/// <summary>
/// creates the global database
/// </summary>
public void CreateTranscriptCacheFile(string outputPrefix)
{
if (!_hasData)
{
throw new GeneralException("Data was not loaded before running CreateTranscriptCacheFile");
}
Console.Write("- creating transcript cache file... ");
var createBenchmark = new Benchmark();
var globalOutputPath = CacheConstants.TranscriptPath(outputPrefix);
var customHeader = new GlobalCustomHeader(_transcriptReader.Header.VepReleaseTicks,
_transcriptReader.Header.VepVersion);
var header = new FileHeader(CacheConstants.Identifier, CacheConstants.SchemaVersion,
CacheConstants.DataVersion, _transcriptReader.Header.TranscriptSource, _currentTimeTicks, _transcriptReader.Header.GenomeAssembly, customHeader);
var genes = ConvertGenes();
using (var writer = new GlobalCacheWriter(globalOutputPath, header))
{
var cache = new VD.GlobalCache(header, _transcripts.ToArray(), _regulatoryElements.ToArray(),
genes, _introns.ToArray(), _microRnas.ToArray(), _peptideSeqs.ToArray());
writer.Write(cache);
}
Console.WriteLine("{0}", Benchmark.ToHumanReadable(createBenchmark.GetElapsedTime()));
}
public static void WriteTranscriptCache(GlobalCache cache, string outputStub, List <string> outputFiles)
{
var outputPath = outputStub + ".ndb" + TempCacheExt;
outputFiles.Add(outputPath);
using (var writer = new GlobalCacheWriter(outputPath, (FileHeader)cache.Header))
{
writer.Write(cache);
}
}
public void Combine()
{
using (var reader1 = new GlobalCacheReader(_cachePath1))
using (var reader2 = new GlobalCacheReader(_cachePath2))
{
var cache1 = reader1.Read();
var cache2 = reader2.Read();
//todo: hardcoding the combined custom header, note that the date is March 2016 on the vep website but we useds to say 2016-04-29
var customHeader = new GlobalCustomHeader(DateTime.Parse("2016-04-29").Ticks, 84);
var header = new FileHeader(CacheConstants.Identifier, CacheConstants.SchemaVersion,
CacheConstants.DataVersion, TranscriptDataSource.BothRefSeqAndEnsembl, DateTime.Now.Ticks, reader1.FileHeader.GenomeAssembly, customHeader);
CombinePredictionsCaches();
using (var writer = new GlobalCacheWriter(_outputCachePath, header))
{
List <RegulatoryElement> combinedRegElements;
List <Gene> combinedGenes;
List <SimpleInterval> combinedIntrons;
List <SimpleInterval> combinedMirnas;
List <string> combinedPeptides;
var combinedTranscripts = GetCombinedCacheElements(cache1, cache2, out combinedRegElements, out combinedGenes, out combinedIntrons, out combinedMirnas, out combinedPeptides);
var combinedCache = new GlobalCache(header, combinedTranscripts.ToArray(),
combinedRegElements.ToArray(),
combinedGenes.ToArray(),
combinedIntrons.ToArray(),
combinedMirnas.ToArray(),
combinedPeptides.ToArray()
);
Console.WriteLine("Writing combined cache...");
writer.Write(combinedCache);
Console.WriteLine("Done");
}
}
}
