private static ExitCodes ProgramExecution()
{
var dosageSensitivityVersion = DataSourceVersionReader.GetSourceVersion(_dosageSensitivityFile + ".version");
string outFileName = $"{dosageSensitivityVersion.Name.Replace(' ','_')}_{dosageSensitivityVersion.Version}";
using (var dosageSensitivityParser = new DosageSensitivityParser(GZipUtilities.GetAppropriateReadStream(_dosageSensitivityFile)))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.NgaFileSuffix)))
using (var ngaWriter = new NgaWriter(stream, dosageSensitivityVersion, SaCommon.DosageSensitivityTag, SaCommon.SchemaVersion, false))
{
ngaWriter.Write(dosageSensitivityParser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
//create universal gene archive
using (var exacParser = new ExacScoresParser(GZipUtilities.GetAppropriateStreamReader(_inputFile)))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.NgaFileSuffix)))
using (var ngaWriter = new NgaWriter(stream, version, SaCommon.ExacScoreTag, SaCommon.SchemaVersion, false))
{
ngaWriter.Write(exacParser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var dosageSensitivityVersion = DataSourceVersionReader.GetSourceVersion(_diseaseValidityFile + ".version");
string outFileName = $"{dosageSensitivityVersion.Name.Replace(' ', '_')}_{dosageSensitivityVersion.Version}";
// read uga file to get hgnc id to gene symbols dictionary
using (var diseaseValidityParser = new GeneDiseaseValidityParser(GZipUtilities.GetAppropriateReadStream(_diseaseValidityFile), GetHgncIdToGeneSymbols()))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.GeneFileSuffix)))
using (var ngaWriter = new NgaWriter(stream, dosageSensitivityVersion, SaCommon.DiseaseValidityTag, SaCommon.SchemaVersion, true))
{
ngaWriter.Write(diseaseValidityParser.GetItems());
}
return(ExitCodes.Success);
}
public void ReadBackGeneAnnotations()
{
var writeStream = new MemoryStream();
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks);
var ngaWriter = new NgaWriter(writeStream, version, "mimo", SaCommon.SchemaVersion, true);
ngaWriter.Write(GetGeneAnnotations());
var readStream = new MemoryStream(writeStream.ToArray());
using (var ngaReader = new NgaReader(readStream))
{
Assert.Null(ngaReader.GetAnnotation("gene3"));
Assert.Equal("[{\"mimNumber\":123,\"geneName\":\"gene name 1 ('minibrain', Drosophila, homolog of)\",\"description\":\"describing gene 1\\n\\\"some citation\\\"\",\"phenotypes\":[{\"phenotype\":\"disease 1\",\"mapping\":\"mapping of the wildtype gene\",\"inheritances\":[\"autosomal recessive\"],\"comments\":\"unconfirmed or possibly spurious mapping\"}]}]", ngaReader.GetAnnotation("gene1"));
Assert.Equal("[{\"mimNumber\":124,\"geneName\":\"gene name 2\",\"phenotypes\":[{\"phenotype\":\"disease 2\",\"mapping\":\"chromosome deletion or duplication syndrome\",\"inheritances\":[\"whatever\",\"never-ever\"],\"comments\":\"nondiseases\"}]}]", ngaReader.GetAnnotation("gene2"));
}
ngaWriter.Dispose();
}
private static ExitCodes ProgramExecution()
{
var omimSchema = OmimSchema.Get();
var omimParser = new OmimParser(_mimToGeneFile, _omimJsonFile, omimSchema);
var version = omimParser.GetVersion();
string outFileName = $"{version.Name}_{version.Version}";
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.GeneFileSuffix)))
using (var ngaWriter = new NgaWriter(nsaStream, version, SaCommon.OmimTag, SaCommon.SchemaVersion, true))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.GeneFileSuffix + SaCommon.JsonSchemaSuffix)))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
var omimItems = omimParser.GetItems();
var geneToItems = OmimUtilities.GetGeneToOmimEntriesAndSchema(omimItems);
ngaWriter.Write(geneToItems);
schemaWriter.Write(omimSchema);
}
return(ExitCodes.Success);
}
public void ReadBackGeneAnnotations()
{
NgaReader reader;
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks);
const string jsonKey = "mimo";
const bool isArray = true;
using (var ms = new MemoryStream())
{
using (var writer = new NgaWriter(ms, version, jsonKey, SaCommon.SchemaVersion, isArray, true))
{
writer.Write(GetGeneAnnotations());
}
ms.Position = 0;
reader = NgaReader.Read(ms);
}
Assert.NotNull(reader);
Assert.Null(reader.GetAnnotation("gene3"));
Assert.Equal("[{\"mimNumber\":123,\"geneName\":\"gene name 1 ('minibrain', Drosophila, homolog of)\",\"description\":\"describing gene 1\\n\\\"some citation\\\"\",\"phenotypes\":[{\"phenotype\":\"disease 1\",\"description\":\"This is disease 1\",\"mapping\":\"mapping of the wildtype gene\",\"inheritances\":[\"autosomal recessive\"],\"comments\":[\"unconfirmed or possibly spurious mapping\"]}]}]", reader.GetAnnotation("gene1"));
Assert.Equal("[{\"mimNumber\":124,\"geneName\":\"gene name 2\",\"phenotypes\":[{\"phenotype\":\"disease 2\",\"description\":\"COVID-19\",\"mapping\":\"chromosome deletion or duplication syndrome\",\"inheritances\":[\"whatever\",\"never-ever\"],\"comments\":[\"nondiseases\"]}]}]", reader.GetAnnotation("gene2"));
}
private static ExitCodes ProgramExecution()
{
_apiKey = GetEnvironmentVariable(OmimApiKeyEnvironmentVariableName);
if (_apiKey == null)
{
throw new InvalidDataException("Please set the OMIM API key as the environment variable \"OmimApiKey\".");
}
var version = OmimVersion.GetVersion();
string outFileName = $"{version.Name}_{version.Version}";
string dumpFilePath = Path.Combine(_outputDirectory, OmimDumpFileBaseName + version.Version + OmimDumpFileSuffix);
var(entrezGeneIdToSymbol, ensemblGeneIdToSymbol) = OmimUtilities.ParseUniversalGeneArchive(_inputReferencePath, _universalGeneArchivePath);
var geneSymbolUpdater = new GeneSymbolUpdater(entrezGeneIdToSymbol, ensemblGeneIdToSymbol);
var omimSchema = OmimSchema.Get();
using (var omimParser = new OmimParser(geneSymbolUpdater, omimSchema, _apiKey, dumpFilePath))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.NgaFileSuffix)))
using (var ngaWriter = new NgaWriter(nsaStream, version, SaCommon.OmimTag, SaCommon.SchemaVersion, true))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.NgaFileSuffix + SaCommon.JsonSchemaSuffix)))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
var omimItems = omimParser.GetItems();
var geneToItems = OmimUtilities.GetGeneToOmimEntriesAndSchema(omimItems);
ngaWriter.Write(geneToItems);
schemaWriter.Write(omimSchema);
}
geneSymbolUpdater.DisplayStatistics();
using (var writer = new StreamWriter(FileUtilities.GetCreateStream("UpdatedGeneSymbols.txt")))
{
geneSymbolUpdater.WriteUpdatedGeneSymbols(writer);
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
Dictionary <string, string> geneIdToSymbols;
using (var cacheStream = FileUtilities.GetReadStream(CacheConstants.TranscriptPath(_cachePrefix)))
using (var transcriptCacheReader = new TranscriptCacheReader(cacheStream))
using (var refProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_referenceSequncePath)))
{
geneIdToSymbols = LoadGenesFromCache(refProvider, transcriptCacheReader);
Console.WriteLine($"Loaded {geneIdToSymbols.Count} gene symbols from cache.");
}
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
var outFileName = $"{version.Name}_{version.Version}";
using (var gnomadGeneParser = new GnomadGeneParser(GZipUtilities.GetAppropriateStreamReader(_inputFile), geneIdToSymbols))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.NgaFileSuffix)))
using (var ngaWriter = new NgaWriter(stream, version, SaCommon.GnomadGeneScoreTag, SaCommon.SchemaVersion, false))
{
ngaWriter.Write(gnomadGeneParser.GetItems());
}
return(ExitCodes.Success);
}