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));
}
