public void ParseHeaderLines_InconsistentFields()
{
const string invalidHeaderLines = "#title=InternalGeneAnnotation\n" +
"#geneSymbol\tgeneId\tphenotype\tmimNumber\tnotes\n" +
"#categories\t\t\tstring\tnumber\t.\n" +
"#descriptions\t.\t.\t.\t.\tSome\tText\tHere\n" +
"#type\t\t\tstring\tnumber\t.\n";
using (var parser = new GeneAnnotationsParser(GetReadStream(invalidHeaderLines), EntrezGeneIdToSymbol, EnsemblIdToSymbol))
{
Assert.Throws <UserErrorException>(() => parser.ParseHeaderLines());
}
}
public void GetItems_UnrecognizedGeneId_ThrowException()
{
const string lines = "#title=InternalGeneAnnotation\n" +
"#geneSymbol\tgeneId\tOMIM Description\tIs Oncogene\tphenotype\tmimNumber\tnotes\n" +
"#categories\t.\tDescription\tFilter\t\tIdentifier\t.\n" +
"#descriptions\t.\tGene description from OMIM\t\tGene phenotype\t\tFree text\n" +
"#type\t\tstring\tbool\tstring\tnumber\tstring\n" +
"Abc\t3\tsome text\ttrue\tgood\t234\ttest\n";
using (var parser = GeneAnnotationsParser.Create(GetReadStream(lines), EntrezGeneIdToSymbol, EnsemblIdToSymbol))
{
Assert.Throws <UserErrorException>(() => parser.GetItems());
}
}
public void ParseHeaderLines_version_and_Description()
{
const string headerLines = "#title=InternalGeneAnnotation\n" +
"#version=v1.1\n" +
"#description=Internal Gene Annotation\n" +
"#geneSymbol\tgeneId\tOMIM Description\tIs Oncogene\tphenotype\tmimNumber\tnotes\n" +
"#categories\t.\tDescription\tFilter\t\tIdentifier\t.\n" +
"#descriptions\t.\tGene description from OMIM\t\tGene phenotype\t\tFree text\n" +
"#type\t\tstring\tbool\tstring\tnumber\tstring\n";
using (var parser = new GeneAnnotationsParser(GetReadStream(headerLines), EntrezGeneIdToSymbol, EnsemblIdToSymbol))
{
parser.ParseHeaderLines();
Assert.Equal("v1.1", parser.Version);
Assert.Equal("Internal Gene Annotation", parser.DataSourceDescription);
}
}
public void GetItems_AsExpected()
{
const string lines = "#title=InternalGeneAnnotation\n" +
"#geneSymbol\tgeneId\tOMIM Description\tIs Oncogene\tphenotype\tmimNumber\tnotes\n" +
"#categories\t.\tDescription\tFilter\t\tIdentifier\t.\n" +
"#descriptions\t.\tGene description from OMIM\t\tGene phenotype\t\tFree text\n" +
"#type\t\tstring\tbool\tstring\tnumber\tstring\n" +
"Abc\t1\tsome text\ttrue\tgood\t234\ttest\n" +
"Abc\tENSG2\tsome other text\tfalse\tbad\t200\ttest2\n";
using (var parser = GeneAnnotationsParser.Create(GetReadStream(lines), EntrezGeneIdToSymbol, EnsemblIdToSymbol))
{
var geneSymbol2Items = parser.GetItems();
Assert.Equal(2, geneSymbol2Items.Count);
Assert.Single(geneSymbol2Items["Gene1"]);
Assert.Single(geneSymbol2Items["Gene2"]);
Assert.Equal("{\"OMIM Description\":\"some text\",\"Is Oncogene\":true,\"phenotype\":\"good\",\"mimNumber\":234,\"notes\":\"test\"}", geneSymbol2Items["Gene1"][0].GetJsonString());
Assert.Equal("{\"OMIM Description\":\"some other text\",\"phenotype\":\"bad\",\"mimNumber\":200,\"notes\":\"test2\"}", geneSymbol2Items["Gene2"][0].GetJsonString());
}
}
public void ParseHeaderLines_AsExpected()
{
const string headerLines = "#title=InternalGeneAnnotation\n" +
"#geneSymbol\tgeneId\tOMIM Description\tIs Oncogene\tphenotype\tmimNumber\tnotes\n" +
"#categories\t.\tDescription\tFilter\t\tIdentifier\t.\n" +
"#descriptions\t.\tGene description from OMIM\t\tGene phenotype\t\tFree text\n" +
"#type\t\tstring\tbool\tstring\tnumber\tstring\n";
using (var parser = new GeneAnnotationsParser(GetReadStream(headerLines), EntrezGeneIdToSymbol, EnsemblIdToSymbol))
{
parser.ParseHeaderLines();
var expectedJsonKeys = new[] { "OMIM Description", "Is Oncogene", "phenotype", "mimNumber", "notes" };
var expectedCategories = new[]
{
CustomAnnotationCategories.Description, CustomAnnotationCategories.Filter,
CustomAnnotationCategories.Unknown, CustomAnnotationCategories.Identifier,
CustomAnnotationCategories.Unknown
};
var expectedDescriptions = new[] { "Gene description from OMIM", null, "Gene phenotype", null, "Free text" };
var expectedTypes = new[]
{
SaJsonValueType.String,
SaJsonValueType.Bool,
SaJsonValueType.String,
SaJsonValueType.Number,
SaJsonValueType.String
};
Assert.Equal("InternalGeneAnnotation", parser.JsonTag);
Assert.Equal(expectedJsonKeys, parser.JsonKeys);
Assert.Equal(expectedCategories, parser.Categories);
Assert.Equal(expectedDescriptions, parser.Descriptions);
Assert.Equal(expectedTypes, parser.ValueTypes);
}
}
private static GeneAnnotationsParser GetGeneAnnotationsParserFromCustomTsvStream(PersistentStream customTsvStream)
{
var(entrezGeneIdToSymbol, ensemblGeneIdToSymbol) = GeneUtilities.ParseUniversalGeneArchive(null, LambdaUrlHelper.GetUgaUrl());
return(GeneAnnotationsParser.Create(new StreamReader(GZipUtilities.GetAppropriateStream(customTsvStream)), entrezGeneIdToSymbol, ensemblGeneIdToSymbol));
}
