Exemple #1
0
        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());
        }
Exemple #2
0
        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());
        }
Exemple #3
0
        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());
        }