public void DecideAnnotationStatus_Flanking_ReturnFlankingAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 100),
new Interval(102, 305), AnnotationBehavior.SmallVariants);
Assert.Equal(TranscriptAnnotationFactory.Status.FlankingAnnotation, observedStatus);
}
public void GetAnnotatedTranscripts_ReturnEmptyList()
{
var variant = new Mock <IVariant>();
var transcript1 = new Mock <ITranscript>();
var transcript2 = new Mock <ITranscript>();
var transcripts = new[] { transcript1.Object, transcript2.Object };
variant.SetupGet(x => x.Behavior).Returns(new AnnotationBehavior(true, false, false, true, false));
variant.SetupGet(x => x.Start).Returns(123456);
variant.SetupGet(x => x.End).Returns(123456);
transcript1.SetupGet(x => x.Id).Returns(CompactId.Convert("NR_046018.2"));
transcript1.SetupGet(x => x.Start).Returns(108455);
transcript1.SetupGet(x => x.End).Returns(118455);
transcript1.SetupGet(x => x.Gene.Start).Returns(108455);
transcript1.SetupGet(x => x.Gene.End).Returns(118455);
transcript2.SetupGet(x => x.Id).Returns(CompactId.Convert("NR_106918.1"));
transcript2.SetupGet(x => x.Start).Returns(128460);
transcript2.SetupGet(x => x.End).Returns(129489);
transcript2.SetupGet(x => x.Gene.Start).Returns(128460);
transcript2.SetupGet(x => x.Gene.End).Returns(129489);
var compressedSequence = new Mock <ISequence>();
var observedAnnotatedTranscripts =
TranscriptAnnotationFactory.GetAnnotatedTranscripts(variant.Object, transcripts,
compressedSequence.Object, null, null);
Assert.Empty(observedAnnotatedTranscripts);
}
public void DecideAnnotationStatus_ROH_Return_RohAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), AnnotationBehavior.RohBehavior);
Assert.Equal(TranscriptAnnotationFactory.Status.RohAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Full_CompleteOverlap_ReturnFullAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), new AnnotationBehavior(false, true, false, false, false));
Assert.Equal(TranscriptAnnotationFactory.Status.FullAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Full_PartialOverlap_ReturnFullAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 105),
new Interval(102, 305), AnnotationBehavior.SmallVariants);
Assert.Equal(TranscriptAnnotationFactory.Status.FullAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Reduced_TranscriptPartialOverlap_ReturnReducedAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 200),
new Interval(102, 305), AnnotationBehavior.StructuralVariants, Chromosome.ShortFlankingLength);
Assert.Equal(TranscriptAnnotationFactory.Status.ReducedAnnotation, observedStatus);
}
public void GetAnnotatedTranscripts_RohAnnotation_ReturnsCanonicalOnly()
{
var variant = new Mock <IVariant>();
var transcript1 = new Mock <ITranscript>();
var transcript2 = new Mock <ITranscript>();
var transcripts = new[] { transcript1.Object, transcript2.Object };
variant.SetupGet(x => x.Behavior).Returns(AnnotationBehavior.RohBehavior);
variant.SetupGet(x => x.Start).Returns(10000);
variant.SetupGet(x => x.End).Returns(20000);
transcript1.SetupGet(x => x.Id).Returns(CompactId.Convert("NM_123.1"));
transcript1.SetupGet(x => x.Start).Returns(11000);
transcript1.SetupGet(x => x.End).Returns(15000);
transcript1.SetupGet(x => x.IsCanonical).Returns(true);
transcript2.SetupGet(x => x.Id).Returns(CompactId.Convert("NM_456.2"));
transcript2.SetupGet(x => x.Start).Returns(11000);
transcript2.SetupGet(x => x.End).Returns(15000);
transcript2.SetupGet(x => x.IsCanonical).Returns(false);
var observedAnnotatedTranscripts =
TranscriptAnnotationFactory.GetAnnotatedTranscripts(variant.Object, transcripts, null, null, null);
Assert.Single(observedAnnotatedTranscripts);
Assert.Equal("NM_123", observedAnnotatedTranscripts[0].Transcript.Id.WithVersion);
}
public void Annotate_return_null_when_no_flanking_over_transcript()
{
var variant = new Mock <IVariant>();
var transcript1 = new Mock <ITranscript>();
var transcript2 = new Mock <ITranscript>();
var transcripts = new[] { transcript1.Object, transcript2.Object };
variant.SetupGet(x => x.Behavior).Returns(new AnnotationBehavior(true, false, false, true, false, false));
variant.SetupGet(x => x.Start).Returns(123456);
variant.SetupGet(x => x.End).Returns(123456);
transcript1.SetupGet(x => x.Start).Returns(108455);
transcript1.SetupGet(x => x.End).Returns(118455);
transcript1.SetupGet(x => x.Gene.Start).Returns(108455);
transcript1.SetupGet(x => x.Gene.End).Returns(118455);
transcript2.SetupGet(x => x.Start).Returns(128460);
transcript2.SetupGet(x => x.End).Returns(129489);
transcript2.SetupGet(x => x.Gene.Start).Returns(128460);
transcript2.SetupGet(x => x.Gene.End).Returns(129489);
var compressedSequence = new Mock <ISequence>();
var observedAnnotatedTranscripts = new List <IAnnotatedTranscript>();
TranscriptAnnotationFactory.GetAnnotatedTranscripts(variant.Object, transcripts, compressedSequence.Object, observedAnnotatedTranscripts, null, null, null, null);
Assert.Empty(observedAnnotatedTranscripts);
}
public void When_not_reducedTranscriptAnnotation_partially_overlapped_variant_get_full_annotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 105),
new Interval(102, 305), new AnnotationBehavior(false, true, false, false, false, false), new Interval(102, 305));
Assert.Equal(TranscriptAnnotationFactory.Status.FullAnnotation, observedStatus);
}
public void When_needFlankingTranscript_flankingTranscript_get_flankingAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 100),
new Interval(102, 305), new AnnotationBehavior(false, true, false, true, false, false), new Interval(102, 305));
Assert.Equal(TranscriptAnnotationFactory.Status.FlankingAnnotation, observedStatus);
}
public void When_reducedTranscriptAnnotation_and_gene_is_completely_overlapped_with_variant_get_SvCompleteOverlapAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), new AnnotationBehavior(false, true, true, false, false, false), new Interval(102, 305));
Assert.Equal(TranscriptAnnotationFactory.Status.SvCompleteOverlapAnnotation, observedStatus);
}
public void When_reducedTranscriptAnnotation_and_transcript_completely_overlapped_variant_but_gene_partial_overlap_get_reducedAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), new AnnotationBehavior(false, true, true, false, false, false), new Interval(102, 503));
Assert.Equal(TranscriptAnnotationFactory.Status.ReducedAnnotation, observedStatus);
}
public void GetAnnotatedTranscripts_ReturnEmptyList()
{
var variant = new Mock <IVariant>();
var transcript1 = new Mock <ITranscript>();
var transcript2 = new Mock <ITranscript>();
ITranscript[] transcripts = { transcript1.Object, transcript2.Object };
variant.SetupGet(x => x.Behavior).Returns(AnnotationBehavior.SmallVariants);
variant.SetupGet(x => x.Chromosome.FlankingLength).Returns(Chromosome.ShortFlankingLength);
variant.SetupGet(x => x.Start).Returns(123456);
variant.SetupGet(x => x.End).Returns(123456);
transcript1.SetupGet(x => x.Id).Returns(CompactId.Convert("NR_046018.2"));
transcript1.SetupGet(x => x.Start).Returns(108455);
transcript1.SetupGet(x => x.End).Returns(118455);
transcript1.SetupGet(x => x.Gene.Start).Returns(108455);
transcript1.SetupGet(x => x.Gene.End).Returns(118455);
transcript2.SetupGet(x => x.Id).Returns(CompactId.Convert("NR_106918.1"));
transcript2.SetupGet(x => x.Start).Returns(128460);
transcript2.SetupGet(x => x.End).Returns(129489);
transcript2.SetupGet(x => x.Gene.Start).Returns(128460);
transcript2.SetupGet(x => x.Gene.End).Returns(129489);
var compressedSequence = new Mock <ISequence>();
IList <IAnnotatedTranscript> observedAnnotatedTranscripts =
TranscriptAnnotationFactory.GetAnnotatedTranscripts(variant.Object, transcripts,
compressedSequence.Object, null, null);
Assert.Empty(observedAnnotatedTranscripts);
}
public void NonOverlap_transcript_get_no_annotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 101),
new Interval(5102, 6100), new AnnotationBehavior(true, false, false, true, false, false), new Interval(5102, 6100));
Assert.Equal(TranscriptAnnotationFactory.Status.NoAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Full_CompleteOverlap_ReturnFullAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), AnnotationBehavior.SmallVariants, Chromosome.ShortFlankingLength);
Assert.Equal(TranscriptAnnotationFactory.Status.FullAnnotation, observedStatus);
}
public void DecideAnnotationStatus_ROH_Return_RohAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), AnnotationBehavior.RunsOfHomozygosity, Chromosome.ShortFlankingLength);
Assert.Equal(TranscriptAnnotationFactory.Status.RohAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Reduced_TranscriptPartialOverlap_ReturnReducedAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 200),
new Interval(102, 305), new AnnotationBehavior(false, true, true, false, false));
Assert.Equal(TranscriptAnnotationFactory.Status.ReducedAnnotation, observedStatus);
}
public void DecideAnnotationStatus_NoOverlap_ReturnNoAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 101),
new Interval(5102, 6100), AnnotationBehavior.SmallVariants, Chromosome.ShortFlankingLength);
Assert.Equal(TranscriptAnnotationFactory.Status.NoAnnotation, observedStatus);
}
public void GetAnnotatedTranscripts_RohAnnotation_ReturnsCanonicalOnly()
{
var variant = new Mock <IVariant>();
var transcript1 = new Mock <ITranscript>();
var transcript2 = new Mock <ITranscript>();
ITranscript[] transcripts = { transcript1.Object, transcript2.Object };
variant.SetupGet(x => x.Behavior).Returns(AnnotationBehavior.RunsOfHomozygosity);
variant.SetupGet(x => x.Chromosome.FlankingLength).Returns(Chromosome.ShortFlankingLength);
variant.SetupGet(x => x.Start).Returns(10000);
variant.SetupGet(x => x.End).Returns(20000);
transcript1.SetupGet(x => x.Id).Returns(CompactId.Convert("NM_123.1"));
transcript1.SetupGet(x => x.Start).Returns(11000);
transcript1.SetupGet(x => x.End).Returns(15000);
transcript1.SetupGet(x => x.IsCanonical).Returns(true);
transcript2.SetupGet(x => x.Id).Returns(CompactId.Convert("NM_456.2"));
transcript2.SetupGet(x => x.Start).Returns(11000);
transcript2.SetupGet(x => x.End).Returns(15000);
transcript2.SetupGet(x => x.IsCanonical).Returns(false);
IList <IAnnotatedTranscript> observedAnnotatedTranscripts =
TranscriptAnnotationFactory.GetAnnotatedTranscripts(variant.Object, transcripts, null, null, null);
Assert.Single(observedAnnotatedTranscripts);
Assert.Equal("NM_123", observedAnnotatedTranscripts[0].Transcript.Id.WithVersion);
}
private void AddTranscripts(IAnnotatedVariant[] annotatedVariants, IIntervalForest <ITranscript> transcriptIntervalForest)
{
foreach (var annotatedVariant in annotatedVariants)
{
var variant = annotatedVariant.Variant;
if (variant.Behavior.Equals(AnnotationBehavior.MinimalAnnotationBehavior))
{
continue;
}
ITranscript[] geneFusionCandidates = GetGeneFusionCandidates(variant.BreakEnds, transcriptIntervalForest);
ITranscript[] transcripts = transcriptIntervalForest.GetAllFlankingValues(variant);
if (transcripts == null)
{
continue;
}
IList <IAnnotatedTranscript> annotatedTranscripts =
TranscriptAnnotationFactory.GetAnnotatedTranscripts(variant, transcripts, _sequence, _siftCache,
_polyphenCache, geneFusionCandidates);
if (annotatedTranscripts.Count == 0)
{
continue;
}
foreach (var annotatedTranscript in annotatedTranscripts)
{
annotatedVariant.Transcripts.Add(annotatedTranscript);
}
}
}
private void AddTranscripts(IAnnotatedVariant[] annotatedVariants)
{
foreach (var annotatedVariant in annotatedVariants)
{
var variant = annotatedVariant.Variant;
if (variant.Behavior.MinimalTranscriptAnnotation)
{
continue;
}
ITranscript[] transcripts = _transcriptCache.TranscriptIntervalForest.GetAllFlankingValues(variant);
if (transcripts == null)
{
continue;
}
IList <IAnnotatedTranscript> annotatedTranscripts =
TranscriptAnnotationFactory.GetAnnotatedTranscripts(variant, transcripts, _sequence, _siftCache,
_polyphenCache);
if (annotatedTranscripts.Count == 0)
{
continue;
}
foreach (var annotatedTranscript in annotatedTranscripts)
{
AddConservationScore(annotatedTranscript);
}
foreach (var annotatedTranscript in annotatedTranscripts)
{
annotatedVariant.Transcripts.Add(annotatedTranscript);
}
}
}
private void AddTranscripts(IAnnotatedPosition annotatedPosition)
{
var overlappingTranscripts = _transcriptCache.GetOverlappingTranscripts(annotatedPosition.Position);
if (overlappingTranscripts == null)
{
return;
}
foreach (var annotatedVariant in annotatedPosition.AnnotatedVariants)
{
var geneFusionCandidates = GetGeneFusionCandiates(annotatedVariant.Variant.BreakEnds);
var annotatedTranscripts = new List <IAnnotatedTranscript>();
TranscriptAnnotationFactory.GetAnnotatedTranscripts(annotatedVariant.Variant, overlappingTranscripts,
_sequence, annotatedTranscripts, annotatedVariant.OverlappingGenes,
annotatedVariant.OverlappingTranscripts, _siftCache, _polyphenCache, geneFusionCandidates);
if (annotatedTranscripts.Count == 0)
{
continue;
}
foreach (var annotatedTranscript in annotatedTranscripts)
{
if (annotatedTranscript.Transcript.Source == Source.Ensembl)
{
annotatedVariant.EnsemblTranscripts.Add(annotatedTranscript);
}
else
{
annotatedVariant.RefSeqTranscripts.Add(annotatedTranscript);
}
}
}
}