private IGeneralAttributes GetGeneralAttributes(ITranscript transcript) { string bioType = AnnotatedTranscript.GetBioType(transcript.BioType); int internalGeneId = _geneToInternalId[transcript.Gene]; string geneId = transcript.Source == Source.Ensembl ? transcript.Gene.EnsemblId.WithVersion : transcript.Gene.EntrezGeneId.WithVersion; return(new GeneralAttributes(geneId, transcript.Gene.Symbol, transcript.Id.WithVersion, transcript.Translation?.ProteinId?.WithVersion, bioType, transcript.IsCanonical, internalGeneId)); }
public static void Annotate(AnnotatedVariant variant) { _countToDelay--; if (_countToDelay == 0) { _countToDelay = RateLimit; Thread.Sleep(1); } var position = variant.Position; var n = 1 + position % 13;// that its never 0 var transcripts = new AnnotatedTranscript[n]; for (int i = 0; i < n; i++) { transcripts[i] = AnnotatedTranscript.Create(position, i); } variant.Transcripts = transcripts; }
public static AnnotatedVariant Create() { var chrom = ChromNames[_random.Next(0, ChromNames.Length - 1)]; var position = _random.Next(1_000, 250_000_000); var refAllele = Alleles[_random.Next(0, Alleles.Length - 1)]; var altAllele = Alleles[_random.Next(0, Alleles.Length - 1)]; var alleleFrequency = _random.Next(0, 1_000_000) * 1.0 / 1_000_000; var pathogenicity = PathogenicitySet[_random.Next(0, PathogenicitySet.Length - 1)]; var transcripts = new AnnotatedTranscript[_random.Next(1, 15)]; for (int i = 0; i < transcripts.Length; i++) { transcripts[i] = AnnotatedTranscript.Create(); } var pubmedIds = new int[_random.Next(2, 20)]; for (int i = 0; i < pubmedIds.Length; i++) { pubmedIds[i] = _random.Next(10_000, 100_000); } return(new AnnotatedVariant(chrom, position, refAllele, altAllele, transcripts, alleleFrequency, pathogenicity, pubmedIds)); }