public void TranscriptCacheReader_EndToEnd()
{
TranscriptCacheData observedCache;
using (var ms = new MemoryStream())
{
using (var writer = new TranscriptCacheWriter(ms, _expectedHeader, true))
{
writer.Write(_expectedCacheData);
}
ms.Position = 0;
using (var reader = new TranscriptCacheReader(ms))
{
observedCache = reader.Read(_refIndexToChromosome);
}
}
Assert.NotNull(observedCache);
Assert.Equal(_expectedCacheData.PeptideSeqs, observedCache.PeptideSeqs);
CheckChromosomeIntervals(_expectedCacheData.Genes, observedCache.Genes);
CheckIntervalArrays(_expectedCacheData.RegulatoryRegionIntervalArrays, observedCache.RegulatoryRegionIntervalArrays);
CheckIntervalArrays(_expectedCacheData.TranscriptIntervalArrays, observedCache.TranscriptIntervalArrays);
CheckIntervals(_expectedCacheData.TranscriptRegions, observedCache.TranscriptRegions);
CheckIntervals(_expectedCacheData.Mirnas, observedCache.Mirnas);
}
public void ReadItems_EndToEnd()
{
var expectedStrings = new[] { "Huey", "Duey", "Louie" };
string[] observedStrings;
using (var ms = new MemoryStream())
{
// ReSharper disable AccessToDisposedClosure
using (var writer = new ExtendedBinaryWriter(ms, Encoding.UTF8, true))
{
TranscriptCacheWriter.WriteItems(writer, expectedStrings, x => writer.WriteOptAscii(x));
}
ms.Position = 0;
using (var reader = new ExtendedBinaryReader(ms))
{
observedStrings = TranscriptCacheReader.ReadItems(reader, () => reader.ReadAsciiString());
}
// ReSharper restore AccessToDisposedClosure
}
Assert.NotNull(observedStrings);
Assert.Equal(expectedStrings, observedStrings);
}
public void CreateIndex_EmptyDictionary_WhenInputNull()
{
var dict = TranscriptCacheWriter.CreateIndex(null, EqualityComparer <string> .Default);
Assert.NotNull(dict);
Assert.Empty(dict);
}
public void CreateIndex_PopulatedDictionary()
{
var strings = new[] { "A", "B", "D", "P", "Z" };
var dict = TranscriptCacheWriter.CreateIndex(strings, EqualityComparer <string> .Default);
Assert.NotNull(dict);
Assert.Equal(3, dict["P"]);
}
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);
}
