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));
}
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 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");
}