private static void WriteGeneralAttributes(TextWriter writer, IRegulatoryRegion regulatoryRegion)
{
if (!regulatoryRegion.Id.IsEmpty())
{
writer.Write($"regulatory_feature_id \"{regulatoryRegion.Id}\"; ");
}
writer.Write($"regulatory_feature_type \"{regulatoryRegion.Type}\"; ");
}
public static IAnnotatedRegulatoryRegion Annotate(IVariant variant, IRegulatoryRegion regulatoryRegion)
{
var featureEffect = new FeatureVariantEffects(regulatoryRegion, variant.Type, variant, variant.IsStructuralVariant);
var consequence = new Consequences(null, featureEffect);
consequence.DetermineRegulatoryVariantEffects();
return(new AnnotatedRegulatoryRegion(regulatoryRegion, consequence.GetConsequences()));
}
private static void MergeRegulatoryRegion(IRegulatoryRegion previous, IRegulatoryRegion current,
RegulatoryRegionComparer comparer)
{
if (comparer.Equals(previous, current))
{
return;
}
throw new InvalidDataException("Found different regulatory regions");
}
private IRegulatoryRegion[] GetRegulatoryRegions()
{
var regulatoryRegions = new IRegulatoryRegion[7];
regulatoryRegions[0] = new RegulatoryRegion(_chr17, 100,200,CompactId.Empty, RegulatoryRegionType.enhancer);
regulatoryRegions[1] = new RegulatoryRegion(_chr17, 200, 300, CompactId.Empty, RegulatoryRegionType.enhancer);
regulatoryRegions[2] = new RegulatoryRegion(_chr17, 300, 400, CompactId.Empty, RegulatoryRegionType.enhancer);
regulatoryRegions[3] = new RegulatoryRegion(_chr1, 1000, 2000, CompactId.Empty, RegulatoryRegionType.enhancer);
regulatoryRegions[4] = new RegulatoryRegion(_chr1, 2000, 3000, CompactId.Empty, RegulatoryRegionType.enhancer);
regulatoryRegions[5] = new RegulatoryRegion(_chr11, 150, 250, CompactId.Empty, RegulatoryRegionType.enhancer);
regulatoryRegions[6] = new RegulatoryRegion(_chr11, 250, 350, CompactId.Empty, RegulatoryRegionType.enhancer);
return regulatoryRegions;
}
public static IAnnotatedRegulatoryRegion Annotate(IVariant variant, IRegulatoryRegion regulatoryRegion)
{
OverlapType overlapType = Intervals.Utilities.GetOverlapType(regulatoryRegion.Start, regulatoryRegion.End,
variant.Start, variant.End);
EndpointOverlapType endpointOverlapType =
Intervals.Utilities.GetEndpointOverlapType(regulatoryRegion.Start, regulatoryRegion.End, variant.Start, variant.End);
var featureEffect = new FeatureVariantEffects(overlapType, endpointOverlapType, false, variant.Type, variant.IsStructuralVariant);
var consequence = new Consequences(VariantType.unknown, null, featureEffect);
consequence.DetermineRegulatoryVariantEffects();
return(new AnnotatedRegulatoryRegion(regulatoryRegion, consequence.GetConsequences()));
}
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);
}
private IRegulatoryRegion[] GetRegulatoryRegions()
{
var regulatoryRegions = new IRegulatoryRegion[3];
regulatoryRegions[0] = new RegulatoryRegion(_chr11, 11000, 12000, CompactId.Empty,
RegulatoryRegionType.promoter);
regulatoryRegions[1] = new RegulatoryRegion(_chr1, 120, 180, CompactId.Empty,
RegulatoryRegionType.promoter);
regulatoryRegions[2] = new RegulatoryRegion(_chr1, 300, 320, CompactId.Empty,
RegulatoryRegionType.promoter);
return(regulatoryRegions);
}
private static IRegulatoryRegion[] GetRegulatoryRegions()
{
var regulatoryRegions = new IRegulatoryRegion[3];
regulatoryRegions[0] = new RegulatoryRegion(ChromosomeUtilities.Chr11, 11000, 12000, CompactId.Empty,
RegulatoryRegionType.promoter);
regulatoryRegions[1] = new RegulatoryRegion(ChromosomeUtilities.Chr1, 120, 180, CompactId.Empty,
RegulatoryRegionType.promoter);
regulatoryRegions[2] = new RegulatoryRegion(ChromosomeUtilities.Chr1, 300, 320, CompactId.Empty,
RegulatoryRegionType.promoter);
return(regulatoryRegions);
}
private static void WriteRegulatoryFeature(TextWriter writer, IRegulatoryRegion regulatoryRegion)
{
writer.Write($"{regulatoryRegion.Chromosome.UcscName}\t.\tregulatory feature\t{regulatoryRegion.Start}\t{regulatoryRegion.End}\t.\t.\t.\t");
WriteGeneralAttributes(writer, regulatoryRegion);
writer.WriteLine();
}
internal void Write(IRegulatoryRegion region) => _writer.WriteLine(
$"{region.Chromosome.UcscName}\t{region.Chromosome.Index}\t{region.Start}\t{region.End}\t{region.Id}\t{region.Type}\t{(byte) region.Type}");
public AnnotatedRegulatoryRegion(IRegulatoryRegion regulatoryRegion, List <ConsequenceTag> consequences)
{
RegulatoryRegion = regulatoryRegion;
Consequences = consequences;
}