public void DetermineExonicEffect_OverlapWithMicroRna()
{
IInterval variant = new Interval(3477284, 3477284);
var position = new MappedPosition(71, 71, -1, -1, -1, -1, 1, 1, -1, -1, 0, 0);
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineExonicEffect(_reverseTranscript.Object, variant, position, 71, 71, -1, -1, "G", false);
Assert.True(positionalEffect.OverlapWithMicroRna);
}
public void DetermineExonicEffect_WithinCds()
{
IInterval variant = new Interval(876543, 876543);
var position = new MappedPosition(206, 206, 206, 206, 69, 69, 2, 2, -1, -1, 2, 2);
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineExonicEffect(_forwardTranscript.Object, variant, position, 206, 206, 206, 206, "G", false);
Assert.True(positionalEffect.WithinCdna);
}
public void DetermineExonicEffect_WithinCdna()
{
IInterval variant = new Interval(879600, 879600);
var position = new MappedPosition(1692, 1692, -1, -1, -1, -1, 7, 7, -1, -1, 12, 12);
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineExonicEffect(_forwardTranscript.Object, variant, position, 1692, 1692, -1, -1, "G", false);
Assert.True(positionalEffect.WithinCdna);
}
public void DetermineExonicEffect_HasExonOverlap()
{
IInterval variant = new Interval(876686, 876686);
var position = new MappedPosition(349, 349, 349, 349, 117, 117, 2, 2, -1, -1, 2, 2);
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineExonicEffect(_forwardTranscript.Object, variant, position, 349, 349, 349, 349, "G", false);
Assert.True(positionalEffect.HasExonOverlap);
}
private static VariantEffect GetVariantEffect(ITranscript transcript, ISimpleVariant variant, IMappedPositions mappedPositions, string refAminoAcids, string altAminoAcids, string refCodons, string altCodons, bool insertionInStartAndNoImpact)
{
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineIntronicEffect(transcript.Introns, variant, variant.Type);
positionalEffect.DetermineExonicEffect(transcript, variant, mappedPositions, variant.AltAllele, insertionInStartAndNoImpact);
var variantEffect = new VariantEffect(positionalEffect, variant, transcript, refAminoAcids,
altAminoAcids,
refCodons, altCodons, mappedPositions.ProteinInterval.Start);
return(variantEffect);
}
private static TranscriptPositionalEffect GetPositionalEffect(ITranscript transcript, ISimpleVariant variant,
IMappedPosition position, string refAminoAcid, string altAminoAcid, int coveredCdnaStart,
int coveredCdnaEnd, int coveredCdsStart, int coveredCdsEnd)
{
bool startCodonInsertionWithNoImpact = variant.Type == VariantType.insertion &&
position.ProteinStart <= 1 &&
altAminoAcid.EndsWith(refAminoAcid);
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineIntronicEffect(transcript.TranscriptRegions, variant, variant.Type);
positionalEffect.DetermineExonicEffect(transcript, variant, position, coveredCdnaStart, coveredCdnaEnd,
coveredCdsStart, coveredCdsEnd, variant.AltAllele, startCodonInsertionWithNoImpact);
return(positionalEffect);
}