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);
}
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
};
}