public void OneTranscriptOneHeterozygousSynonymous()
{
Genome genome = new Genome(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "chr1_sample.fa"));
VCFParser vcf = new VCFParser(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestVcfs", "chr_1_one_heterozygous_synonymous.vcf"));
List <Variant> variants = vcf.Select(x => new Variant(null, x, genome)).ToList();
Assert.AreEqual(1, variants.Count);
GeneModel geneModel = new GeneModel(genome, Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "chr1_one_transcript.gtf"));
List <Protein> proteins_wo_variant = geneModel.Translate(true).ToList();
List <Transcript> transcripts = geneModel.ApplyVariants(variants);
List <Protein> proteins = transcripts.Select(t => t.Protein()).ToList();
Assert.AreEqual(1, geneModel.Genes.Count);
Assert.AreEqual(1, proteins.Count);
Assert.AreEqual(1, proteins_wo_variant.Count);
Assert.AreEqual(1, new HashSet <string> {
proteins[0].BaseSequence, proteins_wo_variant[0].BaseSequence
}.Count);
Assert.IsTrue(proteins.Any(p => p.FullName.Contains(FunctionalClass.SILENT.ToString()))); // synonymous
Assert.IsTrue(proteins.Any(p => p.FullName.Contains(GenotypeType.HETEROZYGOUS.ToString()))); // synonymous
Assert.IsTrue(proteins.Any(p => p.FullName.Contains("1:69666")));
string proteinFasta = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestVcfs", "chr_1_one_heterozygous_synonymous.fasta");
ProteinDbWriter.WriteFastaDatabase(proteins, proteinFasta, " ");
string[] proteinFastaLines = File.ReadLines(proteinFasta).ToArray();
Assert.IsTrue(proteinFastaLines[0].Contains(FunctionalClass.SILENT.ToString())); // synonymous
Assert.IsTrue(proteinFastaLines[0].Contains("1:69666"));
}
public void ProblematicChr19Gene()
{
Genome genome = new Genome(Path.Combine(TestContext.CurrentContext.TestDirectory, "Homo_sapiens.GRCh38.dna.chromosome.19.fa"));
GeneModel geneModel = new GeneModel(genome, Path.Combine(TestContext.CurrentContext.TestDirectory, "ProblematicChr19", "problematicChr19Gene.gff3"));
geneModel.ApplyVariants(new VCFParser(Path.Combine(TestContext.CurrentContext.TestDirectory, "ProblematicChr19", "chr19problematic.vcf")).Select(v => new Variant(null, v, genome.Chromosomes[0])).ToList());
}
public void Chr19VariantTranscript()
{
Genome genome = new Genome(Path.Combine(TestContext.CurrentContext.TestDirectory, "Homo_sapiens.GRCh38.dna.chromosome.19.fa"));
GeneModel geneModel = new GeneModel(genome, Path.Combine(TestContext.CurrentContext.TestDirectory, "ProblematicChr19", "chr19variantTranscript.gff3"));
var variants = new VCFParser(Path.Combine(TestContext.CurrentContext.TestDirectory, "ProblematicChr19", "chr19problematic.vcf"))
.Select(v => new Variant(null, v, genome.Chromosomes[0]))
.Where(v => v.SecondAlleleString.Length == 1 && v.ReferenceAlleleString.Length == 1).ToList();
List <Transcript> transcripts = geneModel.ApplyVariants(variants).ToList();
List <Protein> proteins = transcripts.Select(t => t.Protein(null)).ToList();
}
