コード例 #1
0
        /// <summary>
        /// calculates the cDNA coordinates given the specified genomic coordinates [Transcript.pm:927 cdna_coding_start]
        /// genomic2pep [TransciptMapper:482]
        /// </summary>
        public static void GetCodingDnaEndpoints(CdnaCoordinateMap[] cdnaMaps, int genomicBegin, int genomicEnd, out int cdnaBegin, out int cdnaEnd)
        {
            // find an overlapping mapper pair
            var  coordinateMap = CdnaCoordinateMap.Null();
            bool foundOverlap  = false;

            for (int i = 0; i < cdnaMaps.Length; i++)
            {
                coordinateMap = cdnaMaps[i];

                if (genomicEnd >= coordinateMap.GenomicStart &&
                    genomicBegin <= coordinateMap.GenomicEnd)
                {
                    foundOverlap = true;
                    break;
                }
            }

            if (!foundOverlap)
            {
                throw new GeneralException($"Unable to find an overlapping mapping pair for these genomic coordinates: ({genomicBegin}, {genomicEnd})");
            }

            // calculate the cDNA position
            cdnaBegin = coordinateMap.CdnaEnd - (genomicEnd - coordinateMap.GenomicStart);
            cdnaEnd   = coordinateMap.CdnaEnd - (genomicBegin - coordinateMap.GenomicStart);
        }
コード例 #2
0
        /// <summary>
        /// sets both the exon and intron number strings according to which were affected by the variant [BaseTranscriptVariation.pm:474 _exon_intron_number]
        /// </summary>
        public static void ExonIntronNumber(CdnaCoordinateMap[] cdnaMaps, SimpleInterval[] introns, bool onReverseStrand,
                                            TranscriptAnnotation ta, out string exonNumber, out string intronNumber)
        {
            int exonCount = 0;

            var altAllele       = ta.AlternateAllele;
            var variantInterval = new AnnotationInterval(altAllele.Start, altAllele.End);

            var overlappedExons   = new List <int>();
            var overlappedIntrons = new List <int>();

            var prevExon = CdnaCoordinateMap.Null();

            foreach (var exon in cdnaMaps)
            {
                exonCount++;

                if (variantInterval.Overlaps(exon.GenomicStart, exon.GenomicEnd))
                {
                    overlappedExons.Add(exonCount);
                }

                if (!prevExon.IsNull)
                {
                    int intronStart = prevExon.GenomicEnd + 1;
                    int intronEnd   = exon.GenomicStart - 1;

                    if (variantInterval.Overlaps(intronStart, intronEnd))
                    {
                        overlappedIntrons.Add(exonCount - 1);
                    }
                }

                prevExon = exon;
            }

            exonNumber   = GetExonIntronNumber(overlappedExons, cdnaMaps.Length, onReverseStrand);
            intronNumber = introns != null?GetExonIntronNumber(overlappedIntrons, introns.Length, onReverseStrand) : null;

            if (overlappedExons.Count > 0)
            {
                ta.HasExonOverlap = true;
            }
        }