public void refSeq_gene_return_entrezId()
{
var mockedTranscript = new Mock <ITranscript>();
mockedTranscript.Setup(x => x.Source).Returns(Source.RefSeq);
mockedTranscript.Setup(x => x.Gene.EntrezGeneId.ToString()).Returns("12345");
mockedTranscript.Setup(x => x.Gene.Symbol).Returns("TestGene");
mockedTranscript.Setup(x => x.Id).Returns(CompactId.Convert("NM_124"));
mockedTranscript.Setup(x => x.Version).Returns(1);
mockedTranscript.Setup(x => x.Translation.ProteinId).Returns(CompactId.Convert("NP_342"));
mockedTranscript.Setup(x => x.Translation.ProteinVersion).Returns(2);
var mappedPosition = new Mock <IMappedPositions>();
mappedPosition.Setup(x => x.ProteinInterval).Returns(new NullableInterval(100, 101));
var transcript = new PianoAnnotatedTranscript(mockedTranscript.Object, "AT", "GR", mappedPosition.Object, "KILGF", "ATYRGD",
new List <ConsequenceTag> {
ConsequenceTag.missense_variant, ConsequenceTag.splice_region_variant
});
var expectedOut = "TestGene 12345 NM_124.1 NP_342.2 100-101 KILGF AT/GR ATYRGD missense_variant,splice_region_variant";
Assert.Equal(expectedOut, transcript.ToString());
}
public void Empty_upstreamAminoAcids_return_dot()
{
var mockedTranscript = new Mock <ITranscript>();
mockedTranscript.Setup(x => x.Source).Returns(Source.Ensembl);
mockedTranscript.Setup(x => x.Gene.EnsemblId.ToString()).Returns("ENSG12345");
mockedTranscript.Setup(x => x.Gene.Symbol).Returns("TestGene");
mockedTranscript.Setup(x => x.Id).Returns(CompactId.Convert("ENST124"));
mockedTranscript.Setup(x => x.Version).Returns(1);
mockedTranscript.Setup(x => x.Translation.ProteinId).Returns(CompactId.Convert("ENSP123456"));
mockedTranscript.Setup(x => x.Translation.ProteinVersion).Returns(2);
var mappedPosition = new Mock <IMappedPositions>();
mappedPosition.Setup(x => x.ProteinInterval).Returns(new NullableInterval(100, 100));
var transcript = new PianoAnnotatedTranscript(mockedTranscript.Object, "A", "R", mappedPosition.Object, "", "ATYRGD",
new List <ConsequenceTag> {
ConsequenceTag.missense_variant
});
var expectedOut = "TestGene ENSG12345 ENST124.1 ENSP123456.2 100 . A/R ATYRGD missense_variant";
Assert.Equal(expectedOut, transcript.ToString());
}