public void DistanceCalculationwithTwoContigs() { const int KmerLength = 6; IList <ISequence> sequences = new List <ISequence>() { new Sequence(Alphabets.DNA, "GATCTGATAA") { ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor substrate 1 (IRS1) on chromosome 2.X1:0.5K" }, new Sequence(Alphabets.DNA, "ATCTGATAAG") { ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor on chromosome 2.F:0.5K" }, new Sequence(Alphabets.DNA, "TCTGATAAGG") { ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor on chromosome 2.2:0.5K" }, new Sequence(Alphabets.DNA, "TTTTTGATGG") { ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor substrate 1 (IRS1) on chromosome 2.Y1:0.5K" }, new Sequence(Alphabets.DNA, "TTTTGATGGC") { ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor on chromosome 2.R:0.5K" }, new Sequence(Alphabets.DNA, "TTTGATGGCA") { ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor on chromosome 2.1:0.5K" } }; IList <ISequence> contigs = new List <ISequence> { new Sequence(Alphabets.DNA, "GATCTGATAAGG"), new Sequence(Alphabets.DNA, "TTTTTGATGGCA") }; ReadContigMapper mapper = new ReadContigMapper(); ReadContigMap maps = mapper.Map(contigs, sequences, KmerLength); MatePairMapper mapPairedReads = new MatePairMapper(); ContigMatePairs pairs = mapPairedReads.MapContigToMatePairs(sequences, maps); OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter(); ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairs); DistanceCalculator calc = new DistanceCalculator(contigpairedReads); contigpairedReads = calc.CalculateDistance(); Assert.AreEqual(contigpairedReads.Values.Count, 1); Assert.IsTrue(contigpairedReads.ContainsKey(contigs[0])); Dictionary <ISequence, IList <ValidMatePair> > map = contigpairedReads[contigs[0]]; Assert.IsTrue(map.ContainsKey(contigs[1])); IList <ValidMatePair> valid = map[contigs[1]]; Assert.AreEqual(valid.First().DistanceBetweenContigs[0], (float)478.000031); Assert.AreEqual(valid.First().DistanceBetweenContigs[1], (float)477.0); Assert.AreEqual(valid.First().StandardDeviation[0], (float)14.1421356); Assert.AreEqual(valid.First().StandardDeviation[1], (float)14.1421356); Assert.AreEqual(valid.First().Weight, 2); }
public void DistanceCalculationwithTwoContigsWeightedMean() { const int KmerLength = 6; List <ISequence> sequences = new List <ISequence>(); Sequence seq = new Sequence(Alphabets.DNA, "GATCTGATAA".Select(a => (byte)a).ToArray()); seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor" + "substrate 1 (IRS1) on chromosome 2.x1:2K"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "ATCTGATAAG".Select(a => (byte)a).ToArray()); seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor" + "on chromosome 2.f:0.5K"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TCTGATAAGG".Select(a => (byte)a).ToArray()); seq.ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor" + "on chromosome 2.2:0.5K"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTTTGATGG".Select(a => (byte)a).ToArray()); seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor" + "substrate 1 (IRS1) on chromosome 2.y1:2K"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTTGATGGC".Select(a => (byte)a).ToArray()); seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor" + "on chromosome 2.r:0.5K"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTGATGGCA".Select(a => (byte)a).ToArray()); seq.ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor" + "on chromosome 2.1:0.5K"; sequences.Add(seq); IList <ISequence> contigs = new List <ISequence> { new Sequence(Alphabets.DNA, "GATCTGATAAGG".Select(a => (byte)a).ToArray()), new Sequence(Alphabets.DNA, "TTTTTGATGGCA".Select(a => (byte)a).ToArray()) }; ReadContigMapper mapper = new ReadContigMapper(); ReadContigMap maps = mapper.Map(contigs, sequences, KmerLength); MatePairMapper mapPairedReads = new MatePairMapper(); ContigMatePairs pairedReads = mapPairedReads.MapContigToMatePairs(sequences, maps); OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter(); ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairedReads); DistanceCalculator calc = new DistanceCalculator(contigpairedReads); contigpairedReads = calc.CalculateDistance(); Assert.AreEqual(contigpairedReads.Values.Count, 1); Assert.IsTrue(contigpairedReads.ContainsKey(contigs[0])); Dictionary <ISequence, IList <ValidMatePair> > map = contigpairedReads[contigs[0]]; Assert.IsTrue(map.ContainsKey(contigs[1])); IList <ValidMatePair> valid = map[contigs[1]]; Assert.AreEqual(valid.First().DistanceBetweenContigs[0], (float)1228.0); Assert.AreEqual(valid.First().DistanceBetweenContigs[1], (float)1227.0); Assert.AreEqual(valid.First().StandardDeviation[0], (float)60); Assert.AreEqual(valid.First().StandardDeviation[1], (float)60); Assert.AreEqual(valid.First().Weight, 2); }
/// <summary> /// Distance calculator. /// </summary> /// <param name="contigPairedReads">Contig pair reads.</param> public DistanceCalculator(ContigMatePairs contigPairedReads) { if (contigPairedReads == null) { throw new ArgumentNullException("contigPairedReads"); } this.contigPairedReads = contigPairedReads; }
public void FilterMatePairWithTwoContigs() { const int kmerLength = 6; IList <ISequence> sequences = new List <ISequence>(); Sequence seq = new Sequence(Alphabets.DNA, "GATCTGATAA"); seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor substrate 1 (IRS1) on chromosome 2.X1:0.5K"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "ATCTGATAAG"); seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor on chromosome 2.F:0.5K"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TCTGATAAGG"); seq.ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor on chromosome 2.2:0.5K"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTTTGATGG"); seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor substrate 1 (IRS1) on chromosome 2.Y1:0.5K"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTTGATGGC"); seq.ID = ">gi|263191773|ref|NG_015830.1| H**o sapiens insulin receptor on chromosome 2.R:0.5K"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTGATGGCA"); seq.ID = ">gi|263191773|ref | H**o sapiens ........insulin receptor on chromosome 2.1:0.5K"; sequences.Add(seq); IList <ISequence> contigs = new List <ISequence> { new Sequence(Alphabets.DNA, "GATCTGATAAGG"), new Sequence(Alphabets.DNA, "TTTTTGATGGCA") }; ReadContigMapper mapper = new ReadContigMapper(); ReadContigMap maps = mapper.Map(contigs, sequences, kmerLength); MatePairMapper mapPairedReads = new MatePairMapper(); ContigMatePairs pairs = mapPairedReads.MapContigToMatePairs(sequences, maps); OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter(); ContigMatePairs contigpairedReads = filter.FilterPairedReads(pairs); Assert.AreEqual(contigpairedReads.Values.Count, 1); Assert.IsTrue(contigpairedReads.ContainsKey(contigs[0])); Dictionary <ISequence, IList <ValidMatePair> > map = contigpairedReads[contigs[0]]; Assert.IsTrue(map.ContainsKey(contigs[1])); List <ValidMatePair> valid = Sort(map[contigs[1]], sequences); Assert.AreEqual(valid[0].ForwardReadStartPosition[0], 1); Assert.AreEqual(valid[0].ReverseReadReverseComplementStartPosition[0], 10); Assert.AreEqual(valid[0].ReverseReadStartPosition[0], 10); Assert.AreEqual(valid[1].ForwardReadStartPosition[0], 0); Assert.AreEqual(valid[1].ReverseReadReverseComplementStartPosition[0], 11); Assert.AreEqual(valid[1].ReverseReadStartPosition[0], 9); }
public void ContigPairReadMap() { const int kmerLength = 6; IList <ISequence> readSeqs = new List <ISequence>(); Sequence read = new Sequence(Alphabets.DNA, "GATCTGATAA"); read.DisplayID = "0.x1:abc"; readSeqs.Add(read); read = new Sequence(Alphabets.DNA, "ATCTGATAAG"); read.DisplayID = "1.F:abc"; readSeqs.Add(read); read = new Sequence(Alphabets.DNA, "TCTGATAAGG"); read.DisplayID = "2.2:abc"; readSeqs.Add(read); read = new Sequence(Alphabets.DNA, "TTTTTGATGG"); read.DisplayID = "0.y1:abc"; readSeqs.Add(read); read = new Sequence(Alphabets.DNA, "TTTTGATGGC"); read.DisplayID = "1.R:abc"; readSeqs.Add(read); read = new Sequence(Alphabets.DNA, "TTTGATGGCA"); read.DisplayID = "2.1:abc"; readSeqs.Add(read); IList <ISequence> contigs = new List <ISequence> { new Sequence(Alphabets.DNA, "GATCTGATAAGG"), new Sequence(Alphabets.DNA, "TTTTTGATGGCA") }; ReadContigMapper mapper = new ReadContigMapper(); ReadContigMap maps = mapper.Map(contigs, readSeqs, kmerLength); MatePairMapper pair = new MatePairMapper(); ContigMatePairs map = pair.MapContigToMatePairs(readSeqs, maps); Assert.AreEqual(map.Count, 2); Dictionary <ISequence, IList <ValidMatePair> > reverseContigs; Assert.IsTrue(map.TryGetValue(contigs[0], out reverseContigs)); Assert.AreEqual(reverseContigs.Count, 1); IList <ValidMatePair> matePairs; Assert.IsTrue(reverseContigs.TryGetValue(contigs[1], out matePairs)); Assert.AreEqual(matePairs.Count, 2); Assert.AreEqual(matePairs[0].ForwardReadStartPosition.First(), 0); Assert.AreEqual(matePairs[0].ReverseReadStartPosition.First(), 9); Assert.AreEqual(matePairs[1].ForwardReadStartPosition.First(), 1); Assert.AreEqual(matePairs[1].ReverseReadStartPosition.First(), 10); Assert.IsTrue(map.TryGetValue(contigs[1], out reverseContigs)); Assert.AreEqual(reverseContigs.Count, 1); Assert.IsTrue(reverseContigs.TryGetValue(contigs[0], out matePairs)); Assert.AreEqual(matePairs.Count, 1); Assert.AreEqual(matePairs[0].ForwardReadStartPosition.First(), 2); Assert.AreEqual(matePairs[0].ReverseReadStartPosition.First(), 11); }
/// <summary> /// Performs Breadth First Search to traverse through graph to generate scaffold paths. /// </summary> /// <param name="overlapGraph">Contig Overlap Graph.</param> /// <param name="contigPairedReadMaps">InterContig Distances.</param> /// <param name="lengthOfKmer">Length of Kmer.</param> /// <param name="searchDepth">Depth to which graph is searched.</param> /// <returns>List of paths/scaffold.</returns> public IList<ScaffoldPath> FindPaths( ContigGraph overlapGraph, ContigMatePairs contigPairedReadMaps, int lengthOfKmer, int searchDepth = 10) { if (overlapGraph == null) { throw new ArgumentNullException("deBruijnGraph"); } if (contigPairedReadMaps == null) { throw new ArgumentNullException("contigPairedReadMaps"); } if (lengthOfKmer <= 0) { throw new ArgumentException(Resource.KmerLength); } if (searchDepth <= 0) { throw new ArgumentException(Resource.Depth); } this.graph = overlapGraph; this.kmerLength = lengthOfKmer; this.depth = searchDepth; List<ScaffoldPath> scaffoldPaths = new List<ScaffoldPath>(); Parallel.ForEach( overlapGraph.Nodes, (Node node) => { Dictionary<ISequence, IList<ValidMatePair>> contigPairedReadMap; if (contigPairedReadMaps.TryGetValue(overlapGraph.GetNodeSequence(node), out contigPairedReadMap)) { List<ScaffoldPath> scaffoldPath = TraverseGraph(node, contigPairedReadMap); lock (scaffoldPaths) { scaffoldPaths.AddRange(scaffoldPath); } } }); return scaffoldPaths; }
/// <summary> /// Finds contig pairs having valid mate pairs connection between them. /// </summary> /// <param name="reads">Input list of reads.</param> /// <param name="alignment">Reads contig alignment.</param> /// <returns>Contig Mate pair map.</returns> public ContigMatePairs MapContigToMatePairs(IList <ISequence> reads, ReadContigMap alignment) { if (alignment == null) { throw new ArgumentNullException("alignment"); } if (reads == null) { throw new ArgumentNullException("reads"); } Dictionary <ISequence, IList <ReadMap> > contigs1; Dictionary <ISequence, IList <ReadMap> > contigs2; ContigMatePairs contigMatePairs = new ContigMatePairs(); foreach (ISequence read in reads) { Match match = _readExpression.Match(read.DisplayID); if (match.Success) { String mateDisplayID = GenerateExpression(match); if (alignment.TryGetValue(read.DisplayID, out contigs1) && alignment.TryGetValue(mateDisplayID, out contigs2)) { MatePair pair; if (match.Groups[2].Value == "X1" || match.Groups[2].Value == "F" || match.Groups[2].Value == "1" || match.Groups[2].Value == "x1" || match.Groups[2].Value == "f" || match.Groups[2].Value == "a" || match.Groups[2].Value == "A") { pair = new MatePair(read.DisplayID, mateDisplayID, match.Groups[3].Value); ContigMatePairMapper(contigs1, contigs2, pair, contigMatePairs); } else { pair = new MatePair(mateDisplayID, read.DisplayID, match.Groups[3].Value); ContigMatePairMapper(contigs2, contigs1, pair, contigMatePairs); } alignment.Remove(read.DisplayID); alignment.Remove(mateDisplayID); } } } return(contigMatePairs); }
/// <summary> /// Creates Paired Read Contig Map. /// </summary> /// <param name="forwardContigs">Contigs aligning to forward read.</param> /// <param name="reverseContigs">Contigs aligning to reverse read.</param> /// <param name="pair">Mate Pair.</param> /// <param name="contigMatePairs">Contig mate pair.</param> private static void ContigMatePairMapper( Dictionary <ISequence, IList <ReadMap> > forwardContigs, Dictionary <ISequence, IList <ReadMap> > reverseContigs, MatePair pair, ContigMatePairs contigMatePairs) { foreach (KeyValuePair <ISequence, IList <ReadMap> > forwardContigMaps in forwardContigs) { Dictionary <ISequence, IList <ValidMatePair> > forwardContig; if (!contigMatePairs.TryGetValue(forwardContigMaps.Key, out forwardContig)) { forwardContig = new Dictionary <ISequence, IList <ValidMatePair> >(); contigMatePairs.Add(forwardContigMaps.Key, forwardContig); } foreach (KeyValuePair <ISequence, IList <ReadMap> > reverseContigMaps in reverseContigs) { IList <ValidMatePair> matePairs; if (!forwardContig.TryGetValue(reverseContigMaps.Key, out matePairs)) { matePairs = new List <ValidMatePair>(); forwardContig.Add(reverseContigMaps.Key, matePairs); } foreach (ReadMap forwardMap in forwardContigMaps.Value) { foreach (ReadMap reverseMap in reverseContigMaps.Value) { ValidMatePair validPairedRead = new ValidMatePair(); validPairedRead.PairedRead = pair; validPairedRead.ForwardReadStartPosition.Add(forwardMap.StartPositionOfContig); validPairedRead.ReverseReadStartPosition.Add( reverseMap.StartPositionOfContig + reverseMap.Length - 1); validPairedRead.ReverseReadReverseComplementStartPosition.Add( reverseContigMaps.Key.Count - reverseMap.StartPositionOfContig - 1); matePairs.Add(validPairedRead); } } } } }
/// <summary> /// Performs Breadth First Search in contig overlap graph. /// </summary> /// <param name="contigGraph">Contig Graph.</param> /// <param name="contigMatePairs">Contig Mate Pair map.</param> /// <returns>List of Scaffold Paths.</returns> protected IList<ScaffoldPath> TracePath(ContigGraph contigGraph, ContigMatePairs contigMatePairs) { return this.tracePath.FindPaths(contigGraph, contigMatePairs, this.kmerLength, this.depthField); }
/// <summary> /// Calculate distance between contigs using paired reads. /// </summary> /// <param name="contigMatePairs">Contig Mate Pair map.</param> /// <returns>Number of contig-read pairs.</returns> protected int CalculateDistanceBetweenContigs(ContigMatePairs contigMatePairs) { if (contigMatePairs == null) { throw new ArgumentNullException("contigMatePairs"); } if (this.distanceCalculator == null) { this.distanceCalculator = new DistanceCalculator(contigMatePairs); contigMatePairs = this.distanceCalculator.CalculateDistance(); } else { contigMatePairs = this.distanceCalculator.CalculateDistance(); } // this dictionary is updated in this step. return contigMatePairs.Count; }
/// <summary> /// Filter reads based on orientation of contigs. /// </summary> /// <param name="contigMatePairs">Contig Mate Pair map.</param> /// <returns>Returns Contig Mate Pair map.</returns> protected ContigMatePairs FilterReadsBasedOnOrientation(ContigMatePairs contigMatePairs) { return this.pairedReadFilter.FilterPairedReads(contigMatePairs, this.redundancyField); }
public void TracePathTestWithPalindromicContig() { const int kmerLength = 6; const int dangleThreshold = 3; const int redundantThreshold = 7; List <ISequence> sequences = new List <ISequence>(); Sequence seq = new Sequence(Alphabets.DNA, "ATGCCTC"); seq.DisplayID = ">10.x1:abc"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "CCTCCTAT"); seq.DisplayID = "1"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TCCTATC"); seq.DisplayID = "2"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TGCCTCCT"); seq.DisplayID = "3"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "ATCTTAGC"); seq.DisplayID = "4"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "CTATCTTAG"); seq.DisplayID = "5"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "CTTAGCG"); seq.DisplayID = "6"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "GCCTCCTAT"); seq.DisplayID = ">8.x1:abc"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TAGCGCGCTA"); seq.DisplayID = ">8.y1:abc"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "AGCGCGC"); seq.DisplayID = ">9.x1:abc"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTTTT"); seq.DisplayID = "7"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTTTAAA"); seq.DisplayID = "8"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TAAAAA"); seq.DisplayID = "9"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTTAG"); seq.DisplayID = "10"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTAGC"); seq.DisplayID = "11"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "GCGCGCCGCGCG"); seq.DisplayID = "12"; sequences.Add(seq); KmerLength = kmerLength; SequenceReads.Clear(); AddSequenceReads(sequences); CreateGraph(); DanglingLinksThreshold = dangleThreshold; DanglingLinksPurger = new DanglingLinksPurger(dangleThreshold); RedundantPathLengthThreshold = redundantThreshold; RedundantPathsPurger = new RedundantPathsPurger(redundantThreshold); UnDangleGraph(); RemoveRedundancy(); IList <ISequence> contigs = BuildContigs(); ReadContigMapper mapper = new ReadContigMapper(); ReadContigMap maps = mapper.Map(contigs, sequences, kmerLength); MatePairMapper builder = new MatePairMapper(); CloneLibrary.Instance.AddLibrary("abc", (float)5, (float)15); ContigMatePairs pairedReads = builder.MapContigToMatePairs(sequences, maps); ContigMatePairs overlap; OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter(); overlap = filter.FilterPairedReads(pairedReads, 0); DistanceCalculator dist = new DistanceCalculator(); dist.CalculateDistance(overlap); Graph.BuildContigGraph(contigs, this.KmerLength); TracePath path = new TracePath(); IList <ScaffoldPath> paths = path.FindPaths(Graph, overlap, kmerLength, 3); Assert.AreEqual(paths.Count, 3); Assert.AreEqual(paths.First().Count, 3); ScaffoldPath scaffold = paths.First(); DeBruijnGraph graph = Graph; Assert.IsTrue(graph.GetNodeSequence(scaffold[0].Key).ToString().Equals("ATGCCTCCTATCTTAGC")); Assert.IsTrue(graph.GetNodeSequence(scaffold[1].Key).ToString().Equals("TTAGCGCG")); Assert.IsTrue(graph.GetNodeSequence(scaffold[2].Key).ToString().Equals("GCGCGC")); }
/// <summary> /// Creates Paired Read Contig Map. /// </summary> /// <param name="forwardContigs">Contigs aligning to forward read.</param> /// <param name="reverseContigs">Contigs aligning to reverse read.</param> /// <param name="pair">Mate Pair.</param> /// <param name="contigMatePairs">Contig mate pair.</param> private static void ContigMatePairMapper( Dictionary<ISequence, IList<ReadMap>> forwardContigs, Dictionary<ISequence, IList<ReadMap>> reverseContigs, MatePair pair, ContigMatePairs contigMatePairs) { foreach (KeyValuePair<ISequence, IList<ReadMap>> forwardContigMaps in forwardContigs) { Dictionary<ISequence, IList<ValidMatePair>> forwardContig; if (!contigMatePairs.TryGetValue(forwardContigMaps.Key, out forwardContig)) { forwardContig = new Dictionary<ISequence, IList<ValidMatePair>>(); contigMatePairs.Add(forwardContigMaps.Key, forwardContig); } foreach (KeyValuePair<ISequence, IList<ReadMap>> reverseContigMaps in reverseContigs) { IList<ValidMatePair> matePairs; if (!forwardContig.TryGetValue(reverseContigMaps.Key, out matePairs)) { matePairs = new List<ValidMatePair>(); forwardContig.Add(reverseContigMaps.Key, matePairs); } foreach (ReadMap forwardMap in forwardContigMaps.Value) { foreach (ReadMap reverseMap in reverseContigMaps.Value) { ValidMatePair validPairedRead = new ValidMatePair(); validPairedRead.PairedRead = pair; validPairedRead.ForwardReadStartPosition.Add(forwardMap.StartPositionOfContig); validPairedRead.ReverseReadStartPosition.Add( reverseMap.StartPositionOfContig + reverseMap.Length - 1); validPairedRead.ReverseReadReverseComplementStartPosition.Add( reverseContigMaps.Key.Count - reverseMap.StartPositionOfContig - 1); matePairs.Add(validPairedRead); } } } } }
/// <summary> /// Finds contig pairs having valid mate pairs connection between them. /// </summary> /// <param name="reads">Input list of reads.</param> /// <param name="alignment">Reads contig alignment.</param> /// <returns>Contig Mate pair map.</returns> public ContigMatePairs MapContigToMatePairs(IEnumerable<ISequence> reads, ReadContigMap alignment) { if (alignment == null) { throw new ArgumentNullException("alignment"); } if (reads == null) { throw new ArgumentNullException("reads"); } Dictionary<ISequence, IList<ReadMap>> contigs1; Dictionary<ISequence, IList<ReadMap>> contigs2; ContigMatePairs contigMatePairs = new ContigMatePairs(); foreach (ISequence read in reads) { Match match = this.readExpression.Match(read.ID); if (match.Success) { string mateDisplayID = GenerateExpression(match); if (alignment.TryGetValue(read.ID, out contigs1) && alignment.TryGetValue(mateDisplayID, out contigs2)) { MatePair pair; if (match.Groups[2].Value == "X1" || match.Groups[2].Value == "F" || match.Groups[2].Value == "1" || match.Groups[2].Value == "x1" || match.Groups[2].Value == "f" || match.Groups[2].Value == "a" || match.Groups[2].Value == "A") { pair = new MatePair(read.ID, mateDisplayID, match.Groups[3].Value); ContigMatePairMapper(contigs1, contigs2, pair, contigMatePairs); } else { pair = new MatePair(mateDisplayID, read.ID, match.Groups[3].Value); ContigMatePairMapper(contigs2, contigs1, pair, contigMatePairs); } alignment.Remove(read.ID); alignment.Remove(mateDisplayID); } } } return contigMatePairs; }
public void TracePathTestWithPalindromicContig() { const int kmerLengthConst = 5; const int dangleThreshold = 3; const int redundantThreshold = 6; var sequences = new List <ISequence>() { new Sequence(Alphabets.DNA, "ATGCCTC") { ID = "0" }, new Sequence(Alphabets.DNA, "CCTCCTAT") { ID = "1" }, new Sequence(Alphabets.DNA, "TCCTATC") { ID = "2" }, new Sequence(Alphabets.DNA, "TGCCTCCT") { ID = "3" }, new Sequence(Alphabets.DNA, "ATCTTAGC") { ID = "4" }, new Sequence(Alphabets.DNA, "CTATCTTAG") { ID = "5" }, new Sequence(Alphabets.DNA, "CTTAGCG") { ID = "6" }, new Sequence(Alphabets.DNA, "GCCTCCTAT") { ID = "7" }, new Sequence(Alphabets.DNA, "TAGCGCGCTA") { ID = "8" }, new Sequence(Alphabets.DNA, "AGCGCGC") { ID = "9" }, new Sequence(Alphabets.DNA, "TTTTTT") { ID = "10" }, new Sequence(Alphabets.DNA, "TTTTTAAA") { ID = "11" }, new Sequence(Alphabets.DNA, "TAAAAA") { ID = "12" }, new Sequence(Alphabets.DNA, "TTTTAG") { ID = "13" }, new Sequence(Alphabets.DNA, "TTTAGC") { ID = "14" }, new Sequence(Alphabets.DNA, "GCGCGCCGCGCG") { ID = "15" }, }; KmerLength = kmerLengthConst; SequenceReads.Clear(); SetSequenceReads(sequences); CreateGraph(); DanglingLinksThreshold = dangleThreshold; DanglingLinksPurger = new DanglingLinksPurger(dangleThreshold); RedundantPathLengthThreshold = redundantThreshold; RedundantPathsPurger = new RedundantPathsPurger(redundantThreshold); UnDangleGraph(); RemoveRedundancy(); IList <ISequence> contigs = BuildContigs().ToList(); ReadContigMapper mapper = new ReadContigMapper(); ReadContigMap maps = mapper.Map(contigs, sequences, kmerLengthConst); MatePairMapper builder = new MatePairMapper(); CloneLibrary.Instance.AddLibrary("abc", 5, 15); ContigMatePairs pairedReads = builder.MapContigToMatePairs(sequences, maps); OrientationBasedMatePairFilter filter = new OrientationBasedMatePairFilter(); ContigMatePairs overlap = filter.FilterPairedReads(pairedReads, 0); DistanceCalculator dist = new DistanceCalculator(overlap); overlap = dist.CalculateDistance(); ContigGraph graph = new ContigGraph(); graph.BuildContigGraph(contigs, this.KmerLength); TracePath path = new TracePath(); IList <ScaffoldPath> paths = path.FindPaths(graph, overlap, kmerLengthConst, 3); Assert.AreEqual(paths.Count, 3); Assert.AreEqual(paths.First().Count, 3); ScaffoldPath scaffold = paths.First(); Assert.AreEqual("ATGCCTCCTATCTTAGC", graph.GetNodeSequence(scaffold[0].Key).ConvertToString()); Assert.AreEqual("TTAGCGCG", graph.GetNodeSequence(scaffold[1].Key).ConvertToString()); Assert.AreEqual("GCGCGC", graph.GetNodeSequence(scaffold[2].Key).ConvertToString()); }
/// <summary> /// Filter Paired Read Based on Orientation. /// </summary> /// <param name="matePairMap">Map between contigs using mate pair information.</param> /// <param name="redundancy">Number of mate pairs required to create a link between two contigs. /// Hierarchical Scaffolding With Bambus /// by: Mihai Pop, Daniel S. Kosack, Steven L. Salzberg /// Genome Research, Vol. 14, No. 1. (January 2004), pp. 149-159.</param> public ContigMatePairs FilterPairedReads(ContigMatePairs matePairMap, int redundancy = 2) { if (null == matePairMap) { throw new ArgumentNullException("matePairMap"); } if (redundancy < 0) { throw new ArgumentException(Properties.Resource.NegativeRedundancy); } foreach (KeyValuePair<ISequence, Dictionary<ISequence, IList<ValidMatePair>>> matePair in matePairMap) { foreach (KeyValuePair<ISequence, IList<ValidMatePair>> validMatePair in matePair.Value) { if (matePair.Key != validMatePair.Key) { Dictionary<ISequence, IList<ValidMatePair>> validMatePairs; if (matePairMap.TryGetValue(validMatePair.Key, out validMatePairs)) { IList<ValidMatePair> pair; if (validMatePairs.TryGetValue(matePair.Key, out pair)) { OrientationFilter(pair, validMatePair.Value, redundancy); } else { if (validMatePair.Value.Count < redundancy) { validMatePair.Value.Clear(); } } } else { if (validMatePair.Value.Count < redundancy) { validMatePair.Value.Clear(); } } } else { validMatePair.Value.Clear(); } } } ContigMatePairs newMatePairMap = new ContigMatePairs(); Parallel.ForEach(matePairMap, matePair => { var map = matePair.Value .Where(validMatePair => validMatePair.Value.Count > 0) .ToDictionary(validMatePair => validMatePair.Key, validMatePair => validMatePair.Value); if (map.Count > 0) { lock (newMatePairMap) { newMatePairMap.Add(matePair.Key, map); } } }); return newMatePairMap; }