/// <summary>
/// It assembles the sequences.
/// </summary>
public override void AssembleSequences()
{
TimeSpan algorithmSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
FileInfo refFileinfo = new FileInfo(this.Filename);
long refFileLength = refFileinfo.Length;
Output.WriteLine(OutputLevel.Information, Resources.AssemblyScaffoldStarting);
if (!string.IsNullOrEmpty(this.CloneLibraryName))
{
CloneLibrary.Instance.AddLibrary(this.CloneLibraryName, (float)this.MeanLengthOfInsert, (float)this.StandardDeviationOfInsert);
}
runAlgorithm.Restart();
IEnumerable <ISequence> reads = ParseFile();
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed read file: {0}", Path.GetFullPath(this.Filename));
Output.WriteLine(OutputLevel.Verbose, " Read/Processing time: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", refFileLength);
Output.WriteLine(OutputLevel.Verbose, " k-mer Length : {0}", this.KmerLength);
}
runAlgorithm.Restart();
ValidateAmbiguousReads(reads);
runAlgorithm.Stop();
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Time taken for Validating reads: {0}", runAlgorithm.Elapsed);
}
ParallelDeNovoAssembler assembler = new ParallelDeNovoAssembler();
assembler.StatusChanged += this.AssemblerStatusChanged;
assembler.AllowErosion = AllowErosion;
assembler.AllowKmerLengthEstimation = AllowKmerLengthEstimation;
if (ContigCoverageThreshold != -1)
{
assembler.AllowLowCoverageContigRemoval = true;
assembler.ContigCoverageThreshold = ContigCoverageThreshold;
}
assembler.DanglingLinksThreshold = DangleThreshold;
assembler.ErosionThreshold = ErosionThreshold;
if (!this.AllowKmerLengthEstimation)
{
assembler.KmerLength = this.KmerLength;
}
assembler.RedundantPathLengthThreshold = RedundantPathLengthThreshold;
runAlgorithm.Restart();
IDeNovoAssembly assembly = assembler.Assemble(reads, true);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Compute time: {0}", runAlgorithm.Elapsed);
}
runAlgorithm.Restart();
WriteContigs(assembly);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Write contigs time: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, "Total runtime: {0}", algorithmSpan);
}
}
/// <summary>
/// Scaffold function.
/// </summary>
/// <param name="args">Arguments to Scaffold function.</param>
private static void Scaffold(string[] args)
{
ScaffoldArguments options = new ScaffoldArguments();
CommandLineArguments parser = new CommandLineArguments();
// Add the parameters
parser.Parameter(ArgumentType.Optional, "Quiet", ArgumentValueType.Bool, "q", "Display minimal output during processing.");
parser.Parameter(ArgumentType.Required, "KmerLength", ArgumentValueType.OptionalInt, "k", "Length of k-mer");
parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "h", "");
parser.Parameter(ArgumentType.Optional, "OutputFile", ArgumentValueType.String, "o", "Output file");
parser.Parameter(ArgumentType.DefaultArgument, "Filenames", ArgumentValueType.MultipleUniqueStrings, "", "Input file of reads and contigs.");
parser.Parameter(ArgumentType.Optional, "CloneLibraryName", ArgumentValueType.String, "n", "Clone Library Name");
parser.Parameter(ArgumentType.Optional, "MeanLengthOfInsert", ArgumentValueType.Int, "m", "Mean Length of clone library.");
parser.Parameter(ArgumentType.Optional, "StandardDeviationOfInsert", ArgumentValueType.Int, "s", "Standard Deviation of Clone Library.");
parser.Parameter(ArgumentType.Optional, "Redundancy", ArgumentValueType.Int, "r", "Number of paired read required to connect two contigs.");
parser.Parameter(ArgumentType.Optional, "Depth", ArgumentValueType.Int, "d", "Depth for graph traversal.");
parser.Parameter(ArgumentType.Optional, "Verbose", ArgumentValueType.Bool, "v", "Display verbose logging during processing.");
parser.Parameter(ArgumentType.Optional, "ForceKmer", ArgumentValueType.Bool, "fk", "Force specified k-mer to be used without a warning prompt.");
if (args.Length > 0)
{
try
{
parser.Parse(args, options);
}
catch (ArgumentParserException ex)
{
Output.WriteLine(OutputLevel.Error, ex.Message);
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
Environment.Exit(-1);
}
if (options.Help)
{
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
}
else if (options.FileNames != null)
{
if (!options.ForceKmer)
{
ValidateKmerLength(options.KmerLength, false);
}
if (options.Verbose)
{
Output.TraceLevel = OutputLevel.Information | OutputLevel.Verbose;
}
else if (!options.Quiet)
{
Output.TraceLevel = OutputLevel.Information;
}
options.GenerateScaffold();
}
else
{
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
}
}
else
{
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
}
}
/// <summary>
/// It assembles the sequences.
/// </summary>
public virtual void AssembleSequences()
{
TimeSpan algorithmSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
FileInfo refFileinfo = new FileInfo(this.Filename);
long refFileLength = refFileinfo.Length;
runAlgorithm.Restart();
IEnumerable <ISequence> reads = this.ParseFile();
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Information, Resources.AssemblyStarting);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed read file: {0}", Path.GetFullPath(this.Filename));
Output.WriteLine(OutputLevel.Verbose, " Read/Processing time: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", refFileLength);
Output.WriteLine(OutputLevel.Verbose, " k-mer Length : {0}", this.KmerLength);
}
runAlgorithm.Restart();
if (reads.Any(s => s.Alphabet.HasAmbiguity))
{
throw new ArgumentException(Resources.AmbiguousReadsNotSupported);
}
runAlgorithm.Stop();
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Time taken for Validating reads: {0}", runAlgorithm.Elapsed);
}
using (ParallelDeNovoAssembler assembler = new ParallelDeNovoAssembler())
{
assembler.StatusChanged += this.AssemblerStatusChanged;
assembler.AllowErosion = this.AllowErosion;
assembler.AllowKmerLengthEstimation = this.AllowKmerLengthEstimation;
if (ContigCoverageThreshold != -1)
{
assembler.AllowLowCoverageContigRemoval = true;
assembler.ContigCoverageThreshold = ContigCoverageThreshold;
}
assembler.DanglingLinksThreshold = this.DangleThreshold;
assembler.ErosionThreshold = this.ErosionThreshold;
if (!this.AllowKmerLengthEstimation)
{
assembler.KmerLength = this.KmerLength;
}
assembler.RedundantPathLengthThreshold = this.RedundantPathLengthThreshold;
runAlgorithm.Restart();
IDeNovoAssembly assembly = assembler.Assemble(reads);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Compute time: {0}", runAlgorithm.Elapsed);
}
runAlgorithm.Restart();
this.WriteContigs(assembly);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Write contigs time: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, "Total runtime: {0}", algorithmSpan);
}
}
}
