public void Gene_in_gene_annotation_database_get_annotated()
{
var annotatedGene = new AnnotatedGene("A2M",
new IGeneAnnotationSource[] { new GeneAnnotationSource("omim", new[] { "{\"mimNumber\":103950,\"description\":\"Alpha-2-macroglobulin\",\"phenotypes\":[{\"mimNumber\":614036,\"phenotype\":\"Alpha-2-macroglobulin deficiency\",\"mapping\":\"mapping of the wildtype gene\",\"inheritances\":[\"Autosomal dominant\"]}", "{\"mimNumber\":104300,\"phenotype\":\"Alzheimer disease, susceptibility to\",\"mapping\":\"molecular basis of the disorder is known\",\"inheritances\":[\"Autosomal dominant\"],\"comments\":\"contribute to susceptibility to multifactorial disorders or to susceptibility to infection\"}]}" }, true) });
var ms = new MemoryStream();
var header = new SupplementaryAnnotationHeader("", DateTime.Now.Ticks, 1, new IDataSourceVersion[] { }, GenomeAssembly.Unknown);
using (var writer = new GeneDatabaseWriter(ms, header, true))
{
writer.Write(annotatedGene);
}
ms.Position = 0;
var reader = new GeneDatabaseReader(ms);
var geneAnnotationProvider = new GeneAnnotationProvider(reader);
var observedAnnotation = geneAnnotationProvider.Annotate("A2M");
var observedAnnotation2 = geneAnnotationProvider.Annotate("A2M2L");
Assert.NotNull(observedAnnotation);
Assert.Null(observedAnnotation2);
Assert.Single(observedAnnotation.Annotations);
Assert.Equal("omim", observedAnnotation.Annotations[0].DataSource);
}
public void SaReader_And_SaWriter_Tests()
{
var saMs = new MemoryStream();
var indexMs = new MemoryStream();
var dataSourceVersions = new[]
{
new DataSourceVersion("clinvar", "20", DateTime.Today.Ticks, "clinvar dataset"),
new DataSourceVersion("dbSnp", "18", DateTime.Parse("12/20/2010").Ticks, "dbSNP")
};
var header = new SupplementaryAnnotationHeader("chr1", DateTime.Now.Ticks, 1, dataSourceVersions, GenomeAssembly.GRCh37);
var smallIntervals = new List <ISupplementaryInterval>
{
new SupplementaryInterval("data1", "chr1", 100, 150, "", ReportFor.SmallVariants)
};
var svIntervals = new List <ISupplementaryInterval>
{
new SupplementaryInterval("data2", "chr1", 100, 1000, "", ReportFor.StructuralVariants)
};
var allIntervals = new List <ISupplementaryInterval>
{
new SupplementaryInterval("data3", "chr1", 100, 1000, "", ReportFor.AllVariants)
};
var saDataSources = new ISaDataSource[4];
saDataSources[0] = new SaDataSource("data1", "data1", "A", false, true, "acd", new[] { "\"id\":\"123\"" });
saDataSources[1] = new SaDataSource("data2", "data2", "T", false, true, "acd", new[] { "\"id\":\"123\"" });
saDataSources[2] = new SaDataSource("data3", "data3", "A", false, false, "acd", new[] { "\"id\":\"123\"" });
saDataSources[3] = new SaDataSource("data4", "data4", "T", false, false, "acd", new[] { "\"id\":\"123\"" });
var saPos = new SaPosition(saDataSources, "A");
using (var saWriter = new SaWriter(saMs, indexMs, header, smallIntervals, svIntervals, allIntervals, new List <(int, string)>(), true))
{
saWriter.Write(saPos, 150);
}
saMs.Position = 0;
indexMs.Position = 0;
ISaPosition obseveredPosition, obseveredPosition2;
using (var saReader = new SaReader(saMs, indexMs))
{
obseveredPosition = saReader.GetAnnotation(150);
obseveredPosition2 = saReader.GetAnnotation(200);
}
Assert.Equal("A", obseveredPosition.GlobalMajorAllele);
Assert.Equal(4, obseveredPosition.DataSources.Length);
Assert.Null(obseveredPosition2);
}
private static void MergeGene(IReadOnlyList <GeneTsvReader> geneReaders, IEnumerable <SaHeader> geneHeaders, string outputDirectory, GenomeAssembly assembly)
{
var geneAnnotationDatabasePath = Path.Combine(outputDirectory, SaDataBaseCommon.GeneLevelAnnotationFileName);
var geneAnnotationStream = FileUtilities.GetCreateStream(geneAnnotationDatabasePath);
var databaseHeader = new SupplementaryAnnotationHeader("", DateTime.Now.Ticks, SaDataBaseCommon.DataVersion, geneHeaders.Select(x => x.GetDataSourceVersion()), assembly);
using (var writer = new GeneDatabaseWriter(geneAnnotationStream, databaseHeader))
{
foreach (var annotatedGene in GetAnnotatedGenes(geneReaders) ?? Enumerable.Empty <IAnnotatedGene>())
{
writer.Write(annotatedGene);
}
}
}
private void MergeChrom(string refName)
{
var creationBench = new Benchmark();
var currentChrAnnotationCount = 0;
int refMinorCount;
var saEnumerators = GetSaEnumerators(refName);
//return;
var globalMajorAlleleInRefMinors = GetGlobalMajorAlleleForRefMinors(refName);
var dataSourceVersions = MergeUtilities.GetDataSourceVersions(_saHeaders);
var ucscRefName = _refNameToChromosome[refName].UcscName;
var header = new SupplementaryAnnotationHeader(ucscRefName, DateTime.Now.Ticks,
SaDataBaseCommon.DataVersion, dataSourceVersions, _genomeAssembly);
//we need a list because we will enumerate over it multiple times
var intervals = MergeUtilities.GetIntervals(_intervalReaders, refName).OrderBy(x => x.Start).ThenBy(x => x.End).ToList();
var svIntervals = MergeUtilities.GetSpecificIntervals(ReportFor.StructuralVariants, intervals);
var allVariantsIntervals = MergeUtilities.GetSpecificIntervals(ReportFor.AllVariants, intervals);
var smallVariantIntervals = MergeUtilities.GetSpecificIntervals(ReportFor.SmallVariants, intervals);
var saPath = Path.Combine(_outputDirectory, $"{ucscRefName}.nsa");
using (var stream = FileUtilities.GetCreateStream(saPath))
using (var idxStream = FileUtilities.GetCreateStream(saPath + ".idx"))
using (var blockSaWriter = new SaWriter(stream, idxStream, header, smallVariantIntervals, svIntervals, allVariantsIntervals, globalMajorAlleleInRefMinors))
{
int position;
ISaPosition saPosition;
(position, saPosition) = GetNextInterimPosition(saEnumerators);
while (saPosition != null)
{
blockSaWriter.Write(saPosition, position);
currentChrAnnotationCount++;
(position, saPosition) = GetNextInterimPosition(saEnumerators);
}
refMinorCount = blockSaWriter.RefMinorCount;
}
Console.WriteLine($"{ucscRefName,-23} {currentChrAnnotationCount,10:n0} {intervals.Count,6:n0} {refMinorCount,6:n0} {creationBench.GetElapsedIterationTime(currentChrAnnotationCount, "variants", out double _)}");
}
