private bool Compare(ScaffoldPath path, IList <DeBruijnNode> contig)
{
if (path.Count == contig.Count)
{
for (int index = 0; index < contig.Count; index++)
{
if (path[index].Key != contig[index])
{
return(false);
}
}
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// Remove containing paths.
/// </summary>
/// <param name="scaffoldPath">Current path.</param>
/// <param name="path">Path to be compared with.</param>
/// <returns>Containing paths or not.</returns>
private static bool RemoveContainingPaths(
ScaffoldPath scaffoldPath,
ScaffoldPath path)
{
if (scaffoldPath.Count >= path.Count)
{
if (path.All(t => scaffoldPath.Where(k => k.Key == t.Key).ToList().Count > 0))
{
return true;
}
return false;
}
if (scaffoldPath.All(t => path.Where(k => k.Key == t.Key).ToList().Count > 0))
{
scaffoldPath.Clear();
scaffoldPath.AddRange(path);
return true;
}
return false;
}
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"));
}
public void PathPurger1()
{
const int kmerLength = 7;
List <ISequence> sequences = new List <ISequence>();
sequences.Add(new Sequence(Alphabets.DNA, "GATTCAAGGGCTGGGGG"));
this.KmerLength = kmerLength;
this.AddSequenceReads(sequences);
this.CreateGraph();
List <DeBruijnNode> contigs = this.Graph.Nodes.ToList();
IList <ScaffoldPath> paths =
new List <ScaffoldPath>();
ScaffoldPath path = new ScaffoldPath();
foreach (DeBruijnNode node in contigs)
{
path.Add(new KeyValuePair <DeBruijnNode, DeBruijnEdge>(node, null));
}
paths.Add(path);
path = new ScaffoldPath();
foreach (DeBruijnNode node in contigs.GetRange(2, 5))
{
path.Add(new KeyValuePair <DeBruijnNode, DeBruijnEdge>(node, null));
}
paths.Add(path);
path = new ScaffoldPath();
foreach (DeBruijnNode node in contigs.GetRange(3, 5))
{
path.Add(new KeyValuePair <DeBruijnNode, DeBruijnEdge>(node, null));
}
paths.Add(path);
path = new ScaffoldPath();
foreach (DeBruijnNode node in contigs.GetRange(6, 5))
{
path.Add(new KeyValuePair <DeBruijnNode, DeBruijnEdge>(node, null));
}
paths.Add(path);
path = new ScaffoldPath();
foreach (DeBruijnNode node in contigs.GetRange(0, 11))
{
path.Add(new KeyValuePair <DeBruijnNode, DeBruijnEdge>(node, null));
}
paths.Add(path);
path = new ScaffoldPath();
foreach (DeBruijnNode node in contigs.GetRange(7, 4))
{
path.Add(new KeyValuePair <DeBruijnNode, DeBruijnEdge>(node, null));
}
paths.Add(path);
path = new ScaffoldPath();
foreach (DeBruijnNode node in contigs.GetRange(11, 0))
{
path.Add(new KeyValuePair <DeBruijnNode, DeBruijnEdge>(node, null));
}
paths.Add(path);
path = new ScaffoldPath();
foreach (DeBruijnNode node in contigs.GetRange(2, 9))
{
path.Add(new KeyValuePair <DeBruijnNode, DeBruijnEdge>(node, null));
}
paths.Add(path);
path = new ScaffoldPath();
foreach (DeBruijnNode node in contigs.GetRange(1, 10))
{
path.Add(new KeyValuePair <DeBruijnNode, DeBruijnEdge>(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 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));
}
/// <summary>
/// Removes Overlapping paths by generating pairwise overlaps between paths.
/// </summary>
/// <param name="scaffoldPath">Current path.</param>
/// <param name="path">Path to be compared with.</param>
/// <returns>Overlapping paths or not.</returns>
private static bool RemoveOverlappingPaths(
ScaffoldPath scaffoldPath,
ScaffoldPath path)
{
// Generate Overlap Matrix [Similar To Pairwise Overlap aligner]
bool[,] matrix = new bool[scaffoldPath.Count, path.Count];
for (int index = 0; index < scaffoldPath.Count; index++)
{
for (int index1 = 0; index1 < path.Count; index1++)
{
matrix.SetValue(scaffoldPath[index].Key == path[index1].Key, index, index1);
}
}
// Search in last row for a match.
int startPosOfRow = -1;
for (int index = scaffoldPath.Count - 1; index >= 0; index--)
{
if ((bool)matrix.GetValue(index, path.Count - 1))
{
int index1 = 1;
while (path.Count - 1 - index1 >= 0 && index - index1 >= 0)
{
if ((bool)matrix.GetValue(index - index1, path.Count - 1 - index1))
{
index1++;
}
else
{
break;
}
}
if (path.Count - 1 - index1 <= 0 || index - index1 <= 0)
{
startPosOfRow = index;
break;
}
}
}
// Search in last column for match.
int startPosOfCol = -1;
for (int index = path.Count - 2; index >= 0; index--)
{
if ((bool)matrix.GetValue(scaffoldPath.Count - 1, index))
{
int index1 = 1;
while (scaffoldPath.Count - 1 - index1 > 0 && index - index1 > 0)
{
if ((bool)matrix.GetValue(scaffoldPath.Count - 1 - index1, index - index1))
{
index1++;
}
else
{
break;
}
}
if (scaffoldPath.Count - 1 - index1 <= 0 || index - index1 <= 0)
{
startPosOfCol = index;
break;
}
}
}
if (startPosOfCol != -1 || startPosOfRow != -1)
{
if (startPosOfRow >= startPosOfCol)
{
StitchPath(scaffoldPath, path, startPosOfRow, path.Count - 1);
return true;
}
StitchPath(scaffoldPath, path, scaffoldPath.Count - 1, startPosOfCol);
return true;
}
return false;
}
/// <summary>
/// Search for containing and overlapping paths.
/// </summary>
/// <param name="scaffoldPath">Current Path.</param>
/// <param name="isConsumed">Path status.</param>
/// <returns>Update list or not.</returns>
private bool SearchContainingAndOverlappingPaths(
ScaffoldPath scaffoldPath,
bool[] isConsumed)
{
bool isUpdated = false;
for (int index = 0; index < this.internalScaffoldPaths.Count; index++)
{
if (!isConsumed[index] && scaffoldPath != this.internalScaffoldPaths[index])
{
if (RemoveContainingPaths(scaffoldPath, this.internalScaffoldPaths[index]))
{
isConsumed[index] = true;
isUpdated = true;
}
else
{
if (RemoveOverlappingPaths(scaffoldPath, this.internalScaffoldPaths[index]))
{
isConsumed[index] = true;
isUpdated = true;
}
}
}
}
return isUpdated;
}
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 ValidateBuildSequenceFromPath()
{
const int KmerLength = 7;
ISequence sequence = new Sequence(Alphabets.DNA, "GATTCAAGGGCTGGGGG");
ISequence sequenceNew;
IList<ISequence> contigsSequence = SequenceToKmerBuilder.GetKmerSequences(sequence, KmerLength).ToList();
using (ContigGraph graph = new ContigGraph())
{
graph.BuildContigGraph(contigsSequence, KmerLength);
List<Node> contigs = graph.Nodes.ToList();
ScaffoldPath path = new ScaffoldPath();
foreach (Node node in contigs.GetRange(0, 11))
{
path.Add(new KeyValuePair<Node, Edge>(node, new Edge(true)));
}
sequenceNew = path.BuildSequenceFromPath(graph, KmerLength);
}
Assert.IsNotNull(sequenceNew);
Assert.AreEqual((new string(sequenceNew.Select(a => (char)a).ToArray())), "GATTCAAGGGCTGGGGG");
}
/// <summary>
/// Add right extension of the nodes to queue.
/// </summary>
/// <param name="node">Current node.</param>
/// <param name="search">Queue for BFS.</param>
/// <param name="paths">List of paths.</param>
/// <param name="familyTree">Nodes visited for construction of paths.</param>
/// <param name="contigPairedReadMap">Contig and valid mate pair map.</param>
private void RightExtension(
KeyValuePair<Node, Edge> node,
Queue<Paths> search,
List<Paths> paths,
ScaffoldPath familyTree,
Dictionary<ISequence, IList<ValidMatePair>> contigPairedReadMap)
{
Paths childPath;
if (node.Key.RightExtensionNodes.Count > 0)
{
foreach (KeyValuePair<Node, Edge> child in node.Key.RightExtensionNodes)
{
childPath = new Paths();
childPath.CurrentNode = child;
if (familyTree == null)
{
childPath.FamilyTree.Add(node);
}
else
{
childPath.FamilyTree.AddRange(familyTree);
childPath.FamilyTree.Add(node);
}
childPath.NodeOrientation = true;
if (this.DistanceConstraint(childPath, contigPairedReadMap) &&
childPath.FamilyTree.Count < this.depth &&
!contigPairedReadMap.All(
t => childPath.FamilyTree.Any(k => t.Key == this.graph.GetNodeSequence(k.Key))))
{
search.Enqueue(childPath);
}
else
{
if (contigPairedReadMap.All(
t => childPath.FamilyTree.Any(k => t.Key == this.graph.GetNodeSequence(k.Key))))
{
paths.Add(childPath);
}
}
}
}
else
{
childPath = new Paths();
if (familyTree == null)
{
childPath.FamilyTree.Add(node);
}
else
{
childPath.FamilyTree.AddRange(familyTree);
childPath.FamilyTree.Add(node);
}
if (contigPairedReadMap.All(
t => childPath.FamilyTree.Any(k => t.Key == this.graph.GetNodeSequence(k.Key))))
{
paths.Add(childPath);
}
}
}
