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 static string GetGeneAnnotation(GeneConfig input, string saManifestFilePath, string saPathPrefix)
{
var geneAnnotationProvider = new GeneAnnotationProvider(PersistentStreamUtils.GetStreams(
GetNgaFileList(saManifestFilePath, saPathPrefix, input.ngaUrls).ToList()));
var sb = new StringBuilder(1024 * 1024);
var jsonObject = new JsonObject(sb);
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue(JasixCommons.HeaderSectionTag, GetHeader(geneAnnotationProvider), false);
//not all gene symbols have annotations. So, we need to check and only output the ones that are not null
var geneAnnotations = input.geneSymbols.Select(geneSymbol => geneAnnotationProvider.Annotate(geneSymbol))
.Where(annotation => !string.IsNullOrEmpty(annotation))
.ToList();
jsonObject.AddStringValues("genes", geneAnnotations, false);
sb.Append(JsonObject.CloseBrace);
// AWS lambda response message can not be larger than 6MB
if (sb.Length > 6_000_000)
{
throw new UserErrorException("Too many genes provided in the request. Please decrease the number of genes and try again later.");
}
return(sb.ToString());
}
public void Dispose()
{
SequenceProvider?.Dispose();
TranscriptAnnotationProvider?.Dispose();
SaProvider?.Dispose();
ConservationProvider?.Dispose();
RefMinorProvider?.Dispose();
GeneAnnotationProvider?.Dispose();
}
public static IGeneAnnotationProvider GetGeneAnnotationProvider(IEnumerable <string> supplementaryAnnotationDirectories)
{
var reader = SaReaderUtils.GetGeneAnnotationDatabaseReader(supplementaryAnnotationDirectories.ToList());
if (reader == null)
{
return(null);
}
var geneAnnotationProvider = new GeneAnnotationProvider(reader);
return(geneAnnotationProvider);
}
