public void CacheHeader_EndToEnd()
{
const Source expectedTranscriptSource = Source.BothRefSeqAndEnsembl;
const long expectedCreationTimeTicks = long.MaxValue;
const GenomeAssembly expectedAssembly = GenomeAssembly.hg19;
const ushort expectedVepVersion = ushort.MaxValue;
var expectedBaseHeader = new Header("VEP", 1, 2, expectedTranscriptSource, expectedCreationTimeTicks, expectedAssembly);
var expectedCustomHeader = new TranscriptCacheCustomHeader(expectedVepVersion, 0);
var expectedHeader = new CacheHeader(expectedBaseHeader, expectedCustomHeader);
CacheHeader observedHeader;
using (var ms = new MemoryStream())
{
using (var writer = new BinaryWriter(ms, Encoding.UTF8, true))
{
expectedHeader.Write(writer);
}
ms.Position = 0;
observedHeader = CacheHeader.Read(ms);
}
Assert.NotNull(observedHeader);
Assert.Equal(expectedTranscriptSource, observedHeader.Source);
Assert.Equal(expectedCreationTimeTicks, observedHeader.CreationTimeTicks);
Assert.Equal(expectedAssembly, observedHeader.Assembly);
Assert.Equal(expectedVepVersion, observedHeader.Custom.VepVersion);
}
public TranscriptCacheReaderTests()
{
var chr1 = new Chromosome("chr1", "1", 0);
var chr2 = new Chromosome("chr2", "2", 1);
var chr3 = new Chromosome("chr3", "3", 2);
_refIndexToChromosome = new Dictionary <ushort, IChromosome>
{
[chr1.Index] = chr1,
[chr2.Index] = chr2,
[chr3.Index] = chr3
};
const GenomeAssembly genomeAssembly = GenomeAssembly.GRCh38;
var baseHeader = new Header("test", 2, 3, Source.BothRefSeqAndEnsembl, 4, genomeAssembly);
var customHeader = new TranscriptCacheCustomHeader(1, 2);
_expectedHeader = new CacheHeader(baseHeader, customHeader);
var transcriptRegions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 100, 199, 300, 399),
new TranscriptRegion(TranscriptRegionType.Intron, 1, 200, 299, 399, 400),
new TranscriptRegion(TranscriptRegionType.Exon, 2, 300, 399, 400, 499)
};
var mirnas = new IInterval[2];
mirnas[0] = new Interval(100, 200);
mirnas[1] = new Interval(300, 400);
var peptideSeqs = new[] { "MASE*" };
var genes = new IGene[1];
genes[0] = new Gene(chr3, 100, 200, true, "TP53", 300, CompactId.Convert("7157"),
CompactId.Convert("ENSG00000141510"));
var regulatoryRegions = new IRegulatoryRegion[2];
regulatoryRegions[0] = new RegulatoryRegion(chr3, 1200, 1300, CompactId.Convert("123"), RegulatoryRegionType.enhancer);
regulatoryRegions[1] = new RegulatoryRegion(chr3, 1250, 1450, CompactId.Convert("456"), RegulatoryRegionType.enhancer);
var regulatoryRegionIntervalArrays = regulatoryRegions.ToIntervalArrays(3);
var transcripts = GetTranscripts(chr3, genes, transcriptRegions, mirnas);
var transcriptIntervalArrays = transcripts.ToIntervalArrays(3);
_expectedCacheData = new TranscriptCacheData(_expectedHeader, genes, transcriptRegions, mirnas, peptideSeqs,
transcriptIntervalArrays, regulatoryRegionIntervalArrays);
}
private static Stream GetCacheStream()
{
const GenomeAssembly genomeAssembly = GenomeAssembly.GRCh38;
var baseHeader = new Header("test", 2, 3, Source.BothRefSeqAndEnsembl, 4, genomeAssembly);
var customHeader = new TranscriptCacheCustomHeader(1, 2);
var expectedHeader = new CacheHeader(baseHeader, customHeader);
var transcriptRegions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 100, 199, 300, 399),
new TranscriptRegion(TranscriptRegionType.Intron, 1, 200, 299, 399, 400),
new TranscriptRegion(TranscriptRegionType.Exon, 2, 300, 399, 400, 499)
};
var mirnas = new IInterval[2];
mirnas[0] = new Interval(100, 200);
mirnas[1] = new Interval(300, 400);
var peptideSeqs = new[] { "MASE*" };
var genes = new IGene[1];
genes[0] = new Gene(ChromosomeUtilities.Chr3, 100, 200, true, "TP53", 300, CompactId.Convert("7157"),
CompactId.Convert("ENSG00000141510"));
var regulatoryRegions = new IRegulatoryRegion[2];
regulatoryRegions[0] = new RegulatoryRegion(ChromosomeUtilities.Chr3, 1200, 1300, CompactId.Convert("123"), RegulatoryRegionType.enhancer);
regulatoryRegions[1] = new RegulatoryRegion(ChromosomeUtilities.Chr3, 1250, 1450, CompactId.Convert("456"), RegulatoryRegionType.enhancer);
var regulatoryRegionIntervalArrays = regulatoryRegions.ToIntervalArrays(3);
var transcripts = GetTranscripts(ChromosomeUtilities.Chr3, genes, transcriptRegions, mirnas);
var transcriptIntervalArrays = transcripts.ToIntervalArrays(3);
var expectedCacheData = new TranscriptCacheData(expectedHeader, genes, transcriptRegions, mirnas, peptideSeqs,
transcriptIntervalArrays, regulatoryRegionIntervalArrays);
var ms = new MemoryStream();
using (var writer = new TranscriptCacheWriter(ms, expectedHeader, true))
{
writer.Write(expectedCacheData);
}
ms.Position = 0;
return(ms);
}
public TranscriptCacheStaging CreateTranscriptCache(MutableTranscript[] mutableTranscripts,
IEnumerable <IRegulatoryRegion> regulatoryRegions, IIntervalForest <UgaGene> geneForest, int numRefSeqs)
{
Logger.Write("- assigning UGA genes to transcripts... ");
AssignUgaGenesToTranscripts(mutableTranscripts, geneForest);
Logger.WriteLine("finished.");
var transcriptIntervalArrays = mutableTranscripts.ToTranscripts().ToIntervalArrays(numRefSeqs);
var regulatoryRegionIntervalArrays = regulatoryRegions.ToIntervalArrays(numRefSeqs);
var customHeader = new TranscriptCacheCustomHeader(_vepVersion, _vepReleaseTicks);
var header = new CacheHeader(HeaderUtilities.GetHeader(_source, _genomeAssembly), customHeader);
return(TranscriptCacheStaging.GetStaging(header, transcriptIntervalArrays, regulatoryRegionIntervalArrays));
}
private static (ushort Schema, ushort Data, ushort Vep) GetHeaderInformation(string cachePath)
{
CacheHeader header;
TranscriptCacheCustomHeader customHeader = null;
using (var stream = FileUtilities.GetReadStream(cachePath))
using (var blockStream = new BlockStream(new Zstandard(), stream, CompressionMode.Decompress))
{
header = blockStream.ReadHeader(CacheHeader.Read, TranscriptCacheCustomHeader.Read) as CacheHeader;
if (header != null)
{
customHeader = header.CustomHeader as TranscriptCacheCustomHeader;
}
}
if (header == null || customHeader == null)
{
throw new InvalidFileFormatException($"Could not parse the header information correctly for {cachePath}");
}
return(header.SchemaVersion, header.DataVersion, customHeader.VepVersion);
}
