/// <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);
}
/// <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));
}
/// <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>
/// Generate sequences from list of contig nodes.
/// </summary>
/// <param name="contigGraph">Contig Overlap Graph.</param>
/// <param name="paths">Scaffold paths.</param>
/// <returns>List of sequences of scaffolds.</returns>
protected IList <ISequence> GenerateScaffold(
ContigGraph contigGraph,
IList <ScaffoldPath> paths)
{
if (contigGraph == null)
{
throw new ArgumentNullException("contigGraph");
}
if (paths == null)
{
throw new ArgumentNullException("paths");
}
List <ISequence> scaffolds = paths.AsParallel().Select(t => t.BuildSequenceFromPath(contigGraph, this.kmerLength)).ToList();
IEnumerable <Node> visitedNodes = contigGraph.Nodes.AsParallel().Where(t => !t.IsMarked());
scaffolds.AddRange(visitedNodes.AsParallel().Select(t => contigGraph.GetNodeSequence(t)));
contigGraph.Dispose();
return(scaffolds);
}
/// <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>
/// Builds scaffolds from list of reads and contigs.
/// </summary>
/// <param name="reads">List of reads.</param>
/// <param name="contigs">List of contigs.</param>
/// <param name="lengthofKmer">Kmer Length.</param>
/// <param name="depth">Depth for graph traversal.</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>
/// <returns>List of scaffold sequences.</returns>
public IList <ISequence> BuildScaffold(
IEnumerable <ISequence> reads,
IList <ISequence> contigs,
int lengthofKmer,
int depth = 10,
int redundancy = 2)
{
if (contigs == null)
{
throw new ArgumentNullException("contigs");
}
if (null == reads)
{
throw new ArgumentNullException("reads");
}
if (lengthofKmer <= 0)
{
throw new ArgumentException(Properties.Resource.KmerLength);
}
if (depth <= 0)
{
throw new ArgumentException(Resource.Depth);
}
if (redundancy < 0)
{
throw new ArgumentException(Resource.NegativeRedundancy);
}
this.depthField = depth;
this.redundancyField = redundancy;
this.kmerLength = lengthofKmer;
IEnumerable <ISequence> readSeqs = ValidateReads(reads);
//Step1: Generate contig overlap graph.
IList <ISequence> contigsList = new List <ISequence>(contigs);
ContigGraph contigGraph = GenerateContigOverlapGraph(contigsList);
IEnumerable <Node> nodes = contigGraph.Nodes.Where(t => t.ExtensionsCount == 0);
foreach (Node node in nodes)
{
contigsList.Remove(contigGraph.GetNodeSequence(node));
}
// Step2: Map Reads to contigs.
ReadContigMap readContigMaps = ReadContigMap(contigsList, readSeqs);
contigsList = null;
// Step3: Generate Contig Mate Pair Map.
ContigMatePairs contigMatePairs = MapPairedReadsToContigs(readContigMaps, readSeqs);
readContigMaps = null;
// Step4: Filter Paired Reads.
contigMatePairs = FilterReadsBasedOnOrientation(contigMatePairs);
// Step5: Distance Calculation.
CalculateDistanceBetweenContigs(contigMatePairs);
// Step6: Trace Scaffold Paths.
IList <ScaffoldPath> paths = TracePath(contigGraph, contigMatePairs);
contigMatePairs = null;
// Step7: Assemble paths.
PathPurger(paths);
// Step8: Generate sequence of scaffolds.
return(GenerateScaffold(contigGraph, paths));
}
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 = 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"));
}
