protected void solveIntergenic(List<ConsequenceType> consequenceTypeList, boolean isIntergenic) { if (consequenceTypeList.size() == 0 && isIntergenic) { HashSet<String> intergenicName = new HashSet<>(); intergenicName.add(VariantAnnotationUtils.INTERGENIC_VARIANT); ConsequenceType consequenceType = new ConsequenceType(); consequenceType.setSequenceOntologyTerms(getSequenceOntologyTerms(intergenicName)); consequenceTypeList.add(consequenceType); } }
protected void solveIntergenic(List<ConsequenceType> consequenceTypeList, boolean isIntergenic) { if (consequenceTypeList.size() == 0 && isIntergenic) { HashSet<String> intergenicName = new HashSet<>(); intergenicName.add(VariantAnnotationUtils.INTERGENIC_VARIANT); ConsequenceType consequenceType = new ConsequenceType(); consequenceType.setSequenceOntologyTerms(getSequenceOntologyTerms(intergenicName)); consequenceTypeList.add(consequenceType); } }
private ConsequenceType buildConsequenceType(String geneName, String ensemblGeneId, String ensemblTranscriptId, String strand, String biotype, List<Document> exonOverlap, List<String> transcriptAnnotationFlags, Integer cDnaPosition, Integer cdsPosition, String codon, List<String> soNameList, ProteinVariantAnnotation proteinVariantAnnotation) { List<SequenceOntologyTerm> soTerms = new ArrayList<>(soNameList.size()); for (String soName : soNameList) { soTerms.add(new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(soName), soName)); } List<ExonOverlap> exonOverlapList = new ArrayList<>(exonOverlap.size()); for (Document document : exonOverlap) { ExonOverlap e = new ExonOverlap( document.getString(CT_EXON_OVERLAP_NUMBER_FIELD), getDefault(document, CT_EXON_OVERLAP_PERCENTAGE_FIELD, 0F)); exonOverlapList.add(e); } return new ConsequenceType(geneName, ensemblGeneId, ensemblTranscriptId, strand, biotype, exonOverlapList, transcriptAnnotationFlags, cDnaPosition, cdsPosition, codon, proteinVariantAnnotation, soTerms); }
protected void solveRegulatoryRegions(boolean[] overlapsRegulatoryRegion, List<ConsequenceType> consequenceTypeList) { if (overlapsRegulatoryRegion[0]) { ConsequenceType consequenceType = new ConsequenceType(); SequenceOntologyTerm sequenceOntologyTerm = newSequenceOntologyTerm(VariantAnnotationUtils.REGULATORY_REGION_VARIANT); consequenceType.setSequenceOntologyTerms(Collections.singletonList(sequenceOntologyTerm)); consequenceTypeList.add(consequenceType); if (overlapsRegulatoryRegion[1]) { consequenceType = new ConsequenceType(); sequenceOntologyTerm = newSequenceOntologyTerm(VariantAnnotationUtils.TF_BINDING_SITE_VARIANT); consequenceType.setSequenceOntologyTerms(Collections.singletonList(sequenceOntologyTerm));
protected void solveRegulatoryRegions(boolean[] overlapsRegulatoryRegion, List<ConsequenceType> consequenceTypeList) { if (overlapsRegulatoryRegion[0]) { ConsequenceType consequenceType = new ConsequenceType(); SequenceOntologyTerm sequenceOntologyTerm = newSequenceOntologyTerm(VariantAnnotationUtils.REGULATORY_REGION_VARIANT); consequenceType.setSequenceOntologyTerms(Collections.singletonList(sequenceOntologyTerm)); consequenceTypeList.add(consequenceType); if (overlapsRegulatoryRegion[1]) { consequenceType = new ConsequenceType(); sequenceOntologyTerm = newSequenceOntologyTerm(VariantAnnotationUtils.TF_BINDING_SITE_VARIANT); consequenceType.setSequenceOntologyTerms(Collections.singletonList(sequenceOntologyTerm));
private List<ConsequenceType> getConsequenceTypes(List<TranscriptVariation> transcriptVariations) { List<ConsequenceType> consequenceTypes = null; for (TranscriptVariation transcriptVariation : transcriptVariations) { ProteinVariantAnnotation proteinVariantAnnotation = getProteinVariantAnnotation(transcriptVariation); List<SequenceOntologyTerm> soTerms = null; try { soTerms = getSequenceOntologyTerms(transcriptVariation.getConsequenceTypes()); } catch (SOTermNotAvailableException e) { logger.warn(e.getMessage()); } if (consequenceTypes == null) { consequenceTypes = new ArrayList<>(); } consequenceTypes.add(new ConsequenceType(null, null, transcriptVariation.getTranscriptId(), null, null, null, null, transcriptVariation.getCdnaStart() != 0 ? transcriptVariation.getCdnaStart() : null, transcriptVariation.getCdsStart() != 0 ? transcriptVariation.getCdsStart() : null, transcriptVariation.getCodonAlleleString(), proteinVariantAnnotation, soTerms)); } return consequenceTypes; }
isIntergenic = isIntergenic && (variantEnd < currentTranscript.getStart() || variantStart > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
isIntergenic = isIntergenic && (variantEnd < currentTranscript.getStart() || variantStart > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
isIntergenic = isIntergenic && (variantEnd < currentTranscript.getStart() || variantStart > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
isIntergenic = isIntergenic && (variantEnd < currentTranscript.getStart() || variantStart > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
isIntergenic = isIntergenic && (variantEnd < currentTranscript.getStart() || variantStart > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
isIntergenic = isIntergenic && (variantEnd < currentTranscript.getStart() || variantStart > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
isIntergenic = isIntergenic && (variantEnd < currentTranscript.getStart() || variantStart > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
isIntergenic = isIntergenic && (variantEnd < currentTranscript.getStart() || variantStart > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
isIntergenic = isIntergenic && (variantEnd < currentTranscript.getStart() || variantStart > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
isIntergenic = isIntergenic && (variantEnd < currentTranscript.getStart() || variantStart > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
@Override public List<VariantAnnotation> annotate(List<Variant> variants) throws VariantAnnotatorException { if (fail) { throw new VariantAnnotatorException("Fail because reasons"); } return variants.stream().map(v -> { VariantAnnotation a = new VariantAnnotation(); a.setChromosome(v.getChromosome()); a.setStart(v.getStart()); a.setEnd(v.getEnd()); a.setReference(v.getReference()); a.setAlternate(v.getAlternate()); a.setId("an id -- " + key); ConsequenceType ct = new ConsequenceType(); ct.setGeneName("a gene"); ct.setSequenceOntologyTerms(Collections.emptyList()); ct.setExonOverlap(Collections.emptyList()); ct.setTranscriptAnnotationFlags(Collections.emptyList()); a.setConsequenceTypes(Collections.singletonList(ct)); a.setAdditionalAttributes( Collections.singletonMap(GROUP_NAME.key(), new AdditionalAttribute(Collections.singletonMap(VARIANT_ID.key(), v.toString())))); return a; }).collect(Collectors.toList()); }
|| variant.getStart() > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
|| variant.getStart() > currentTranscript.getEnd()); transcript = currentTranscript; consequenceType = new ConsequenceType(); consequenceType.setGeneName(gene.getName()); consequenceType.setEnsemblGeneId(gene.getId());
@Override public ConsequenceType build() { try { ConsequenceType record = new ConsequenceType(); record.geneName = fieldSetFlags()[0] ? this.geneName : (java.lang.String) defaultValue(fields()[0]); record.ensemblGeneId = fieldSetFlags()[1] ? this.ensemblGeneId : (java.lang.String) defaultValue(fields()[1]); record.ensemblTranscriptId = fieldSetFlags()[2] ? this.ensemblTranscriptId : (java.lang.String) defaultValue(fields()[2]); record.strand = fieldSetFlags()[3] ? this.strand : (java.lang.String) defaultValue(fields()[3]); record.biotype = fieldSetFlags()[4] ? this.biotype : (java.lang.String) defaultValue(fields()[4]); record.exonOverlap = fieldSetFlags()[5] ? this.exonOverlap : (java.util.List<org.opencb.biodata.models.variant.avro.ExonOverlap>) defaultValue(fields()[5]); record.transcriptAnnotationFlags = fieldSetFlags()[6] ? this.transcriptAnnotationFlags : (java.util.List<java.lang.String>) defaultValue(fields()[6]); record.cdnaPosition = fieldSetFlags()[7] ? this.cdnaPosition : (java.lang.Integer) defaultValue(fields()[7]); record.cdsPosition = fieldSetFlags()[8] ? this.cdsPosition : (java.lang.Integer) defaultValue(fields()[8]); record.codon = fieldSetFlags()[9] ? this.codon : (java.lang.String) defaultValue(fields()[9]); record.proteinVariantAnnotation = fieldSetFlags()[10] ? this.proteinVariantAnnotation : (org.opencb.biodata.models.variant.avro.ProteinVariantAnnotation) defaultValue(fields()[10]); record.sequenceOntologyTerms = fieldSetFlags()[11] ? this.sequenceOntologyTerms : (java.util.List<org.opencb.biodata.models.variant.avro.SequenceOntologyTerm>) defaultValue(fields()[11]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }