public void missense_variant_in_TSS_returns()
{
var transcript = GetMockedTranscriptOnForwardStrand();
var chromosome = new Chromosome("chr1", "1", 0);
var variant = new Variant(chromosome, 1262291, 1262291, "A", "C", VariantType.SNV, "1:1262291:A>C", false, false, null, null, new AnnotationBehavior(false, false, false, false, false, false));
var refSequence = new SimpleSequence(Enst00000343938GenomicSequence, 1260147 - 1);
var result = PianoTranscriptAnnotator.GetAnnotatedTranscript(transcript, variant, refSequence, new AminoAcids(false));
var expectedResult =
"CPTP ENSG000000224051 ENST00000343938.4 ENST00000343938.4 1 . M/L DDSETGFNLKVVLVS start_lost";
Assert.Equal(expectedResult, result.ToString());
}
public void synounymous_mutation_returns_no_change()
{
var transcript = GetMockedTranscriptOnForwardStrand();
var chromosome = new Chromosome("chr1", "1", 0);
var variant = new Variant(chromosome, 1262347, 1262347, "G", "A", VariantType.SNV, "1:1262347:G>A", false, false, null, null, new AnnotationBehavior(false, false, false, false, false, false));
var refSequence = new SimpleSequence(Enst00000343938GenomicSequence, 1260147 - 1);
var result = PianoTranscriptAnnotator.GetAnnotatedTranscript(transcript, variant, refSequence, new AminoAcids(false));
var expectedResult =
"CPTP ENSG000000224051 ENST00000343938.4 ENST00000343938.4 19 SETGFNLKVVLVSFK Q CLDEKEEVLLDPYIA synonymous_variant";
Assert.Equal(expectedResult, result.ToString());
}
public void Frameshift_mutation_returns_no_downStreamAminoAcids()
{
var transcript = GetMockedTranscriptOnForwardStrand();
var chromosome = new Chromosome("chr1", "1", 0);
var variant = new Variant(chromosome, 1262347, 1262348, "GT", "G", VariantType.deletion, "vid", false, false, null, null, new AnnotationBehavior(false, false, false, false, false, false));
var refSequence = new SimpleSequence(Enst00000343938GenomicSequence, 1260147 - 1);
var result = PianoTranscriptAnnotator.GetAnnotatedTranscript(transcript, variant, refSequence, new AminoAcids(false));
var expectedResult =
"CPTP ENSG000000224051 ENST00000343938.4 ENST00000343938.4 19-20 SETGFNLKVVLVSFK QCLDEKEEVLLDPYIAS/QVSMRRKRSCWTPTLPX . frameshift_variant";
Assert.Equal(expectedResult, result.ToString());
}