public void TwoStudyCosmicCoding()
{
var vcfReader = GZipUtilities.GetAppropriateStreamReader(Resources.TopPath("cosm5428243.vcf"));
var tsvReader = GZipUtilities.GetAppropriateStreamReader(Resources.TopPath("cosm5428243.tsv"));
var cosmicReader = new MergedCosmicReader(vcfReader, tsvReader, _refChromDict);
var cosmicItems = cosmicReader.GetCosmicItems();
var count = 0;
foreach (var cosmicItem in cosmicItems)
{
switch (count)
{
case 0:
foreach (var study in cosmicItem.Studies)
{
Assert.Equal("544", study.Id);
Assert.Equal(new [] { "haematopoietic_and_lymphoid_tissue" }, study.Sites);
Assert.Equal(new [] { "haematopoietic_neoplasm", "acute_myeloid_leukaemia" }, study.Histologies);
}
break;
case 1:
foreach (var study in cosmicItem.Studies)
{
Assert.Equal("544", study.Id);
Assert.Equal(new[] { "haematopoietic;lymphoid_tissue" }, study.Sites);
Assert.Equal(new[] { "haematopoietic_neoplasm", "acute_myeloid_leukaemia" }, study.Histologies);
}
break;
}
count++;
}
}
public void CosmicAlleleSpecificIndel()
{
var vcfReader = GZipUtilities.GetAppropriateStreamReader(Resources.TopPath("COSM18152.vcf"));
var tsvReader = GZipUtilities.GetAppropriateStreamReader(Resources.TopPath("COSM18152.tsv"));
var cosmicReader = new MergedCosmicReader(vcfReader, tsvReader, _refChromDict);
var items = cosmicReader.GetCosmicItems();
Assert.Single(items);
}
public void CosmicAltAllele()
{
var vcfReader = GZipUtilities.GetAppropriateStreamReader(Resources.TopPath("COSM983708.vcf"));
var tsvReader = GZipUtilities.GetAppropriateStreamReader(Resources.TopPath("COSM983708.tsv"));
var cosmicReader = new MergedCosmicReader(vcfReader, tsvReader, _refChromDict);
var items = cosmicReader.GetCosmicItems().ToList();
Assert.Single(items);
Assert.Contains("\"refAllele\":\"C\"", items[0].GetJsonString());
}
private void CreateCosmicTsv(string vcfFile, string tsvFile)
{
if (string.IsNullOrEmpty(tsvFile) || string.IsNullOrEmpty(vcfFile))
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(vcfFile);
using (var writer = new CosmicTsvWriter(version, _outputDirectory, _genomeAssembly, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath))))
{
var tsvReader = GZipUtilities.GetAppropriateStreamReader(tsvFile);
var vcfReader = GZipUtilities.GetAppropriateStreamReader(vcfFile);
var reader = new MergedCosmicReader(vcfReader, tsvReader, _refNamesDictionary);
TsvWriterUtilities.WriteSortedItems(reader.GetCosmicItems(), writer);
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("COSMIC", version.Version, timeSpan);
}
