public void TrackAffectedGenes()
{
var taProvider = new Mock <IAnnotationProvider>();
taProvider.SetupGet(x => x.GenomeAssembly).Returns(GenomeAssembly.GRCh37);
taProvider.Setup(x => x.Annotate(It.IsAny <IAnnotatedPosition>())).Callback((IAnnotatedPosition x) => { });//do nothing
var geneAnnotationProvider = new Mock <IGeneAnnotationProvider>();
geneAnnotationProvider.SetupGet(x => x.GenomeAssembly).Returns(GenomeAssembly.GRCh37);
var annotator = new Annotator(taProvider.Object, null, null, null, geneAnnotationProvider.Object);
var annotatedPosition = new Mock <IAnnotatedPosition>();
var annotatedVariant = new Mock <IAnnotatedVariant>();
var ensembleTranscript = new Mock <IAnnotatedTranscript>();
annotatedVariant.SetupGet(x => x.EnsemblTranscripts)
.Returns(new List <IAnnotatedTranscript> {
ensembleTranscript.Object
});
ensembleTranscript.SetupGet(x => x.Transcript.Gene.Symbol).Returns("ensembl1");
var refSeqTranscript = new Mock <IAnnotatedTranscript>();
annotatedVariant.SetupGet(x => x.RefSeqTranscripts)
.Returns(new List <IAnnotatedTranscript> {
refSeqTranscript.Object
});
refSeqTranscript.SetupGet(x => x.Transcript.Gene.Symbol).Returns("refseq1");
annotatedPosition.SetupGet(x => x.AnnotatedVariants).Returns(new[] { annotatedVariant.Object });
annotator.TrackAffectedGenes(annotatedPosition.Object);
var geneAnnotation = new Mock <IAnnotatedGene>();
geneAnnotationProvider.Setup(x => x.Annotate("ensembl1")).Returns(geneAnnotation.Object);
geneAnnotationProvider.Setup(x => x.Annotate("refseq1")).Returns((IAnnotatedGene)null);
var annotatedGenes = annotator.GetAnnotatedGenes();
Assert.Equal(1, annotatedGenes.Count);
}