public static IAnnotatedTranscript GetAnnotatedTranscript(ITranscript transcript, IVariant leftShiftedVariant,
ISequence refSequence, IPredictionCache siftCache, IPredictionCache polyphenCache, AminoAcids aminoAcids)
{
var rightShiftedVariant = VariantRotator.Right(leftShiftedVariant, transcript, refSequence,
transcript.Gene.OnReverseStrand);
var leftAnnotation = AnnotateTranscript(transcript, leftShiftedVariant, aminoAcids, refSequence);
var rightAnnotation = ReferenceEquals(leftShiftedVariant, rightShiftedVariant)
? leftAnnotation
: AnnotateTranscript(transcript, rightShiftedVariant, aminoAcids, refSequence);
var consequences = GetConsequences(transcript, leftShiftedVariant, leftAnnotation.VariantEffect);
var hgvsCoding = HgvsCodingNomenclature.GetHgvscAnnotation(transcript, rightShiftedVariant, refSequence,
rightAnnotation.Position.RegionStartIndex, rightAnnotation.Position.RegionEndIndex);
var hgvsProtein = HgvsProteinNomenclature.GetHgvsProteinAnnotation(transcript,
rightAnnotation.RefAminoAcids, rightAnnotation.AltAminoAcids, rightAnnotation.TranscriptAltAllele,
rightAnnotation.Position, rightAnnotation.VariantEffect, rightShiftedVariant, refSequence, hgvsCoding,
leftShiftedVariant.Chromosome.UcscName == "chrM");
var predictionScores = GetPredictionScores(leftAnnotation.Position, leftAnnotation.RefAminoAcids,
leftAnnotation.AltAminoAcids, siftCache, polyphenCache, transcript.SiftIndex, transcript.PolyPhenIndex);
return(new AnnotatedTranscript(transcript, leftAnnotation.RefAminoAcids, leftAnnotation.AltAminoAcids,
leftAnnotation.RefCodons, leftAnnotation.AltCodons, leftAnnotation.Position, hgvsCoding, hgvsProtein,
predictionScores.Sift, predictionScores.PolyPhen, consequences, false));
}
public void Insertion()
{
var variantEffect = new Mock <IVariantEffect>();
variantEffect.Setup(x => x.IsFrameshiftVariant()).Returns(false);
variantEffect.Setup(x => x.IsStopRetained()).Returns(false);
variantEffect.Setup(x => x.IsStartLost()).Returns(false);
variantEffect.Setup(x => x.IsStopLost()).Returns(false);
var proteinChange = HgvsProteinNomenclature.GetProteinChange(4, "", "A", "MACTAWR", variantEffect.Object);
Assert.Equal(ProteinChange.Insertion, proteinChange);
}
public void IsDuplicatedAminoAcidsTests(string refAminoAcids, string altAminoAcids, bool result)
{
Assert.Equal(result, HgvsProteinNomenclature.IsDuplicatedAminoAcids(refAminoAcids, altAminoAcids));
}
