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}\"; ");
 }
예제 #2
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        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()));
        }
예제 #3
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 private static void MergeRegulatoryRegion(IRegulatoryRegion previous, IRegulatoryRegion current,
                                           RegulatoryRegionComparer comparer)
 {
     if (comparer.Equals(previous, current))
     {
         return;
     }
     throw new InvalidDataException("Found different regulatory regions");
 }
예제 #4
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 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;
 }
예제 #5
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        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()));
        }
예제 #6
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        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);
        }
예제 #7
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        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);
        }
예제 #8
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        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);
        }
예제 #9
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        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);
        }
예제 #10
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 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();
 }
예제 #11
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 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;
 }