public void PalindromicAssembleTest()
{
const int KmerLength = 19;
string testSeq = @"TTTTTTCAATTGAAAAAAAC";
//Will these two sequences be assembled differently?
//Key is that there is no additional kmer added by the first sequence relative to the second sequence
//TTTTTTTCAATTGAAAAAAATC
// TTTTTTCAATTGAAAAAAATC
var testSequence = new Sequence(NoGapDnaAlphabet.Instance, testSeq);
List <ISequence> seqs = new List <ISequence>();
seqs.Add(testSequence);
using (MitoPaintedAssembler assembler = new MitoPaintedAssembler())
{
//assembler.ReferenceGenome = testSequence;
assembler.KmerLength = 19;
assembler.DiagnosticFileOutputPrefix = "tmp";
assembler.DanglingLinksThreshold = 1;
var assembly = assembler.Assemble(seqs);
// Compare the two graphs
Assert.IsTrue(assembly.AssembledSequences.Count == 1);
Assert.AreEqual(1, assembly.AssembledSequences.Count());
bool correctContig = assembly.AssembledSequences[0].SequenceEqual(testSequence);
if (!correctContig)
{
correctContig = assembly.AssembledSequences[0].GetReverseComplementedSequence().Equals(testSequence);
}
Assert.IsTrue(correctContig);
}
}
public void OutputGraph(string fname)
{
SW = new StreamWriter(fname);
MitoPaintedAssembler.RaiseStatusEvent("\tBuilding Graph File");
SW.Write(HEADER);
//make verticies
foreach (MetaNode node in MetaNodes)
{
OutNode(node);
}
int edgeCount = 0;
//make edges
foreach (MetaNode node in MetaNodes)
{
foreach (var leftNode in node.GetLeftEdges())
{
edgeCount++;
OutEdge(node, leftNode.ToNode, leftNode.DifferentOrientation, 0, leftNode.Weight);
}
//Remove all relatives
foreach (var rightNode in node.GetRightEdges())
{
edgeCount++;
OutEdge(node, rightNode.ToNode, rightNode.DifferentOrientation, 100, rightNode.Weight);
}
}
MitoPaintedAssembler.RaiseStatusEvent("\tWrote " + edgeCount.ToString() + " edges");
SW.Write(FOOTER);
SW.Close();
}
public void AssembleDataWithNoErrors()
{
MitoPaintedAssembler mpa = new MitoPaintedAssembler();
MitoPaintedAssembler assembler = new MitoPaintedAssembler();
// assembler.ReferenceGenome = refAsSequence;
assembler.KmerLength = 19;
var assembly = assembler.Assemble(DoDeterministicSimulation(25, 75, true));
Assert.AreEqual(assembly.AssembledSequences.Count, 1);
var seq1 = assembly.AssembledSequences.First();
Assert.IsTrue(seq1.SequenceEqual(refAsSequence) || seq1.GetReverseComplementedSequence().SequenceEqual(refAsSequence));
}
private void makeSlidingWindowOccurencePlot()
{
MitoPaintedAssembler.RaiseStatusEvent("\tStarting sliding window plot");
var list = GetAverageInSlidingCoverageWindows().ToList();
double[] xvals = list.Select(x => (double)x.Key).ToArray();
double[] yvals = list.Select(x => x.Value).ToArray();
var scutoff = PoissonCoverageCutoffCount.ToString();
string line = "lines(c(0,16569),c(" + scutoff + "," + scutoff + "),col=\"red\",lwd=3)";
rInt.PlotPDF(xvals, yvals, OutputFilePrefix + "Windowed" + this.ScanningWindowSize.ToString() + ".pdf", "Windowed occurence", "Insert Size", "Window Average", new List <string>()
{
line
});
MitoPaintedAssembler.RaiseStatusEvent("\tFinished sliding window plot");
}
public void OutputDotGraph(string fname)
{
StreamWriter SW = new StreamWriter(fname);
SW.WriteLine("digraph g {");
foreach (MetaNode node in MetaNodes)
{
if (node.Lowest_Reference_Position != 0)
{
SW.WriteLine("N" + node.NodeNumber.ToString() + " [label=\"" + node.Lowest_Reference_Position.ToString() + "-" + node.Highest_Reference_Position.ToString() + " -AvgCov=" + node.AvgKmerCoverage.ToString() + "\"];");
}
else
{
SW.WriteLine("N" + node.NodeNumber.ToString() + " [label=\"" + node.Sequence + " -N=" + node.AvgKmerCoverage.ToString() + "\"];");
}
}
int edgeCount = 0;
//make edges
foreach (MetaNode node in MetaNodes)
{
foreach (var leftNode in node.GetLeftEdges().Where(x => !x.IsInferiorEdge))
{
edgeCount++;
string edge = "N" + leftNode.FromNode.NodeNumber.ToString() + " -> " + "N" + leftNode.ToNode.NodeNumber.ToString() + ";";
SW.WriteLine(edge);
}
//Remove all relatives
foreach (var rightNode in node.GetRightEdges().Where(x => !x.IsInferiorEdge))
{
edgeCount++;
string edge = "N" + rightNode.FromNode.NodeNumber.ToString() + " -> " + "N" + rightNode.ToNode.NodeNumber.ToString() + ";";
SW.WriteLine(edge);
}
}
SW.WriteLine("}");
MitoPaintedAssembler.RaiseStatusEvent("\tWrote " + edgeCount.ToString() + " edges in dot file");
SW.Close();
}
