private static ExitCodes ProgramExecution()
{
var logger = new ConsoleLogger();
string transcriptPath = _inputPrefix + ".transcripts.gz";
string siftPath = _inputPrefix + ".sift.gz";
string polyphenPath = _inputPrefix + ".polyphen.gz";
string regulatoryPath = _inputPrefix + ".regulatory.gz";
(var refIndexToChromosome, var refNameToChromosome, int numRefSeqs) = SequenceHelper.GetDictionaries(_inputReferencePath);
using (var transcriptReader = new MutableTranscriptReader(GZipUtilities.GetAppropriateReadStream(transcriptPath), refIndexToChromosome))
using (var regulatoryReader = new RegulatoryRegionReader(GZipUtilities.GetAppropriateReadStream(regulatoryPath), refIndexToChromosome))
using (var siftReader = new PredictionReader(GZipUtilities.GetAppropriateReadStream(siftPath), refIndexToChromosome, IntermediateIoCommon.FileType.Sift))
using (var polyphenReader = new PredictionReader(GZipUtilities.GetAppropriateReadStream(polyphenPath), refIndexToChromosome, IntermediateIoCommon.FileType.Polyphen))
using (var geneReader = new UgaGeneReader(GZipUtilities.GetAppropriateReadStream(ExternalFiles.UniversalGeneFilePath), refNameToChromosome))
{
var genomeAssembly = transcriptReader.Header.Assembly;
var source = transcriptReader.Header.Source;
long vepReleaseTicks = transcriptReader.Header.VepReleaseTicks;
ushort vepVersion = transcriptReader.Header.VepVersion;
logger.Write("- loading universal gene archive file... ");
var genes = geneReader.GetGenes();
var geneForest = CreateGeneForest(genes, numRefSeqs, genomeAssembly);
logger.WriteLine($"{genes.Length:N0} loaded.");
logger.Write("- loading regulatory region file... ");
var regulatoryRegions = regulatoryReader.GetRegulatoryRegions();
logger.WriteLine($"{regulatoryRegions.Length:N0} loaded.");
logger.Write("- loading transcript file... ");
var transcripts = transcriptReader.GetTranscripts();
var transcriptsByRefIndex = transcripts.GetMultiValueDict(x => x.Chromosome.Index);
logger.WriteLine($"{transcripts.Length:N0} loaded.");
MarkCanonicalTranscripts(logger, transcripts);
var predictionBuilder = new PredictionCacheBuilder(logger, genomeAssembly);
var predictionCaches = predictionBuilder.CreatePredictionCaches(transcriptsByRefIndex, siftReader, polyphenReader, numRefSeqs);
logger.Write("- writing SIFT prediction cache... ");
predictionCaches.Sift.Write(FileUtilities.GetCreateStream(CacheConstants.SiftPath(_outputCacheFilePrefix)));
logger.WriteLine("finished.");
logger.Write("- writing PolyPhen prediction cache... ");
predictionCaches.PolyPhen.Write(FileUtilities.GetCreateStream(CacheConstants.PolyPhenPath(_outputCacheFilePrefix)));
logger.WriteLine("finished.");
var transcriptBuilder = new TranscriptCacheBuilder(logger, genomeAssembly, source, vepReleaseTicks, vepVersion);
var transcriptStaging = transcriptBuilder.CreateTranscriptCache(transcripts, regulatoryRegions, geneForest, numRefSeqs);
logger.Write("- writing transcript cache... ");
transcriptStaging.Write(FileUtilities.GetCreateStream(CacheConstants.TranscriptPath(_outputCacheFilePrefix)));
logger.WriteLine("finished.");
}
return(ExitCodes.Success);
}
public (PredictionCacheStaging Sift, PredictionCacheStaging PolyPhen) CreatePredictionCaches(
Dictionary <ushort, List <MutableTranscript> > transcriptsByRefIndex, PredictionReader siftReader,
PredictionReader polyphenReader, int numRefSeqs)
{
_logger.Write("- converting prediction strings... ");
var siftRoundedPredictionsPerRef = new RoundedEntryPrediction[numRefSeqs][];
var polyPhenRoundedPredictionsPerRef = new RoundedEntryPrediction[numRefSeqs][];
for (ushort refIndex = 0; refIndex < numRefSeqs; refIndex++)
{
var sift = siftReader.GetPredictionData();
var polyphen = polyphenReader.GetPredictionData();
if (sift.Chromosome.Index != refIndex || polyphen.Chromosome.Index != refIndex)
{
throw new InvalidDataException(
$"Found mismatch between transcript chromosome index ({refIndex}) and prediction chromosome indices (SIFT: {sift.Chromosome.Index}, PolyPhen: {polyphen.Chromosome.Index}.");
}
if (!transcriptsByRefIndex.TryGetValue(refIndex, out var refTranscripts))
{
continue;
}
var(siftPredictions, polyPhenPredictions) = ProcessReference(refTranscripts,
sift.TranscriptToPredictionIndex, polyphen.TranscriptToPredictionIndex, sift.PredictionData,
polyphen.PredictionData);
siftRoundedPredictionsPerRef[refIndex] = siftPredictions;
polyPhenRoundedPredictionsPerRef[refIndex] = polyPhenPredictions;
}
_logger.WriteLine("finished.");
var siftStaging = BuildCacheStaging("SIFT", siftRoundedPredictionsPerRef, numRefSeqs);
var polyPhenStaging = BuildCacheStaging("PolyPhen", polyPhenRoundedPredictionsPerRef, numRefSeqs);
return(siftStaging, polyPhenStaging);
}
