public void TestDanglingLinksPurger()
{
const int KmerLength = 11;
const int DangleThreshold = 3;
List <ISequence> readSeqs = TestInputs.GetDanglingReads();
SequenceReads.Clear();
this.AddSequenceReads(readSeqs);
this.KmerLength = KmerLength;
DanglingLinksThreshold = DangleThreshold;
DanglingLinksPurger = new DanglingLinksPurger(DangleThreshold);
CreateGraph();
int graphCount = Graph.Nodes.Count;
int graphEdges = Graph.Nodes.Select(n => n.ExtensionsCount).Sum();
HashSet <string> graphNodes = new HashSet <string>(
Graph.Nodes.Select(n => Graph.GetNodeSequence(n).ToString()));
DanglingLinksThreshold = DangleThreshold;
UnDangleGraph();
int dangleRemovedGraphCount = Graph.Nodes.Count;
int dangleRemovedGraphEdge = Graph.Nodes.Select(n => n.ExtensionsCount).Sum();
HashSet <string> dangleRemovedGraphNodes = new HashSet <string>(
Graph.Nodes.Select(n => Graph.GetNodeSequence(n).ToString()));
// Compare the two graphs
Assert.AreEqual(2, graphCount - dangleRemovedGraphCount);
Assert.AreEqual(4, graphEdges - dangleRemovedGraphEdge);
graphNodes.ExceptWith(dangleRemovedGraphNodes);
Assert.IsTrue(graphNodes.Contains("TCGAACGATGA"));
Assert.IsTrue(graphNodes.Contains("ATCGAACGATG"));
}
public void AssemblerTest()
{
const int KmerLength = 11;
const int DangleThreshold = 3;
const int RedundantThreshold = 10;
List <ISequence> readSeqs = TestInputs.GetDanglingReads();
using (ParallelDeNovoAssembler assembler = new ParallelDeNovoAssembler())
{
assembler.KmerLength = KmerLength;
assembler.DanglingLinksThreshold = DangleThreshold;
assembler.RedundantPathLengthThreshold = RedundantThreshold;
IDeNovoAssembly result = assembler.Assemble(readSeqs);
// Compare the two graphs
Assert.AreEqual(1, result.AssembledSequences.Count);
HashSet <string> expectedContigs = new HashSet <string>()
{
"ATCGCTAGCATCGAACGATCATT"
};
foreach (ISequence contig in result.AssembledSequences)
{
Assert.IsTrue(expectedContigs.Contains(contig.ToString()));
}
}
}
public void TestContigBuilder1()
{
const int KmerLength = 11;
const int DangleThreshold = 3;
const int RedundantThreshold = 10;
List <ISequence> readSeqs = TestInputs.GetDanglingReads();
this.SequenceReads.Clear();
this.AddSequenceReads(readSeqs);
this.KmerLength = KmerLength;
DanglingLinksThreshold = DangleThreshold;
DanglingLinksPurger = new DanglingLinksPurger(DangleThreshold);
RedundantPathLengthThreshold = RedundantThreshold;
RedundantPathsPurger = new RedundantPathsPurger(RedundantThreshold);
ContigBuilder = new SimplePathContigBuilder();
CreateGraph();
UnDangleGraph();
RemoveRedundancy();
int graphCount = Graph.Nodes.Count;
int graphEdges = Graph.Nodes.Select(n => n.ExtensionsCount).Sum();
IList <ISequence> contigs = BuildContigs();
int contigsBuiltGraphCount = this.Graph.Nodes.Count;
int contigsBuilt = Graph.Nodes.Select(n => n.ExtensionsCount).Sum();
// Compare the two graphs
Assert.AreEqual(1, contigs.Count);
HashSet <string> expectedContigs = new HashSet <string>()
{
"ATCGCTAGCATCGAACGATCATT"
};
foreach (ISequence contig in contigs)
{
Assert.IsTrue(expectedContigs.Contains(contig.ToString()));
}
Assert.AreEqual(graphCount, contigsBuiltGraphCount);
Assert.AreEqual(graphEdges, contigsBuilt);
}
public void TestContigGraphBuilder1()
{
const int KmerLength = 11;
const int DangleThreshold = 3;
const int RedundantThreshold = 10;
List <ISequence> readSeqs = TestInputs.GetDanglingReads();
this.SequenceReads.Clear();
this.AddSequenceReads(readSeqs);
this.KmerLength = KmerLength;
this.DanglingLinksThreshold = DangleThreshold;
this.RedundantPathLengthThreshold = RedundantThreshold;
this.DanglingLinksPurger = new DanglingLinksPurger(DangleThreshold);
this.RedundantPathsPurger = new RedundantPathsPurger(RedundantThreshold);
this.ContigBuilder = new SimplePathContigBuilder();
this.CreateGraph();
this.UnDangleGraph();
this.RemoveRedundancy();
IList <ISequence> contigs = this.BuildContigs();
this.Graph.BuildContigGraph(contigs, KmerLength);
int contigGraphCount = this.Graph.Nodes.Count;
int contigGraphEdges = this.Graph.Nodes.Select(n => n.ExtensionsCount).Sum();
Assert.AreEqual(contigs.Count, contigGraphCount);
Assert.AreEqual(0, contigGraphEdges);
HashSet <string> contigSeqs = new HashSet <string>(contigs.Select(c => c.ToString()));
foreach (DeBruijnNode node in this.Graph.Nodes)
{
Assert.IsTrue(contigSeqs.Contains(this.Graph.GetNodeSequence(node).ToString()));
}
}