private static void WriteGeneralAttributes(TextWriter writer, Transcript transcript)
{
var geneId = transcript.TranscriptSource == TranscriptDataSource.Ensembl
? transcript.Gene.EnsemblId.ToString()
: transcript.Gene.EntrezGeneId.ToString();
if (!string.IsNullOrEmpty(geneId))
{
writer.Write($"gene_id \"{geneId}\"; ");
}
if (!string.IsNullOrEmpty(transcript.Gene.Symbol))
{
writer.Write($"gene_name \"{transcript.Gene.Symbol}\"; ");
}
if (!transcript.Id.IsEmpty)
{
writer.Write($"transcript_id \"{FormatUtilities.CombineIdAndVersion(transcript.Id, transcript.Version)}\"; ");
}
writer.Write($"transcript_type \"{BioTypeUtilities.GetBiotypeDescription(transcript.BioType)}\"; ");
if (transcript.IsCanonical)
{
writer.Write("tag \"canonical\"; ");
}
if (!string.IsNullOrEmpty(transcript.Translation?.ProteinId.ToString()))
{
writer.Write($"protein_id \"{FormatUtilities.CombineIdAndVersion(transcript.Translation.ProteinId, transcript.Translation.ProteinVersion)}\"; ");
}
}
public void CreateAnnotationObject(Transcript transcript, VariantAlternateAllele altAllele)
{
FindCorrespondingJsonVariant(altAllele);
if (_currPianoAllele == null)
{
throw new GeneralException("Cannot find jsonVariant corresponding to alternate allele");
}
_currTranscript = new PianoAllele.Transcript
{
IsCanonical = transcript.IsCanonical ? "true" : null,
TranscriptID = transcript.Id.ToString(),
BioType = BioTypeUtilities.GetBiotypeDescription(transcript.BioType),
Gene = transcript.TranscriptSource == TranscriptDataSource.Ensembl ? transcript.Gene.EnsemblId.ToString() : transcript.Gene.EntrezGeneId.ToString(),
Hgnc = transcript.Gene.Symbol
};
}
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
};
}
private static void TranscriptDump(DataStructures.VEP.Transcript t)
{
Console.WriteLine("==================================");
Console.WriteLine($"ReferenceIndex: {t.ReferenceIndex}");
Console.WriteLine($"Start: {t.Start}");
Console.WriteLine($"End: {t.End}");
Console.WriteLine($"BioType: {BioTypeUtilities.GetBiotypeDescription(t.BioType)}");
Console.WriteLine($"OnReverseStrand: {t.OnReverseStrand}");
Console.WriteLine($"IsCanonical: {t.IsCanonical}");
Console.WriteLine($"CompDnaCodingStart: {t.CompDnaCodingStart}");
Console.WriteLine($"CompDnaCodingEnd: {t.CompDnaCodingEnd}");
Console.WriteLine($"Version: {t.Version}");
Console.WriteLine($"CcdsId: {t.CcdsId}");
Console.WriteLine($"DatabaseId: {t.DatabaseId}");
Console.WriteLine($"ProteinId: {t.ProteinId}");
Console.WriteLine($"RefSeqId: {t.RefSeqId}");
Console.WriteLine($"GeneStableId: {t.GeneStableId}");
Console.WriteLine($"StableId: {t.StableId}");
Console.WriteLine($"GeneSymbol: {t.GeneSymbol}");
Console.WriteLine($"GeneSymbolSource: {t.GeneSymbolSource}");
Console.WriteLine($"HgncId: {t.HgncId}");
Console.WriteLine("==================================");
}
/// <summary>
/// returns the biotype given the specialized string key/value type
/// </summary>
public static BioType GetBiotype(AbstractData ad)
{
return(BioTypeUtilities.GetBiotypeFromString(DumperUtilities.GetString(ad)));
}
