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(new string(contig.Select(a => (char)a).ToArray())));
}
}
}
public void TestContigBuilder1()
{
const int KmerLength = 11;
const int DangleThreshold = 3;
const int RedundantThreshold = 10;
List<ISequence> readSeqs = TestInputs.GetDanglingReads();
this.SequenceReads.Clear();
this.SetSequenceReads(readSeqs);
this.KmerLength = KmerLength;
DanglingLinksThreshold = DangleThreshold;
DanglingLinksPurger = new DanglingLinksPurger(DangleThreshold);
RedundantPathLengthThreshold = RedundantThreshold;
RedundantPathsPurger = new RedundantPathsPurger(RedundantThreshold);
ContigBuilder = new SimplePathContigBuilder();
CreateGraph();
UnDangleGraph();
RemoveRedundancy();
long graphCount = Graph.NodeCount;
long graphEdges = Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
IEnumerable<ISequence> contigs = BuildContigs();
long contigsBuiltGraphCount = this.Graph.NodeCount;
long contigsBuilt = Graph.GetNodes().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)
{
string s = new string(contig.Select(a => (char)a).ToArray());
Assert.IsTrue(expectedContigs.Contains(s));
}
Assert.AreEqual(graphCount, contigsBuiltGraphCount);
Assert.AreEqual(graphEdges, contigsBuilt);
}
public void TestDanglingLinksPurger()
{
const int KmerLength = 11;
const int DangleThreshold = 3;
List <ISequence> readSeqs = TestInputs.GetDanglingReads();
SequenceReads.Clear();
this.SetSequenceReads(readSeqs);
this.KmerLength = KmerLength;
DanglingLinksThreshold = DangleThreshold;
DanglingLinksPurger = new DanglingLinksPurger(DangleThreshold);
CreateGraph();
long graphCount = Graph.NodeCount;
long graphEdges = Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
var graphNodes = Graph.GetNodes().Select(n => Graph.GetNodeSequence(n)).ToList();
DanglingLinksThreshold = DangleThreshold;
UnDangleGraph();
long dangleRemovedGraphCount = Graph.NodeCount;
long dangleRemovedGraphEdge = Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
var dangleRemovedGraphNodes = Graph.GetNodes().Select(n => Graph.GetNodeSequence(n)).ToList();
// Compare the two graphs
Assert.AreEqual(2, graphCount - dangleRemovedGraphCount);
Assert.AreEqual(4, graphEdges - dangleRemovedGraphEdge);
var checkList = graphNodes.Except(dangleRemovedGraphNodes, new SequenceEqualityComparer());
HashSet <string> expected = new HashSet <string> {
"ATCGAACGATG", "TCGAACGATGA"
};
AlignmentHelpers.CompareSequenceLists(expected, checkList);
}
