private void CreateTranscriptDictionary(List <Transcript> transcripts)
{
_transcriptsById.Clear();
foreach (var transcript in transcripts)
{
_transcriptsById[TranscriptUtilities.GetTranscriptId(transcript)] = transcript;
}
}
public SvOverlapTranscript(DataStructures.Transcript transcript, VariantAlternateAllele altAllele)
{
TranscriptID = TranscriptUtilities.GetTranscriptId(transcript);
IsCanonical = transcript.IsCanonical ? "true" : null;
Hgnc = transcript.Gene.Symbol;
var isFullOverlap = altAllele.Start <= transcript.Start && altAllele.End >= transcript.End;
IsPartialOverlap = isFullOverlap ? null : "true";
}
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
};
}
public BreakendTranscriptAnnotation(Transcript transcript, int breakendPosition, char isBreakendSuffix)
{
var transcriptId = TranscriptUtilities.GetTranscriptId(transcript);
TranscriptDataSource = transcript.TranscriptSource;
GeneName = transcript.Gene.Symbol;
if (transcript.Translation == null || breakendPosition < transcript.Translation.CodingRegion.GenomicStart || breakendPosition > transcript.Translation.CodingRegion.GenomicEnd)
{
InCodingRegion = false;
return;
}
InCodingRegion = true;
var transcriptCdnaLength = transcript.Translation.CodingRegion.CdnaEnd - transcript.Translation.CodingRegion.CdnaStart + 1;
_referenceName = "chr";
_codingStart = transcript.Translation.CodingRegion.GenomicStart;
_codingEnd = transcript.Translation.CodingRegion.GenomicEnd;
// map cdn position
var complementaryCdnaPosDescription = MapCdnaPosition(transcript, breakendPosition);
LocateExonIntron(transcript, breakendPosition);
var transcriptOrientation = transcript.Gene.OnReverseStrand ? '-' : '+';
ConsistentOrientation = transcriptOrientation == isBreakendSuffix;
if (ConsistentOrientation)
{
HgvsDescription = GeneName + "{" + transcriptId + "}" + ":c." + complementaryCdnaPosDescription + "_" +
transcriptCdnaLength;
}
else
{
HgvsDescription = GeneName + "{" + transcriptId + "}" + ":c." + 1 + "_" + complementaryCdnaPosDescription;
}
}