public void DetermineIntronicEffect_IsStartSpliceSite()
{
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineIntronicEffect(_otherTranscriptRegions, new Interval(300, 303), VariantType.deletion);
Assert.True(positionalEffect.IsStartSpliceSite);
}
public void DetermineIntronicEffect_IsEndSpliceSite()
{
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineIntronicEffect(_otherTranscriptRegions, new Interval(400, 400), VariantType.SNV);
Assert.True(positionalEffect.IsEndSpliceSite);
}
public void DetermineIntronicEffect_IsWithinFrameshiftIntron()
{
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineIntronicEffect(_otherTranscriptRegions, new Interval(702, 705), VariantType.deletion);
Assert.True(positionalEffect.IsWithinFrameshiftIntron);
}
public void DetermineIntronicEffect_IsWithinSpliceSiteRegion()
{
var positionalEffect = new TranscriptPositionalEffect();
IInterval variant = new Interval(298, 302);
positionalEffect.DetermineIntronicEffect(_otherTranscriptRegions, variant, VariantType.deletion);
Assert.True(positionalEffect.IsWithinSpliceSiteRegion);
}
public void DetermineIntronicEffect_IsWithinFrameshiftIntron_NotInSpliceSite()
{
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineIntronicEffect(_otherTranscriptRegions, new Interval(701, 709), VariantType.deletion);
Assert.True(positionalEffect.IsWithinFrameshiftIntron);
Assert.False(positionalEffect.IsStartSpliceSite);
Assert.False(positionalEffect.IsEndSpliceSite);
}
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);
}
public void DetermineIntronicEffect_IsWithinIntron()
{
IInterval variant = new Interval(300, 302);
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineIntronicEffect(_otherTranscriptRegions, variant, VariantType.deletion);
Assert.False(positionalEffect.IsWithinIntron);
IInterval variant2 = new Interval(303, 303);
var positionalEffect2 = new TranscriptPositionalEffect();
positionalEffect2.DetermineIntronicEffect(_otherTranscriptRegions, variant2, VariantType.deletion);
Assert.True(positionalEffect2.IsWithinIntron);
}
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);
}
public void DetermineIntronicEffect_NotWithinFrameshiftIntron()
{
var transcriptRegions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 201342300, 201342340, 1, 186),
new TranscriptRegion(TranscriptRegionType.Intron, 1, 201342340, 201342343, 186, 187),
new TranscriptRegion(TranscriptRegionType.Exon, 2, 201342344, 201342400, 187, 349)
};
IInterval variant = new Interval(201342344, 201342344);
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineIntronicEffect(transcriptRegions, variant, VariantType.SNV);
Assert.True(positionalEffect.IsWithinSpliceSiteRegion);
}
public void DetermineIntronicEffect_NullIntrons()
{
var positionalEffect = new TranscriptPositionalEffect();
positionalEffect.DetermineIntronicEffect(null, new Interval(400, 400), VariantType.SNV);
Assert.False(positionalEffect.IsEndSpliceSite);
Assert.False(positionalEffect.IsStartSpliceSite);
Assert.False(positionalEffect.IsWithinFrameshiftIntron);
Assert.False(positionalEffect.IsWithinIntron);
Assert.False(positionalEffect.IsWithinSpliceSiteRegion);
Assert.False(positionalEffect.HasExonOverlap);
Assert.False(positionalEffect.AfterCoding);
Assert.False(positionalEffect.BeforeCoding);
Assert.False(positionalEffect.WithinCdna);
Assert.False(positionalEffect.WithinCds);
Assert.False(positionalEffect.HasFrameShift);
Assert.False(positionalEffect.IsCoding);
}