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))); }