/// <summary>
/// Validate scaffold sequence for a given input reads.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateScaffoldSequence(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
string daglingThreshold = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.DanglingLinkThresholdNode);
string redundantThreshold = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.RedundantThreshold);
string libraray = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.LibraryName);
string stdDeviation = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.StdDeviation);
string mean = utilityObj.xmlUtil.GetTextValue(nodeName,Constants.Mean);
string inputRedundancy = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.InputRedundancy);
string expectedSeq = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ScaffoldSeq);
string[] scaffoldSeqNodes = expectedSeq.Split(',');
// Get the input reads and build kmers
using (FastAParser parser = new FastAParser(filePath))
{
IEnumerable<ISequence> sequenceReads = parser.Parse();
// Build kmers from step1,graph in step2
// Remove the dangling links from graph in step3
// Remove bubbles form the graph in step4
// Pass the graph and build contigs
// Validate contig reads
this.KmerLength = Int32.Parse(kmerLength, null);
this.DanglingLinksThreshold = Int32.Parse(daglingThreshold, null);
this.DanglingLinksPurger = new DanglingLinksPurger(Int32.Parse(daglingThreshold, null));
this.RedundantPathsPurger = new RedundantPathsPurger(Int32.Parse(redundantThreshold, null));
this.RedundantPathLengthThreshold = Int32.Parse(redundantThreshold, null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
this.CreateGraph();
this.UnDangleGraph();
// Build contig.
this.RemoveRedundancy();
IEnumerable<ISequence> contigs = this.BuildContigs();
// Find map paired reads.
CloneLibrary.Instance.AddLibrary(libraray, float.Parse(mean, null),
float.Parse(stdDeviation, null));
IEnumerable<ISequence> scaffoldSeq;
using (GraphScaffoldBuilder scaffold = new GraphScaffoldBuilder())
{
scaffoldSeq = scaffold.BuildScaffold(
sequenceReads, contigs.ToList(), this.KmerLength, redundancy: Int32.Parse(inputRedundancy, null));
}
AlignmentHelpers.CompareSequenceLists(new HashSet<string>(scaffoldSeqNodes), scaffoldSeq.ToList());
}
ApplicationLog.WriteLine("PADENA P1 : Scaffold sequence : validation for Padena step6:step8 completed successfully");
}
/// <summary>
/// Build scaffolds from contigs and paired reads (uses Padena Step 6 for assembly).
/// </summary>
/// <param name="contigs">List of contigs.</param>
/// <param name="reads">List of paired reads.</param>
/// <returns>List of scaffold sequences.</returns>
private IEnumerable<ISequence> ScaffoldsGenerator(IEnumerable<ISequence> contigs, IEnumerable<ISequence> reads)
{
using (GraphScaffoldBuilder scaffoldBuilder = new GraphScaffoldBuilder())
{
return scaffoldBuilder.BuildScaffold(reads, contigs.ToList(), this.KmerLength, this.Depth, this.ScaffoldRedundancy);
}
}
/// <summary>
/// Refine layout in the delta alignments.
/// </summary>
public void GenerateScaffolds()
{
TimeSpan timeSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
FileInfo inputFileinfo = new FileInfo(this.FilePath[0]);
long inputFileLength = inputFileinfo.Length;
inputFileinfo = null;
if (!string.IsNullOrEmpty(this.CloneLibraryName))
{
CloneLibrary.Instance.AddLibrary(this.CloneLibraryName, (float)this.MeanLengthOfInsert, (float)this.StandardDeviationOfInsert);
}
runAlgorithm.Restart();
FastAParser parser = new FastAParser();
IEnumerable<ISequence> contigs = parser.Parse(this.FilePath[0]);
runAlgorithm.Stop();
if (this.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed Contig file: {0}", Path.GetFullPath(this.FilePath[0]));
Console.Error.WriteLine(" Read/Processing time: {0}", runAlgorithm.Elapsed);
Console.Error.WriteLine(" File Size : {0}", inputFileLength);
}
inputFileinfo = new FileInfo(this.FilePath[1]);
inputFileLength = inputFileinfo.Length;
runAlgorithm.Restart();
FastAParser readParser = new FastAParser();
IEnumerable<ISequence> reads = readParser.Parse(this.FilePath[1]);
runAlgorithm.Stop();
if (this.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed reads file: {0}", Path.GetFullPath(this.FilePath[1]));
Console.Error.WriteLine(" Read/Processing time: {0}", runAlgorithm.Elapsed);
Console.Error.WriteLine(" File Size : {0}", inputFileLength);
}
runAlgorithm.Restart();
IEnumerable<ISequence> scaffolds = null;
using (GraphScaffoldBuilder scaffoldBuilder = new GraphScaffoldBuilder())
{
scaffolds = scaffoldBuilder.BuildScaffold(reads, contigs.ToList(), this.KmerLength, this.Depth, this.Redundancy);
}
runAlgorithm.Stop();
timeSpan = timeSpan.Add(runAlgorithm.Elapsed);
runAlgorithm.Restart();
this.WriteSequences(scaffolds);
runAlgorithm.Stop();
if (this.Verbose)
{
Console.Error.WriteLine(" Compute time: {0}", timeSpan);
Console.Error.WriteLine(" Write() time: {0}", runAlgorithm.Elapsed);
}
}
/// <summary>
/// Step 6: Build scaffolds from contig list and paired reads.
/// </summary>
/// <param name="contigs">List of contigs.</param>
/// <returns>List of scaffold sequences.</returns>
protected IList<ISequence> BuildScaffolds(IList<ISequence> contigs)
{
if (ScaffoldBuilder == null)
{
// Scaffold Builder is a required module for this method. Set this to default.
ScaffoldBuilder = new GraphScaffoldBuilder();
}
return ScaffoldBuilder.BuildScaffold(SequenceReads, contigs, KmerLength, Depth, ScaffoldRedundancy);
}
/// <summary>
/// Generates the Scaffold.
/// </summary>
public void GenerateScaffold()
{
Output.WriteLine(OutputLevel.Information, Resources.ScaffoldStarting);
if (this.FileNames.Length != 2)
{
Output.WriteLine(OutputLevel.Error, "\nError: A reference file and 1 query file are required.");
Output.WriteLine(OutputLevel.Required, Resources.ScaffoldHelp);
return;
}
if (!string.IsNullOrEmpty(this.CloneLibraryName))
{
CloneLibrary.Instance.AddLibrary(this.CloneLibraryName, (float)this.MeanLengthOfInsert, (float)this.StandardDeviationOfInsert);
}
TimeSpan algorithmSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
FileInfo refFileinfo = null;
using (GraphScaffoldBuilder scaffoldBuilder = new GraphScaffoldBuilder())
{
refFileinfo = new FileInfo(this.FileNames[0]);
long refFileLength = refFileinfo.Length;
runAlgorithm.Restart();
IEnumerable<ISequence> contigs = AssembleArguments.ParseFile(this.FileNames[0]);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed contigs file : {0}", Path.GetFullPath(this.FileNames[0]));
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);
}
refFileinfo = new FileInfo(this.FileNames[1]);
refFileLength = refFileinfo.Length;
runAlgorithm.Restart();
IEnumerable<ISequence> reads = AssembleArguments.ParseFile(this.FileNames[1]);
runAlgorithm.Stop();
algorithmSpan = algorithmSpan.Add(runAlgorithm.Elapsed);
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed reads file : {0}", Path.GetFullPath(this.FileNames[1]));
Output.WriteLine(OutputLevel.Verbose, " Read/Processing time: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", refFileLength);
}
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);
}
runAlgorithm.Restart();
IList<ISequence> scaffolds = scaffoldBuilder.BuildScaffold(reads, contigs.ToList(), this.KmerLength, this.Depth, this.Redundancy);
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(scaffolds);
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);
}
}
}