public void TestMissenseMutation()
{
// Make a transcript
Sequence seq = new Sequence(Alphabets.DNA, "AAA".Select(cc => (byte)cc).ToArray(), false);
seq.ID = "1";
Chromosome c = new Chromosome(seq, null);
Gene g = new Gene("", c, "", "+", 1, 3, null);
Transcript t = new Transcript("", g, "", "+", 1, 3, "", null, null);
Exon x = new Exon(t, seq, "", 1, 3, seq.ID, "+", null, null);
t.Exons = new List <Exon> {
x
};
CDS cds = new CDS(t, seq.ID, "", "+", 1, 3, null, 0);
t.CodingDomainSequences = new List <CDS> {
cds
};
// Make a missense mutation
// ugh.vcf has a homozygous variation that should change the codon from AAA to AGA, which code for K and R
// # CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
// 1 2 . A G 64.77 . info GT:AD:DP:GQ:PL 1/1:2,3:5:69:93,0,69
List <Variant> variants = new VCFParser(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestVcfs", "ugh.vcf")).Select(v => new Variant(null, v, new Chromosome(seq, null))).ToList();
// Make sure it makes it into the DNA sequence
t.Variants = new HashSet <Variant>(variants);
List <Transcript> variantTranscripts = GeneModel.ApplyVariantsCombinitorially(t);
Assert.AreEqual("AAA", SequenceExtensions.ConvertToString(t.Exons[0].Sequence));
Assert.AreEqual("K", t.Protein().BaseSequence);
Assert.AreEqual("AGA", SequenceExtensions.ConvertToString(variantTranscripts[0].Exons[0].Sequence));
Assert.AreEqual("R", variantTranscripts[0].Protein().BaseSequence);
// Make sure it gets annotated as a missense mutation
Assert.IsTrue(variantTranscripts[0].VariantAnnotations.Any(str => str.Contains(FunctionalClass.MISSENSE.ToString())));
}
/// <summary>
/// Interval is not a variant, nothing to do
/// </summary>
/// <param name="exon"></param>
/// <returns></returns>
protected override bool ChangeCodon(Exon exon)
{
return(false);
}