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 int setCdsAndProteinPosition(int cdnaVariantPosition, int firstCdsPhase, int cdnaCodingStart) { if (cdnaVariantPosition != -1) { // cdnaVariantStart may be null if variantEnd falls in an intron if (transcript.unconfirmedStart()) { cdnaCodingStart -= ((3 - firstCdsPhase) % 3); } int cdsVariantStart = cdnaVariantPosition - cdnaCodingStart + 1; consequenceType.setCdsPosition(cdsVariantStart); // First place where protein variant annotation is added to the Consequence type, // must create the ProteinVariantAnnotation object ProteinVariantAnnotation proteinVariantAnnotation = new ProteinVariantAnnotation(); proteinVariantAnnotation.setPosition(((cdsVariantStart - 1) / 3) + 1); consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation); } return cdnaCodingStart; }
protected int setCdsAndProteinPosition(int cdnaVariantPosition, int firstCdsPhase, int cdnaCodingStart) { if (cdnaVariantPosition != -1) { // cdnaVariantStart may be null if variantEnd falls in an intron if (transcript.unconfirmedStart()) { cdnaCodingStart -= ((3 - firstCdsPhase) % 3); } int cdsVariantStart = cdnaVariantPosition - cdnaCodingStart + 1; consequenceType.setCdsPosition(cdsVariantStart); // First place where protein variant annotation is added to the Consequence type, // must create the ProteinVariantAnnotation object ProteinVariantAnnotation proteinVariantAnnotation = new ProteinVariantAnnotation(); proteinVariantAnnotation.setPosition(((cdsVariantStart - 1) / 3) + 1); consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation); } return cdnaCodingStart; }
private void parseRemainingFields(ConsequenceType consequenceType, String[] lineFields) { consequenceType.setEnsemblGeneId(lineFields[3]); // fill Ensembl gene id consequenceType.setEnsemblTranscriptId(lineFields[4]); // fill Ensembl transcript id ProteinVariantAnnotation proteinVariantAnnotation = new ProteinVariantAnnotation(); if(!lineFields[7].equals("-")) { consequenceType.setCdnaPosition(parseStringInterval(lineFields[7])); // fill cdna position } if(!lineFields[8].equals("-")) { consequenceType.setCdsPosition(parseStringInterval(lineFields[8])); // fill cds position } if(!lineFields[9].equals("-")) { proteinVariantAnnotation.setPosition(parseStringInterval(lineFields[9])); // fill aa position } if(!lineFields[10].equals("-")) { String parts[] = lineFields[10].split("/"); if(parts.length == 2) { proteinVariantAnnotation.setReference(parts[0]); // fill aa change proteinVariantAnnotation.setAlternate(parts[1]); // fill aa change } } consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation); consequenceType.setCodon(lineFields[11]); // fill codon change if(!lineFields[6].equals("") && !lineFields.equals("-")) { // VEP may leave this field empty consequenceType.setSequenceOntologyTerms( getSequenceOntologyTerms(Arrays.asList(lineFields[6].split(",")))); // fill so terms // consequenceType.setSoTermsFromSoNames(Arrays.asList(lineFields[6].split(","))); // fill so terms } }
private List<ConsequenceType> getConsequenceTypeList(Variant variant, List<Gene> geneList, boolean regulatoryAnnotation, QueryOptions queryOptions) { boolean[] overlapsRegulatoryRegion = {false, false}; if (regulatoryAnnotation) { overlapsRegulatoryRegion = getRegulatoryRegionOverlaps(variant); } ConsequenceTypeCalculator consequenceTypeCalculator = getConsequenceTypeCalculator(variant); List<ConsequenceType> consequenceTypeList = consequenceTypeCalculator.run(variant, geneList, overlapsRegulatoryRegion, queryOptions); if (variant.getType() == VariantType.SNV || Variant.inferType(variant.getReference(), variant.getAlternate()) == VariantType.SNV) { for (ConsequenceType consequenceType : consequenceTypeList) { if (nonSynonymous(consequenceType, variant.getChromosome().equals("MT"))) { consequenceType.setProteinVariantAnnotation(getProteinAnnotation(consequenceType)); } } } return consequenceTypeList; }
private List<ConsequenceType> getConsequenceTypeList(Variant variant, List<Gene> geneList, boolean regulatoryAnnotation, QueryOptions queryOptions) { boolean[] overlapsRegulatoryRegion = {false, false}; if (regulatoryAnnotation) { overlapsRegulatoryRegion = getRegulatoryRegionOverlaps(variant); } ConsequenceTypeCalculator consequenceTypeCalculator = getConsequenceTypeCalculator(variant); List<ConsequenceType> consequenceTypeList = consequenceTypeCalculator.run(variant, geneList, overlapsRegulatoryRegion, queryOptions); if (variant.getType() == VariantType.SNV || Variant.inferType(variant.getReference(), variant.getAlternate()) == VariantType.SNV) { for (ConsequenceType consequenceType : consequenceTypeList) { if (nonSynonymous(consequenceType, variant.getChromosome().equals("MT"))) { consequenceType.setProteinVariantAnnotation(getProteinAnnotation(consequenceType)); } } } return consequenceTypeList; }
protVarAnnotation.setAlternate(refAlt[1]); consequenceType.setProteinVariantAnnotation(protVarAnnotation);
consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation);
consequenceType3.setProteinVariantAnnotation(newProteinVariantAnnotation); consequenceType3.setSequenceOntologyTerms(soTerms); consequenceType1.setProteinVariantAnnotation(newProteinVariantAnnotation == null ? getProteinAnnotation(consequenceType1) : newProteinVariantAnnotation); consequenceType1.setSequenceOntologyTerms(soTerms); consequenceType2.setCodon(codon); consequenceType2.setProteinVariantAnnotation(consequenceType1.getProteinVariantAnnotation()); consequenceType2.setSequenceOntologyTerms(soTerms);
consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation);
consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation);
consequenceType3.setProteinVariantAnnotation(newProteinVariantAnnotation); consequenceType3.setSequenceOntologyTerms(soTerms); consequenceType1.setProteinVariantAnnotation(newProteinVariantAnnotation == null ? getProteinAnnotation(consequenceType1) : newProteinVariantAnnotation); consequenceType1.setSequenceOntologyTerms(soTerms); consequenceType2.setCodon(codon); consequenceType2.setProteinVariantAnnotation(consequenceType1.getProteinVariantAnnotation()); consequenceType2.setSequenceOntologyTerms(soTerms);
consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation);