/// <summary> /// Converts the scaffold path into its sequence. /// </summary> /// <param name="graph">De Bruijn graph.</param> /// <param name="kmerLength">Kmer Length.</param> /// <returns>Scaffold Sequence.</returns> public ISequence BuildSequenceFromPath(ContigGraph graph, int kmerLength) { if (graph == null) { throw new ArgumentNullException("graph"); } Node startNode = this[0].Key; bool isForwardDirection = this[0].Value.IsSameOrientation; startNode.MarkNode(); List <byte> scaffoldSequence = new List <byte>(); scaffoldSequence.InsertRange(0, graph.GetNodeSequence(startNode)); this.RemoveAt(0); // There is overlap of (k-1) symbols between adjacent contigs if (kmerLength > 1) { kmerLength--; } bool sameOrientation = true; ISequence nextNodeSequence = null; foreach (KeyValuePair <Node, Edge> extensions in this) { sameOrientation = !(sameOrientation ^ extensions.Value.IsSameOrientation); nextNodeSequence = sameOrientation ? graph.GetNodeSequence(extensions.Key) : graph.GetNodeSequence(extensions.Key).GetReverseComplementedSequence(); // Extend scaffold sequence using symbols from contig beyond the overlap if (isForwardDirection) { scaffoldSequence.InsertRange( scaffoldSequence.Count, nextNodeSequence.GetSubSequence(kmerLength, nextNodeSequence.Count - kmerLength)); } else { scaffoldSequence.InsertRange(0, nextNodeSequence.GetSubSequence(0, nextNodeSequence.Count - kmerLength)); } extensions.Key.MarkNode(); } if (nextNodeSequence == null) { return(null); } return(new Sequence(nextNodeSequence.Alphabet, scaffoldSequence.ToArray(), false)); }
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()); }
public void TracePathTestWithPalindromicContig() { const int KmerLengthConst = 6; const int DangleThreshold = 3; const int RedundantThreshold = 7; List <ISequence> sequences = new List <ISequence>(); Sequence seq = new Sequence(Alphabets.DNA, "ATGCCTC".Select(a => (byte)a).ToArray()); seq.ID = ">10.x1:abc"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "CCTCCTAT".Select(a => (byte)a).ToArray()); seq.ID = "1"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TCCTATC".Select(a => (byte)a).ToArray()); seq.ID = "2"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TGCCTCCT".Select(a => (byte)a).ToArray()); seq.ID = "3"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "ATCTTAGC".Select(a => (byte)a).ToArray()); seq.ID = "4"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "CTATCTTAG".Select(a => (byte)a).ToArray()); seq.ID = "5"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "CTTAGCG".Select(a => (byte)a).ToArray()); seq.ID = "6"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "GCCTCCTAT".Select(a => (byte)a).ToArray()); seq.ID = ">8.x1:abc"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TAGCGCGCTA".Select(a => (byte)a).ToArray()); seq.ID = ">8.y1:abc"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "AGCGCGC".Select(a => (byte)a).ToArray()); seq.ID = ">9.x1:abc"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTTTT".Select(a => (byte)a).ToArray()); seq.ID = "7"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTTTAAA".Select(a => (byte)a).ToArray()); seq.ID = "8"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TAAAAA".Select(a => (byte)a).ToArray()); seq.ID = "9"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTTAG".Select(a => (byte)a).ToArray()); seq.ID = "10"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "TTTAGC".Select(a => (byte)a).ToArray()); seq.ID = "11"; sequences.Add(seq); seq = new Sequence(Alphabets.DNA, "GCGCGCCGCGCG".Select(a => (byte)a).ToArray()); seq.ID = "12"; sequences.Add(seq); 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", (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(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.IsTrue(new string(graph.GetNodeSequence(scaffold[0].Key).Select(a => (char)a).ToArray()).Equals("ATGCCTCCTATCTTAGC")); Assert.IsTrue(new string(graph.GetNodeSequence(scaffold[1].Key).Select(a => (char)a).ToArray()).Equals("TTAGCGCG")); Assert.IsTrue(new string(graph.GetNodeSequence(scaffold[2].Key).Select(a => (char)a).ToArray()).Equals("GCGCGC")); }