/// <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"));
}