private static ExitCodes ProgramExecution()
{
var(entrezGeneIdToSymbol, ensemblGeneIdToSymbol) = GeneUtilities.ParseUniversalGeneArchive(null, _universalGeneArchivePath);
string outputPrefix = GetOutputPrefix(_inputFile);
string ngaFilePath = Path.Combine(_outputDirectory, outputPrefix + SaCommon.NgaFileSuffix);
string ngaSchemaFilePath = ngaFilePath + SaCommon.JsonSchemaSuffix;
using (var parser = GeneAnnotationsParser.Create(GZipUtilities.GetAppropriateStreamReader(_inputFile), entrezGeneIdToSymbol, ensemblGeneIdToSymbol))
using (var ngaStream = FileUtilities.GetCreateStream(ngaFilePath))
using (var ngaWriter = CaUtilities.GetNgaWriter(ngaStream, parser, CaUtilities.GetInputFileName(_inputFile)))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(ngaSchemaFilePath))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
ngaWriter.Write(parser.GetItems());
schemaWriter.Write(parser.JsonSchema);
}
return(ExitCodes.Success);
}
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(entrezGeneIdToSymbol, ensemblGeneIdToSymbol) = GeneUtilities.ParseUniversalGeneArchive(_inputReferencePath, _universalGeneArchivePath);
var geneSymbolUpdater = new GeneSymbolUpdater(entrezGeneIdToSymbol, ensemblGeneIdToSymbol);
using (var omimQuery = new OmimQuery(_apiKey, _outputDirectory))
{
omimQuery.GenerateMimToGeneSymbolFile(geneSymbolUpdater);
omimQuery.GenerateJsonResponse();
}
OmimVersion.WriteToFile(OmimQuery.JsonResponseFile, _outputDirectory);
geneSymbolUpdater.DisplayStatistics();
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var(entrezGeneIdToSymbol, ensemblGeneIdToSymbol) = GeneUtilities.ParseUniversalGeneArchive(null, _universalGeneArchivePath);
string outputPrefix = GetOutputPrefix(_inputFile);
string ngaFilePath = Path.Combine(_outputDirectory, outputPrefix + SaCommon.GeneFileSuffix);
string ngaSchemaFilePath = ngaFilePath + SaCommon.JsonSchemaSuffix;
using (var parser = GeneAnnotationsParser.Create(GZipUtilities.GetAppropriateStreamReader(_inputFile), entrezGeneIdToSymbol, ensemblGeneIdToSymbol))
using (var ngaStream = FileUtilities.GetCreateStream(ngaFilePath))
using (var ngaWriter = CaUtilities.GetNgaWriter(ngaStream, parser, CaUtilities.GetInputFileName(_inputFile)))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(ngaSchemaFilePath))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
ngaWriter.Write(parser.GetItems());
if (parser.GetUnknownGenes().Count > 0)
{
throw new UserErrorException($"The following gene IDs were not recognized in Nirvana: {string.Join(',',parser.GetUnknownGenes())}.");
}
schemaWriter.Write(parser.JsonSchema);
}
return(ExitCodes.Success);
}
private static GeneAnnotationsParser GetGeneAnnotationsParserFromCustomTsvStream(PersistentStream customTsvStream)
{
var(entrezGeneIdToSymbol, ensemblGeneIdToSymbol) = GeneUtilities.ParseUniversalGeneArchive(null, LambdaUrlHelper.GetUgaUrl());
return(GeneAnnotationsParser.Create(new StreamReader(GZipUtilities.GetAppropriateStream(customTsvStream)), entrezGeneIdToSymbol, ensemblGeneIdToSymbol));
}