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]); }