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);
}
