Example #1
0
        public void AddFlankingTranscript(Transcript transcript, TranscriptAnnotation ta, string[] consequences)
        {
            _currTranscript = new JsonVariant.Transcript
            {
                IsCanonical  = transcript.IsCanonical ? TrueTag : null,
                Consequence  = consequences,
                ProteinID    = ta.HasValidCdnaCodingStart ? TranscriptUtilities.GetProteinId(transcript) : null,
                TranscriptID = TranscriptUtilities.GetTranscriptId(transcript),
                BioType      = BioTypeUtilities.GetBiotypeDescription(transcript.BioType),
                Gene         = transcript.TranscriptSource == TranscriptDataSource.Ensembl ? transcript.Gene.EnsemblId.ToString() : transcript.Gene.EntrezGeneId.ToString(),
                Hgnc         = transcript.Gene.Symbol
            };

            if (ta.HasValidCdnaStart && ta.HasValidCdnaEnd)
            {
                _currTranscript.ComplementaryDnaPosition = GetCdnaRangeString(ta);
            }

            _currJsonVariant.AddTranscript(_currTranscript, transcript.TranscriptSource);
        }
Example #2
0
        public void CreateAnnotationObject(Transcript transcript, VariantAlternateAllele altAllele)
        {
            // while annotating alternate allele, the first output function to be called is AddExonData.
            // So, we set the current json variant and transcript here.
            // they will subsequently be used in other output functions.
            FindCorrespondingJsonVariant(altAllele);

            if (_currJsonVariant == null)
            {
                throw new GeneralException("Cannot find jsonVariant corresponding to alternate allele");
            }

            _currTranscript = new JsonVariant.Transcript
            {
                IsCanonical  = transcript.IsCanonical ? TrueTag : null,
                TranscriptID = TranscriptUtilities.GetTranscriptId(transcript),
                BioType      = BioTypeUtilities.GetBiotypeDescription(transcript.BioType),
                Gene         = transcript.TranscriptSource == TranscriptDataSource.Ensembl ? transcript.Gene.EnsemblId.ToString() : transcript.Gene.EntrezGeneId.ToString(),
                Hgnc         = transcript.Gene.Symbol
            };
        }