public void GetOverlapFractions_ReturnNulls_BreakEnd() { var saInterval = new ChromosomeInterval(Chr1, 2, 1); var variant = new SimpleVariant(Chr1, 1, 2, null, null, VariantType.translocation_breakend); var(reciprocalOverlap, annotationOverlap) = SuppIntervalUtilities.GetOverlapFractions(saInterval, variant); Assert.Null(reciprocalOverlap); Assert.Null(annotationOverlap); }
public void GetOverlapFractions_ReturnNulls_Insertion() { var saInterval = new ChromosomeInterval(Chr1, 1, 2); var variant = new SimpleVariant(Chr1, 1, 2, null, null, VariantType.insertion); var(reciprocalOverlap, annotationOverlap) = SuppIntervalUtilities.GetOverlapFractions(saInterval, variant); Assert.Null(reciprocalOverlap); Assert.Null(annotationOverlap); }
public void GetHgvscAnnotation_duplication_at_last_position() { var sequence = new Mock <ISequence>(); sequence.Setup(x => x.Substring(70361156 - 4, 4)).Returns("ACAC"); var variant = new SimpleVariant(chrX, 70361157, 70361156, "", "ACAC", VariantType.insertion);//right shifted variant var observedHgvsc = HgvsCodingNomenclature.GetHgvscAnnotation(GetForwardTranscriptWithoutUtr(), variant, sequence.Object, 0, 0); Assert.Equal("ENST00000579622.1:n.119_122dupACAC", observedHgvsc); }
public void GetHgvscAnnotation_duplication_in_coding_region() { var sequence = new Mock <ISequence>(); sequence.Setup(x => x.Substring(1262626, 2)).Returns("TA"); var variant = new SimpleVariant(Chromosome, 1262629, 1262628, "", "TA", VariantType.insertion); var observedHgvsc = HgvsCodingNomenclature.GetHgvscAnnotation(_forwardTranscript, variant, sequence.Object, 4, 4); Assert.Equal("ENST00000343938.4:c.129_130dupTA", observedHgvsc); }
public void GetHgvscAnnotation_insertion_after_coding_region() { var sequence = new Mock <ISequence>(); sequence.Setup(x => x.Substring(1262627, 1)).Returns("A"); var variant = new SimpleVariant(Chromosome, 1263159, 1263158, "", "G", VariantType.insertion); var observedHgvsc = HgvsCodingNomenclature.GetHgvscAnnotation(_forwardTranscript, variant, sequence.Object, 4, 4); Assert.Equal("ENST00000343938.4:c.*15_*16insG", observedHgvsc); }
public void GetHgvscAnnotation_insertion_at_last_position() { var sequence = new Mock <ISequence>(); sequence.Setup(x => x.Substring(70361157 - 12, 12)).Returns("TATATATATATA"); var variant = new SimpleVariant(ChromosomeUtilities.ChrX, 70361157, 70361156, "", "ACACCAGCAGCA", VariantType.insertion);//right shifted variant var observedHgvsc = HgvsCodingNomenclature.GetHgvscAnnotation(GetForwardTranscriptWithoutUtr(), variant, sequence.Object, 0, 0); Assert.Equal("ENST00000579622.1:n.122_123insACACCAGCAGCA", observedHgvsc); }
public void GetOverlapFractions_NotNull_AsExpected(int varStart, int varEnd, int saStart, int saEnd, double expectedReciprocalOverlap, double expecedAnnotationOverlap) { var saInterval = new ChromosomeInterval(ChromosomeUtilities.Chr1, saStart, saEnd); var variant = new SimpleVariant(ChromosomeUtilities.Chr1, varStart, varEnd, null, null, VariantType.deletion); var(reciprocalOverlap, annotationOverlap) = SuppIntervalUtilities.GetOverlapFractions(saInterval, variant); Assert.NotNull(reciprocalOverlap); Assert.NotNull(annotationOverlap); Assert.Equal(expectedReciprocalOverlap, reciprocalOverlap.Value, 5); Assert.Equal(expecedAnnotationOverlap, annotationOverlap.Value, 5); }
public void GetHgvscAnnotation_in_intron_gap_substitution(int variantStart, int variantEnd, string reference, string alt, string transcriptRef, VariantType variantType, string expectedHgvsc) { var(startIndex, _) = MappedPositionUtilities.FindRegion(_gapTranscript.TranscriptRegions, variantStart); var(endIndex, _) = MappedPositionUtilities.FindRegion(_gapTranscript.TranscriptRegions, variantEnd); var variant = new SimpleVariant(ChromosomeUtilities.Chr10, variantStart, variantEnd, reference, alt, variantType); var observedHgvsc = HgvsCodingNomenclature.GetHgvscAnnotation(_gapTranscript, variant, null, startIndex, endIndex, transcriptRef, null); Assert.Equal(expectedHgvsc, observedHgvsc); }
public void Right_Deletion_ReverseStrand() { var variant = new SimpleVariant(ChromosomeUtilities.Chr1, 966399, 966401, "TG", "", VariantType.deletion); var transcript = new Mock <ITranscript>(); transcript.SetupGet(x => x.Start).Returns(966300); transcript.SetupGet(x => x.End).Returns(966405); transcript.SetupGet(x => x.Gene.OnReverseStrand).Returns(true); var rotatedVariant = VariantRotator.Right(variant, transcript.Object, _refSequence, transcript.Object.Gene.OnReverseStrand); Assert.False(ReferenceEquals(variant, rotatedVariant)); Assert.Equal(966393, rotatedVariant.Start); Assert.Equal("TG", rotatedVariant.RefAllele); }
public void SimpleVariant_Set() { const int expectedStart = 100; const int expectedEnd = 102; const string expectedRef = "AT"; const string expectedAlt = ""; const VariantType expectedType = VariantType.deletion; var variant = new SimpleVariant(ChromosomeUtilities.Chr1, expectedStart, expectedEnd, expectedRef, expectedAlt, expectedType); Assert.Equal(ChromosomeUtilities.Chr1, variant.Chromosome); Assert.Equal(expectedStart, variant.Start); Assert.Equal(expectedEnd, variant.End); Assert.Equal(expectedRef, variant.RefAllele); Assert.Equal(expectedAlt, variant.AltAllele); Assert.Equal(expectedType, variant.Type); }
public void CreateFromTranslocation_Nominal(int position, string refAllele, string altAllele, bool expectedOnReverseStrand, string expectedPartnerChr, int expectedPartnerPosition, bool expectedPartnerOnReverseStrand) { var variant = new SimpleVariant(ChromosomeUtilities.Chr1, position, position, refAllele, altAllele, VariantType.translocation_breakend); BreakEndAdjacency[] adjacencies = BreakEndUtilities.CreateFromTranslocation(variant, ChromosomeUtilities.RefNameToChromosome); Assert.NotNull(adjacencies); Assert.Single(adjacencies); var observed = adjacencies[0]; Assert.Equal(expectedOnReverseStrand, observed.Origin.OnReverseStrand); Assert.Equal(expectedPartnerChr, observed.Partner.Chromosome.EnsemblName); Assert.Equal(expectedPartnerPosition, observed.Partner.Position); Assert.Equal(expectedPartnerOnReverseStrand, observed.Partner.OnReverseStrand); }