private boolean nonSynonymous(ConsequenceType consequenceType, boolean useMitochondrialCode) { if (consequenceType.getCodon() == null) { return false; } else { String[] parts = consequenceType.getCodon().split("/"); String ref = String.valueOf(parts[0]).toUpperCase(); String alt = String.valueOf(parts[1]).toUpperCase(); return !VariantAnnotationUtils.isSynonymousCodon(useMitochondrialCode, ref, alt) && !VariantAnnotationUtils.isStopCodon(useMitochondrialCode, ref); } }
private boolean nonSynonymous(ConsequenceType consequenceType, boolean useMitochondrialCode) { if (consequenceType.getCodon() == null) { return false; } else { String[] parts = consequenceType.getCodon().split("/"); String ref = String.valueOf(parts[0]).toUpperCase(); String alt = String.valueOf(parts[1]).toUpperCase(); return !VariantAnnotationUtils.isSynonymousCodon(useMitochondrialCode, ref, alt) && !VariantAnnotationUtils.isStopCodon(useMitochondrialCode, ref); } }
if (StringUtils.isNotEmpty(conseqType.getCodon()) || (conseqType.getCdnaPosition() != null && conseqType.getCdnaPosition() > 0) || (conseqType.getCdsPosition() != null && conseqType.getCdsPosition() > 0)) { .append(FIELD_SEP) .append(conseqType.getCdsPosition() == null ? 0 : conseqType.getCdsPosition()); if (StringUtils.isNotEmpty(conseqType.getCodon())) { trans.append(FIELD_SEP).append(conseqType.getCodon());
String referenceCodon = consequenceType1.getCodon().split("/")[0].toUpperCase(); int codonIdx1 = getUpperCaseLetterPosition(consequenceType1.getCodon().split("/")[0]); int codonIdx2 = getUpperCaseLetterPosition(consequenceType2.getCodon().split("/")[0]); char[] referenceCodonArray = consequenceType1.getCodon().split("/")[0].toLowerCase().toCharArray(); referenceCodonArray[codonIdx1] = Character.toUpperCase(referenceCodonArray[codonIdx1]); referenceCodonArray[codonIdx2] = Character.toUpperCase(referenceCodonArray[codonIdx2]);
String referenceCodon = consequenceType1.getCodon().split("/")[0].toUpperCase(); int codonIdx1 = getUpperCaseLetterPosition(consequenceType1.getCodon().split("/")[0]); int codonIdx2 = getUpperCaseLetterPosition(consequenceType2.getCodon().split("/")[0]); char[] referenceCodonArray = consequenceType1.getCodon().split("/")[0].toLowerCase().toCharArray(); referenceCodonArray[codonIdx1] = Character.toUpperCase(referenceCodonArray[codonIdx1]); referenceCodonArray[codonIdx2] = Character.toUpperCase(referenceCodonArray[codonIdx2]);
if((codon=consequenceType.getCodon())==null) { codon = "-";
putNotNull(ct, CT_ENSEMBL_TRANSCRIPT_ID_FIELD, consequenceType.getEnsemblTranscriptId()); putNotNull(ct, CT_CODON_FIELD, consequenceType.getCodon()); putNotDefault(ct, CT_STRAND_FIELD, consequenceType.getStrand(), DEFAULT_STRAND_VALUE); putNotNull(ct, CT_BIOTYPE_FIELD, consequenceType.getBiotype());
int outCdnaPosition = outCT.getCdnaPosition() == null ? 0 : outCT.getCdnaPosition(); int outCdsPosition = outCT.getCdsPosition() == null ? 0 : outCT.getCdsPosition(); String inCodon = inCT.getCodon() == null ? "" : inCT.getCodon().trim(); String outCodon = outCT.getCodon() == null ? "" : outCT.getCodon().trim(); System.out.println(inCdnaPosition + " vs " + outCdnaPosition + " ; " + inCdsPosition + " vs " + outCdsPosition
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(); }