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 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());
}
