public void BuildGraph_GenerateDotFile_WriteContigs(string fastaPath)
{
var assemblyName = "IntegrationTests";
var projectPath = Environment.CurrentDirectory.Substring(0, Environment.CurrentDirectory.IndexOf(assemblyName) + assemblyName.Length);
fastaPath = Path.Combine(projectPath, fastaPath);
var fileService = new FileService();
var kmerLength = 19;
var errorCorrector = new ErrorCorrector(kmerLength);
var fastaReader = new FastaReader(fileService);
var reads = fastaReader.ParseFastaFile(fastaPath);
errorCorrector.BuildHistogram(reads);
var graphBuilder = new DeBruijnGraphBuilder(kmerLength, errorCorrector);
var graph = graphBuilder.Build(reads);
errorCorrector.PrintResult();
graph.CleanUp();
var dotFileDirectory = Path.Combine(Path.GetDirectoryName(fastaPath), "graphs");
Directory.CreateDirectory(dotFileDirectory);
graphBuilder.ToDot(fileService, Path.Combine(dotFileDirectory, Path.GetFileNameWithoutExtension(fastaPath) + ".dot"), graph);
var contigs = graph.GetContigs();
var contigsDirectory = Path.Combine(Path.GetDirectoryName(fastaPath), "contigs");
Directory.CreateDirectory(contigsDirectory);
fastaReader.WriteFastaFile(Path.Combine(contigsDirectory, Path.GetFileNameWithoutExtension(fastaPath) + ".contigs.fasta"), contigs);
}
private void Run()
{
var fileService = new FileService();
var kmerLength = K ?? 19;
var errorCorrector = new ErrorCorrector(kmerLength, true);
var fastaReader = new FastaReader(fileService);
var reads = fastaReader.ParseFastaFile(ReadsPath);
// errorCorrector.BuildHistogram(reads);
var graphBuilder = new DeBruijnGraphBuilder(kmerLength, errorCorrector);
var graph = graphBuilder.Build(reads);
errorCorrector.PrintResult();
graph.CleanUp();
if (!string.IsNullOrWhiteSpace(DotFilePath))
{
Directory.CreateDirectory(Path.GetDirectoryName(DotFilePath));
graphBuilder.ToDot(fileService, DotFilePath, graph);
}
var contigs = graph.GetContigs();
Directory.CreateDirectory(Path.GetDirectoryName(ContigsPath));
fastaReader.WriteFastaFile(ContigsPath, contigs);
}
public void Simplify(int mergedNodeCount, int totalMergedNodeValuesLength, params string[] str)
{
var k = 4;
var graphBuilder = new DeBruijnGraphBuilder(k, new TestErrorCorrector(k));
var graph = graphBuilder.Build(str);
graph.Simplify();
Assert.Equal(mergedNodeCount, graph.Nodes.Count());
Assert.Equal(totalMergedNodeValuesLength, graph.Nodes.Select(n => n.Value).Aggregate((a, b) => a + b).Length);
}
public void RemoveShortChains(int chainsCount, params string[] str)
{
var k = 4;
var graphBuilder = new DeBruijnGraphBuilder(k, new TestErrorCorrector(k));
var graph = graphBuilder.Build(str);
graph.Simplify();
graph.RemoveShortChains();
Assert.Equal(chainsCount, graph.Nodes.Count());
}
public void RemoveTips_WithSimplify(int k, int chainsCount, params string[] str)
{
var graphBuilder = new DeBruijnGraphBuilder(k, new TestErrorCorrector(k));
var graph = graphBuilder.Build(str);
graph.Simplify();
graph.RemoveTips();
Assert.Equal(chainsCount, graph.Nodes.Count());
graph.Simplify();
Assert.Single(graph.Nodes);
}