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 ParseVcf([Values("testData/NA12878.knowledgebase.snapshot.20131119.b37.vcf.gz")] string fname)
{
Assert.IsTrue(File.Exists(fname));
VCFParser vcp = new VCFParser(fname);
var j = vcp.First();
var ii = j.Genotypes;
var i = vcp.Select(x => x.NoCallCount).Count();
Console.WriteLine("Count: {0}", i);
}
static void Main(string[] args)
{
fname = "testData/NA12878.knowledgebase.snapshot.20131119.b37.vcf.gz";
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch();
sw.Start();
VCFParser vcp = new VCFParser(fname);
var j = vcp.First();
var ii = j.Genotypes;
var i = vcp.Select(x => x.NoCallCount).Count();
sw.Stop();
Console.WriteLine(sw.Elapsed.ToString());
}
static void Main (string[] args)
{
var fname = "testData/NA12878.knowledgebase.snapshot.20131119.b37.vcf.gz";
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch ();
sw.Start ();
VCFParser vcp = new VCFParser (fname);
var j = vcp.First ();
var ii = j.Genotypes.Count;
var i = vcp.Select (x => x.NoCallCount).Count ();
sw.Stop ();
Console.WriteLine("Count: {0}/{1}", ii,i);
Console.WriteLine ("Elapsed: {0}", sw.Elapsed);
var anyKey = Console.ReadKey();
}
public void test()
{
VCFParser parser = new VCFParser(Path.Combine(TestContext.CurrentContext.TestDirectory, @"testData", @"NA12878.knowledgebase.snapshot.20131119.b37.vcf.gz"));
List <VariantContext> context = parser.Select(x => x).ToList();
}