public static NgaWriter GetNgaWriter(Stream ngaStream, GeneAnnotationsParser parser, string dataVersion)
{
dataVersion = string.IsNullOrEmpty(parser.Version) ? dataVersion : parser.Version;
var version = new DataSourceVersion(parser.JsonTag, dataVersion, DateTime.Now.Ticks, parser.DataSourceDescription);
return(new NgaWriter(ngaStream, version, parser.JsonTag, SaCommon.SchemaVersion, false));
}
public static GeneAnnotationsParser Create(StreamReader reader, Dictionary <string, string> entrezGeneIdToSymbol, Dictionary <string, string> ensemblIdToSymbol)
{
var parser = new GeneAnnotationsParser(reader, entrezGeneIdToSymbol, ensemblIdToSymbol);
parser.ParseHeaderLines();
parser.InitiateSchema();
parser.AddHeaderAnnotation();
return(parser);
}
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()
{
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);
}
public static NgaWriter GetNgaWriter(Stream ngaStream, GeneAnnotationsParser parser, string dataVersion)
{
var version = new DataSourceVersion(parser.JsonTag, dataVersion, DateTime.Now.Ticks);
return(new NgaWriter(ngaStream, version, parser.JsonTag, SaCommon.SchemaVersion, false));
}
