/// <summary> /// Generate contig overlap graph. /// </summary> /// <param name="contigs">List of contig sequences.</param> /// <returns>Contig Graph.</returns> protected ContigGraph GenerateContigOverlapGraph(IList <ISequence> contigs) { if (contigs == null) { throw new ArgumentNullException("contigs"); } ContigGraph contigGraph = new ContigGraph(); contigGraph.BuildContigGraph(contigs, this.kmerLength); return(contigGraph); }
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 PathPurger1() { const int KmerLength = 7; ISequence sequence = new Sequence(Alphabets.DNA, "GATTCAAGGGCTGGGGG"); IList <ISequence> contigsSequence = SequenceToKmerBuilder.GetKmerSequences(sequence, KmerLength).ToList(); ContigGraph graph = new ContigGraph(); graph.BuildContigGraph(contigsSequence, KmerLength); List <Node> contigs = graph.Nodes.ToList(); IList <ScaffoldPath> paths = new List <ScaffoldPath>(); ScaffoldPath path = new ScaffoldPath(); foreach (Node node in contigs) { path.Add(new KeyValuePair <Node, Edge>(node, null)); } paths.Add(path); path = new ScaffoldPath(); foreach (Node node in contigs.GetRange(2, 5)) { path.Add(new KeyValuePair <Node, Edge>(node, null)); } paths.Add(path); path = new ScaffoldPath(); foreach (Node node in contigs.GetRange(3, 5)) { path.Add(new KeyValuePair <Node, Edge>(node, null)); } paths.Add(path); path = new ScaffoldPath(); foreach (Node node in contigs.GetRange(6, 5)) { path.Add(new KeyValuePair <Node, Edge>(node, null)); } paths.Add(path); path = new ScaffoldPath(); foreach (Node node in contigs.GetRange(0, 11)) { path.Add(new KeyValuePair <Node, Edge>(node, null)); } paths.Add(path); path = new ScaffoldPath(); foreach (Node node in contigs.GetRange(7, 4)) { path.Add(new KeyValuePair <Node, Edge>(node, null)); } paths.Add(path); path = new ScaffoldPath(); foreach (Node node in contigs.GetRange(11, 0)) { path.Add(new KeyValuePair <Node, Edge>(node, null)); } paths.Add(path); path = new ScaffoldPath(); foreach (Node node in contigs.GetRange(2, 9)) { path.Add(new KeyValuePair <Node, Edge>(node, null)); } paths.Add(path); path = new ScaffoldPath(); foreach (Node node in contigs.GetRange(1, 10)) { path.Add(new KeyValuePair <Node, Edge>(node, null)); } paths.Add(path); PathPurger assembler = new PathPurger(); assembler.PurgePath(paths); Assert.AreEqual(paths.Count, 1); Assert.IsTrue(Compare(paths.First(), contigs)); }
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")); }