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);
}
private void Flush()
{
var nullGene = AnnotatedGene.CreateEmptyGene();
nullGene.Write(_writer);
_stream.Flush();
}
public void SerializeJson()
{
var geneAnnotation1 = new Mock <IGeneAnnotationSource>();
var geneAnnotation2 = new Mock <IGeneAnnotationSource>();
var geneAnnotations = new [] { geneAnnotation1.Object, geneAnnotation2.Object };
geneAnnotation1.SetupGet(x => x.DataSource).Returns("annotation1");
geneAnnotation1.Setup(x => x.JsonStrings).Returns(new[]
{
"{\"mimNumber\":603024,\"description\":\"AT rich interactive domain 1A, SWI-like\",\"phenotypes\":[{\"mimNumber\":614607,\"phenotype\":\"Coffin-Siris syndrome 2\",\"mapping\":\"molecular basis of the disorder is known\",\"inheritances\":[\"Autosomal dominant\"]}]}",
"{\"mimNumber\":300531,\"description\":\"Sprouty, Drosophila, homolog of, 3\"}"
});
geneAnnotation1.SetupGet(x => x.IsArray).Returns(true);
geneAnnotation2.SetupGet(x => x.DataSource).Returns("annotation2");
geneAnnotation2.Setup(x => x.JsonStrings).Returns(new[] { "0.154" });
geneAnnotation2.SetupGet(x => x.IsArray).Returns(false);
var annotatedGene = new AnnotatedGene("Gene1", geneAnnotations);
const string expectedLine = "{\"name\":\"Gene1\",\"annotation1\":[{\"mimNumber\":603024,\"description\":\"AT rich interactive domain 1A, SWI-like\",\"phenotypes\":[{\"mimNumber\":614607,\"phenotype\":\"Coffin-Siris syndrome 2\",\"mapping\":\"molecular basis of the disorder is known\",\"inheritances\":[\"Autosomal dominant\"]}]},{\"mimNumber\":300531,\"description\":\"Sprouty, Drosophila, homolog of, 3\"}],\"annotation2\":0.154}";
var sb = StringBuilderCache.Acquire();
annotatedGene.SerializeJson(sb);
Assert.Equal(expectedLine, StringBuilderCache.GetStringAndRelease(sb));
}
private static IEnumerable <IAnnotatedGene> GetAnnotatedGenes(IReadOnlyList <GeneTsvReader> geneReaders)
{
if (geneReaders == null)
{
return(null);
}
var geneAnnotations = new Dictionary <string, IAnnotatedGene>();
foreach (var reader in geneReaders)
{
foreach (var annotatedGene in reader.GetItems() ?? Enumerable.Empty <IAnnotatedGene>())
{
var geneName = annotatedGene.GeneName;
if (!geneAnnotations.TryAdd(geneName, annotatedGene))
{
geneAnnotations[geneName] = new AnnotatedGene(geneName, geneAnnotations[geneName].Annotations.Concat(annotatedGene.Annotations).ToArray());
}
}
}
return(geneAnnotations.Values);
}
