/// <summary>
/// updates a regulatory region
/// mini-cache filename example: ENSR00000079256_chr1_Ensembl72_reg.ndb
/// </summary>
public UpdateStatus Update(DataBundle bundle, string outputCacheDir, ushort desiredVepVersion, List <string> outputFiles)
{
var regulatoryElement = MiniCacheUtilities.GetDesiredRegulatoryElement(bundle, _regulatoryId);
if (regulatoryElement == null)
{
return(UpdateStatus.IdNotFound);
}
bundle.Load(regulatoryElement.ReferenceIndex);
var outputCache = CreateCache(bundle.Cache.Header, new[] { regulatoryElement });
var outputStub = GetOutputStub(outputCacheDir, _regulatoryId,
bundle.Sequence.Renamer.UcscReferenceNames[regulatoryElement.ReferenceIndex], TranscriptDataSource,
desiredVepVersion);
var refIndices = new HashSet <ushort> {
regulatoryElement.ReferenceIndex
};
MiniCacheUtilities.WriteTranscriptCache(outputCache, outputStub, outputFiles);
MiniCacheUtilities.WriteEmptyBases(bundle, refIndices, outputStub, outputFiles);
return(UpdateStatus.Current);
}
/// <summary>
/// updates a transcript
/// mini-cache filename example: ENST00000255416_chr1_Ensembl79.ndb
/// </summary>
public UpdateStatus Update(DataBundle bundle, string outputCacheDir, ushort desiredVepVersion, List <string> outputFiles)
{
var transcript = MiniCacheUtilities.GetDesiredTranscript(bundle, _transcriptId, RefIndex);
if (transcript == null)
{
return(UpdateStatus.IdNotFound);
}
var packets = new List <TranscriptPacket> {
new TranscriptPacket(transcript)
};
foreach (var packet in packets)
{
bundle.Load(packet.ReferenceIndex);
packet.SiftPrediction = packet.Transcript.SiftIndex == -1
? null
: bundle.SiftCache.Predictions[packet.Transcript.SiftIndex];
packet.PolyPhenPrediction = packet.Transcript.PolyPhenIndex == -1
? null
: bundle.PolyPhenCache.Predictions[packet.Transcript.PolyPhenIndex];
}
var numRefSeqs = bundle.Sequence.Renamer.NumRefSeqs;
var sift = PredictionUtilities.GetStaging(bundle, true, packets, numRefSeqs);
var polyphen = PredictionUtilities.GetStaging(bundle, false, packets, numRefSeqs);
PredictionUtilities.FixIndices(packets);
var outputCache = MiniCacheUtilities.CreateCache(bundle.Cache.Header, packets);
var outputStub = GetOutputStub(outputCacheDir, _transcriptId,
bundle.Sequence.Renamer.UcscReferenceNames[transcript.ReferenceIndex], TranscriptDataSource,
desiredVepVersion);
MiniCacheUtilities.WriteTranscriptCache(outputCache, outputStub, outputFiles);
MiniCacheUtilities.WritePredictionCaches(sift, polyphen, outputStub, outputFiles);
MiniCacheUtilities.WriteBases(bundle, packets, outputStub, outputFiles);
return(UpdateStatus.Current);
}
/// <summary>
/// updates a position
/// mini-cache filename example: chr1_713044_755966_RefSeq79_pos.ndb
/// </summary>
public UpdateStatus Update(DataBundle bundle, string outputCacheDir, ushort desiredVepVersion, List <string> outputFiles)
{
bundle.Load(RefIndex);
string vcfLine = $"{bundle.Sequence.Renamer.UcscReferenceNames[RefIndex]}\t{_position}\t.\tC\t<CN0>\t100\tPASS\tEND={_endPosition};SVTYPE=CNV";
var transcripts = MiniCacheUtilities.GetTranscriptsByVcf(bundle, vcfLine);
if (transcripts == null)
{
return(UpdateStatus.IdNotFound);
}
var packets = transcripts.Select(transcript => new TranscriptPacket(transcript)).ToList();
foreach (var packet in packets)
{
bundle.Load(packet.ReferenceIndex);
packet.SiftPrediction = packet.Transcript.SiftIndex == -1
? null
: bundle.SiftCache.Predictions[packet.Transcript.SiftIndex];
packet.PolyPhenPrediction = packet.Transcript.PolyPhenIndex == -1
? null
: bundle.PolyPhenCache.Predictions[packet.Transcript.PolyPhenIndex];
}
var numRefSeqs = bundle.Sequence.Renamer.NumRefSeqs;
var sift = PredictionUtilities.GetStaging(bundle, true, packets, numRefSeqs);
var polyphen = PredictionUtilities.GetStaging(bundle, false, packets, numRefSeqs);
PredictionUtilities.FixIndices(packets);
var outputCache = MiniCacheUtilities.CreateCache(bundle.Cache.Header, packets);
var outputStub = GetOutputStub(outputCacheDir, bundle.Sequence.Renamer.UcscReferenceNames[RefIndex],
_position, _endPosition, TranscriptDataSource, desiredVepVersion);
MiniCacheUtilities.WriteTranscriptCache(outputCache, outputStub, outputFiles);
MiniCacheUtilities.WritePredictionCaches(sift, polyphen, outputStub, outputFiles);
MiniCacheUtilities.WriteBases(bundle, packets, outputStub, outputFiles);
return(UpdateStatus.Current);
}
/// <summary>
/// executes the program
/// </summary>
protected override void ProgramExecution()
{
var bundle = GetDataBundle(ConfigurationSettings.InputReferencePath, ConfigurationSettings.InputPrefix);
var header = bundle.Cache.Header.Custom as GlobalCustomHeader;
if (header == null)
{
throw new InvalidCastException("Unable to cast the custom header as a GlobalCustomHeader");
}
var regulatoryElement = MiniCacheUtilities.GetDesiredRegulatoryElement(bundle, ConfigurationSettings.RegulatoryElementId);
if (regulatoryElement == null)
{
throw new UserErrorException($"Unable to find the desired regulatory element: {ConfigurationSettings.RegulatoryElementId}");
}
var updater = new RegulatoryUpdater(ConfigurationSettings.RegulatoryElementId,
regulatoryElement.ReferenceIndex, bundle.Cache.Header.TranscriptSource.ToString());
var outputFiles = new List <string>();
var status = updater.Update(bundle, ConfigurationSettings.OutputDirectory, header.VepVersion, outputFiles);
UnitTestResourceCrawler.CleanupFiles(status, new List <string>(), outputFiles);
if (status != UpdateStatus.Current)
{
throw new UserErrorException($"Unable to create the mini-cache file. Status: {status}");
}
Console.WriteLine();
Console.WriteLine("- created the following files:");
foreach (var path in outputFiles)
{
Console.WriteLine(Path.GetFileNameWithoutExtension(path));
}
}
