/// <summary>
/// reads the transcript from the binary reader
/// </summary>
public static Transcript Read(ExtendedBinaryReader reader, Gene[] cacheGenes, SimpleInterval[] cacheIntrons,
SimpleInterval[] cacheMirnas, string[] cachePeptideSeqs)
{
// transcript
var referenceIndex = reader.ReadUInt16();
var start = reader.ReadOptInt32();
var end = reader.ReadOptInt32();
var id = CompactId.Read(reader);
// gene
var geneIndex = reader.ReadOptInt32();
var gene = cacheGenes[geneIndex];
// encoded data
var encoded = new EncodedTranscriptData(reader.ReadUInt16(), reader.ReadByte());
// exons & introns
var introns = encoded.HasIntrons ? ReadIndices(reader, cacheIntrons) : null;
var cdnaMaps = encoded.HasCdnaMaps ? ReadCdnaMaps(reader) : null;
// protein function predictions
int siftIndex = encoded.HasSift ? reader.ReadOptInt32() : -1;
int polyphenIndex = encoded.HasPolyPhen ? reader.ReadOptInt32() : -1;
// translation
var translation = encoded.HasTranslation ? Translation.Read(reader, cachePeptideSeqs) : null;
// attributes
var mirnas = encoded.HasMirnas ? ReadIndices(reader, cacheMirnas) : null;
return(new Transcript(referenceIndex, start, end, id, encoded.Version, translation, encoded.BioType,
gene, TranscriptUtilities.GetTotalExonLength(cdnaMaps), encoded.StartExonPhase, encoded.IsCanonical,
introns, mirnas, cdnaMaps, siftIndex, polyphenIndex, encoded.TranscriptSource));
}
/// <summary>
/// writes the transcript to the binary writer
/// </summary>
public void Write(ExtendedBinaryWriter writer, Dictionary <Gene, int> geneIndices,
Dictionary <SimpleInterval, int> intronIndices, Dictionary <SimpleInterval, int> microRnaIndices,
Dictionary <string, int> peptideIndices)
{
// transcript
writer.Write(ReferenceIndex);
writer.WriteOpt(Start);
writer.WriteOpt(End);
Id.Write(writer);
// gene
writer.WriteOpt(GetIndex(Gene, geneIndices));
// encoded data
var encoded = new EncodedTranscriptData(BioType, Version, TranscriptSource, IsCanonical, SiftIndex != -1,
PolyPhenIndex != -1, MicroRnas != null, Introns != null, CdnaMaps != null, Translation != null,
StartExonPhase);
encoded.Write(writer);
// exons & introns
if (encoded.HasIntrons)
{
WriteIndices(writer, Introns, intronIndices);
}
if (encoded.HasCdnaMaps)
{
WriteCdnaMaps(writer);
}
// protein function predictions
if (encoded.HasSift)
{
writer.WriteOpt(SiftIndex);
}
if (encoded.HasPolyPhen)
{
writer.WriteOpt(PolyPhenIndex);
}
// translation
if (encoded.HasTranslation)
{
// ReSharper disable once PossibleNullReferenceException
var peptideIndex = GetIndex(Translation.PeptideSeq, peptideIndices);
Translation.Write(writer, peptideIndex);
}
// attributes
if (encoded.HasMirnas)
{
WriteIndices(writer, MicroRnas, microRnaIndices);
}
}
public void EncodedTranscriptData_EndToEnd()
{
const BioType expectedBiotype = BioType.Y_RNA;
const bool expectedCdsStartNotFound = true;
const bool expectedCdsEndNotFound = true;
const Source expectedSource = Source.BothRefSeqAndEnsembl;
const bool expectedCanonical = true;
const bool expectedSift = true;
const bool expectedPolyPhen = true;
const bool expectedMirnas = true;
const bool expectedRnaEdits = true;
const bool expectedSelenocysteines = true;
const bool expectedTranscriptRegions = true;
const bool expectedTranslation = true;
const byte expectedStartExonPhase = 3;
// ReSharper disable ConditionIsAlwaysTrueOrFalse
var encodedData = EncodedTranscriptData.GetEncodedTranscriptData(expectedBiotype, expectedCdsStartNotFound,
expectedCdsEndNotFound, expectedSource, expectedCanonical, expectedSift, expectedPolyPhen,
expectedMirnas, expectedRnaEdits, expectedSelenocysteines, expectedTranscriptRegions,
expectedTranslation, expectedStartExonPhase);
// ReSharper restore ConditionIsAlwaysTrueOrFalse
EncodedTranscriptData observedEncodedTranscriptData;
using (var ms = new MemoryStream())
{
using (var writer = new ExtendedBinaryWriter(ms, Encoding.UTF8, true))
{
encodedData.Write(writer);
}
ms.Position = 0;
using (var reader = new BufferedBinaryReader(ms))
{
observedEncodedTranscriptData = EncodedTranscriptData.Read(reader);
}
}
Assert.NotNull(observedEncodedTranscriptData);
Assert.Equal(expectedBiotype, observedEncodedTranscriptData.BioType);
Assert.Equal(expectedSource, observedEncodedTranscriptData.TranscriptSource);
Assert.Equal(expectedCanonical, observedEncodedTranscriptData.IsCanonical);
Assert.Equal(expectedSift, observedEncodedTranscriptData.HasSift);
Assert.Equal(expectedPolyPhen, observedEncodedTranscriptData.HasPolyPhen);
Assert.Equal(expectedMirnas, observedEncodedTranscriptData.HasMirnas);
Assert.Equal(expectedTranscriptRegions, observedEncodedTranscriptData.HasTranscriptRegions);
Assert.Equal(expectedTranslation, observedEncodedTranscriptData.HasTranslation);
Assert.Equal(expectedStartExonPhase, observedEncodedTranscriptData.StartExonPhase);
}
