public void IsCodingSequenceVariant_WithMoreSpecificConsequence_ReturnFalse(ConsequenceTag ct)
{
var positionalEffect = new TranscriptPositionalEffect
{
BeforeCoding = false,
AfterCoding = true,
WithinCdna = true
};
var cache = new VariantEffectCache();
cache.Add(ct, true);
var variant = new Mock <ISimpleVariant>();
variant.SetupGet(x => x.AltAllele).Returns("ATAGCCC");
variant.SetupGet(x => x.RefAllele).Returns("A");
var variantEffect = new VariantEffect(positionalEffect, variant.Object, null, "", "", "", "",
null, null, null, cache);
Assert.False(variantEffect.IsCodingSequenceVariant());
}
public void DetermineSmallVariantEffects_tier3()
{
var cache = new VariantEffectCache();
cache.Add(ConsequenceTag.mature_miRNA_variant, false);
cache.Add(ConsequenceTag.splice_donor_variant, true);
cache.Add(ConsequenceTag.splice_acceptor_variant, true);
cache.Add(ConsequenceTag.stop_gained, true);
cache.Add(ConsequenceTag.frameshift_variant, true);
cache.Add(ConsequenceTag.stop_lost, true);
cache.Add(ConsequenceTag.start_lost, true);
cache.Add(ConsequenceTag.inframe_insertion, true);
cache.Add(ConsequenceTag.inframe_deletion, true);
cache.Add(ConsequenceTag.missense_variant, true);
cache.Add(ConsequenceTag.protein_altering_variant, true);
cache.Add(ConsequenceTag.splice_region_variant, true);
cache.Add(ConsequenceTag.incomplete_terminal_codon_variant, true);
cache.Add(ConsequenceTag.stop_retained_variant, true);
cache.Add(ConsequenceTag.synonymous_variant, true);
cache.Add(ConsequenceTag.coding_sequence_variant, true);
cache.Add(ConsequenceTag.five_prime_UTR_variant, true);
cache.Add(ConsequenceTag.three_prime_UTR_variant, true);
cache.Add(ConsequenceTag.non_coding_transcript_exon_variant, true);
cache.Add(ConsequenceTag.intron_variant, true);
cache.Add(ConsequenceTag.NMD_transcript_variant, true);
cache.Add(ConsequenceTag.non_coding_transcript_variant, true);
var simpleVariant = new Mock <ISimpleVariant>();
simpleVariant.SetupGet(x => x.RefAllele).Returns("G");
simpleVariant.SetupGet(x => x.AltAllele).Returns("C");
var positionalEffect = new TranscriptPositionalEffect
{
IsWithinIntron = true
};
var variantEffect = new VariantEffect(positionalEffect, simpleVariant.Object, null, null, null, null, null, null, cache);
var featureEffect = new Mock <IFeatureVariantEffects>();
featureEffect.Setup(x => x.Ablation()).Returns(false);
featureEffect.Setup(x => x.Amplification()).Returns(false);
featureEffect.Setup(x => x.Truncation()).Returns(true);
featureEffect.Setup(x => x.Elongation()).Returns(true);
var consequence = new Consequences(variantEffect, featureEffect.Object);
consequence.DetermineSmallVariantEffects();
var observedConsequence = consequence.GetConsequences();
Assert.Equal(ConsequenceTag.splice_donor_variant, observedConsequence[0]);
Assert.Equal(ConsequenceTag.splice_acceptor_variant, observedConsequence[1]);
Assert.Equal(ConsequenceTag.stop_gained, observedConsequence[2]);
Assert.Equal(ConsequenceTag.frameshift_variant, observedConsequence[3]);
Assert.Equal(ConsequenceTag.stop_lost, observedConsequence[4]);
Assert.Equal(ConsequenceTag.start_lost, observedConsequence[5]);
Assert.Equal(ConsequenceTag.inframe_insertion, observedConsequence[6]);
Assert.Equal(ConsequenceTag.inframe_deletion, observedConsequence[7]);
Assert.Equal(ConsequenceTag.missense_variant, observedConsequence[8]);
Assert.Equal(ConsequenceTag.protein_altering_variant, observedConsequence[9]);
Assert.Equal(ConsequenceTag.splice_region_variant, observedConsequence[10]);
Assert.Equal(ConsequenceTag.incomplete_terminal_codon_variant, observedConsequence[11]);
Assert.Equal(ConsequenceTag.stop_retained_variant, observedConsequence[12]);
Assert.Equal(ConsequenceTag.synonymous_variant, observedConsequence[13]);
Assert.Equal(ConsequenceTag.coding_sequence_variant, observedConsequence[14]);
Assert.Equal(ConsequenceTag.five_prime_UTR_variant, observedConsequence[15]);
Assert.Equal(ConsequenceTag.three_prime_UTR_variant, observedConsequence[16]);
Assert.Equal(ConsequenceTag.non_coding_transcript_exon_variant, observedConsequence[17]);
Assert.Equal(ConsequenceTag.intron_variant, observedConsequence[18]);
Assert.Equal(ConsequenceTag.NMD_transcript_variant, observedConsequence[19]);
Assert.Equal(ConsequenceTag.non_coding_transcript_variant, observedConsequence[20]);
}
