedCodon));
@Override protected Iterable<T> featureValueOf(VariantAnnotation actual) { if (actual.getConsequenceTypes() != null) { Set<T> set = new HashSet<>(); for (ConsequenceType ct : actual.getConsequenceTypes()) { if (ct != null && ct.getProteinVariantAnnotation() != null && ct.getProteinVariantAnnotation().getSubstitutionScores() != null) { for (Score score : ct.getProteinVariantAnnotation().getSubstitutionScores()) { if (score != null && source.equals(score.getSource())) { set.add(mapper.apply(score)); } } } } return set; } return Collections.emptyList(); } };
if (consequenceType.getProteinVariantAnnotation() != null && consequenceType.getProteinVariantAnnotation().getSubstitutionScores() != null) { for (Score score : consequenceType.getProteinVariantAnnotation().getSubstitutionScores()) { String source = score.getSource(); if (("sift").equals(source)) {
@Test public void testConvertToDataModelType() throws Exception { DocumentToVariantAnnotationConverter documentToVariantAnnotationConverter = new DocumentToVariantAnnotationConverter(); VariantAnnotation convertedVariantAnnotation = documentToVariantAnnotationConverter.convertToDataModelType(dbObject); assertEquals(convertedVariantAnnotation.getConsequenceTypes().get(2).getProteinVariantAnnotation().getReference(), "CYS"); assertEquals(convertedVariantAnnotation.getVariantTraitAssociation().getCosmic().get(0).getPrimarySite(), "large_intestine"); }
if (variant.getAnnotation().getConsequenceTypes() != null) { for (ConsequenceType consequenceType : variant.getAnnotation().getConsequenceTypes()) { if (consequenceType.getProteinVariantAnnotation() != null && consequenceType.getProteinVariantAnnotation().getKeywords() != null) { keywordsInVariant.addAll(consequenceType.getProteinVariantAnnotation().getKeywords());
public static VariantAnnotationProto.ConsequenceType createConsequenceType(ConsequenceType type) { VariantAnnotationProto.ConsequenceType.Builder builder= VariantAnnotationProto.ConsequenceType.newBuilder() .setGeneName(type.getGeneName()) .setEnsemblGeneId(type.getEnsemblGeneId()) .setEnsemblTranscriptId(type.getEnsemblTranscriptId()) .setStrand(type.getStrand()) .setBiotype(type.getBiotype()) .setCDnaPosition(type.getCdnaPosition()) .setCdsPosition(type.getCdsPosition()) .setCodon(type.getCodon()) .setProteinVariantAnnotation(createProteinVariantAnnotation(type.getProteinVariantAnnotation())); List<SequenceOntologyTerm> sequenceOntologyTerms = type.getSequenceOntologyTerms(); if (sequenceOntologyTerms != null) { for (SequenceOntologyTerm so : sequenceOntologyTerms) { VariantAnnotationProto.SequenceOntologyTerm.Builder soBuilder = VariantAnnotationProto.SequenceOntologyTerm.newBuilder() .setAccession(so.getAccession()) .setName(so.getName()); builder.addSequenceOntologyTerms(soBuilder.build()); } } return builder.build(); }