/// <summary>
/// Assemble the list of sequence reads.
/// </summary>
/// <param name="inputSequences">List of input sequences.</param>
/// <returns>Assembled output.</returns>
public IDeNovoAssembly Assemble(IEnumerable <ISequence> inputSequences)
{
if (inputSequences == null)
{
throw new ArgumentNullException("inputSequences");
}
this.sequenceReads = inputSequences;
// Remove ambiguous reads and set up fields for assembler process
this.Initialize();
// Step 1, 2: Create k-mers from reads and build de bruijn graph
this.CreateGraphStarted();
this.CreateGraph();
this.CreateGraphEnded();
// Estimate and set default value for erosion and coverage thresholds
this.EstimateDefaultValuesStarted();
this.EstimateDefaultThresholds();
this.EstimateDefaultValuesEnded();
// Step 3: Remove dangling links from graph
this.UndangleGraphStarted();
this.UnDangleGraph();
this.UndangleGraphEnded();
// Step 4: Remove redundant paths from graph
this.RemoveRedundancyStarted();
this.RemoveRedundancy();
this.RemoveRedundancyEnded();
// Perform dangling link purger step once more.
// This is done to remove any links created by redundant paths purger.
this.statusMessage = string.Format(CultureInfo.CurrentCulture, "\n UndangleGraph - Start time: {0}", DateTime.Now);
this.RaiseStatusEvent();
this.UnDangleGraph();
this.statusMessage = string.Format(CultureInfo.CurrentCulture, "\n UndangleGraph - End time: {0}", DateTime.Now);
this.RaiseStatusEvent();
// Step 5: Build Contigs
this.BuildContigsStarted();
IEnumerable <ISequence> contigSequences = this.BuildContigs();
this.BuildContigsEnded();
PadenaAssembly result = new PadenaAssembly();
result.AddContigs(contigSequences);
return(result);
}
/// <summary>
/// Assemble the list of sequence reads. Also performs the
/// scaffold building step as part of assembly process.
/// </summary>
/// <param name="inputSequences">List of input sequences.</param>
/// <param name="includeScaffolds">Boolean indicating whether scaffold building step has to be run.</param>
/// <returns>Assembled output.</returns>
public IDeNovoAssembly Assemble(IEnumerable <ISequence> inputSequences, bool includeScaffolds)
{
PadenaAssembly assemblyResult = (PadenaAssembly)this.Assemble(inputSequences);
if (includeScaffolds)
{
// Step 6: Build _scaffolds
IList <ISequence> scaffolds = this.BuildScaffolds(assemblyResult.ContigSequences);
if (scaffolds != null)
{
assemblyResult.AddScaffolds(scaffolds);
}
}
return(assemblyResult);
}
/// <summary>
/// Assemble the list of sequence reads.
/// </summary>
/// <param name="inputSequences">List of input sequences.</param>
/// <returns>Assembled output.</returns>
public IDeNovoAssembly Assemble(IEnumerable <ISequence> inputSequences)
{
if (inputSequences == null)
{
throw new ArgumentNullException("inputSequences");
}
this.sequenceReads = inputSequences;
// Remove ambiguous reads and set up fields for assembler process
this.Initialize();
// Step 1, 2: Create k-mers from reads and build de bruijn graph
this.CreateGraph();
// Estimate and set default value for erosion and coverage thresholds
this.EstimateDefaultThresholds();
// Step 3: Remove dangling links from graph
this.UnDangleGraph();
// Step 4: Remove redundant paths from graph
this.RemoveRedundancy();
// Perform dangling link purger step once more.
// This is done to remove any links created by redundant paths purger.
this.UnDangleGraph();
// Step 5: Build Contigs
IEnumerable <ISequence> contigSequences = this.BuildContigs();
PadenaAssembly result = new PadenaAssembly();
result.AddContigs(contigSequences);
return(result);
}
/// <summary>
/// Assemble the list of sequence reads.
/// </summary>
/// <param name="inputSequences">List of input sequences.</param>
/// <returns>Assembled output.</returns>
public virtual IDeNovoAssembly Assemble(IEnumerable <ISequence> inputSequences)
{
if (inputSequences == null)
{
throw new ArgumentNullException("inputSequences");
}
this._sequenceReads = inputSequences;
// Remove ambiguous reads and set up fields for assembler process
this.Initialize();
// Step 1, 2: Create k-mers from reads and build de bruijn graph
Stopwatch sw = Stopwatch.StartNew();
this.CreateGraphStarted();
this.CreateGraph();
sw.Stop();
this.CreateGraphEnded();
this.TaskTimeSpanReport(sw.Elapsed);
this.NodeCountReport();
// Estimate and set default value for erosion and coverage thresholds
sw = Stopwatch.StartNew();
this.EstimateDefaultValuesStarted();
this.EstimateDefaultThresholds();
sw.Stop();
this.EstimateDefaultValuesEnded();
this.TaskTimeSpanReport(sw.Elapsed);
// Step 3: Remove dangling links from graph
sw = Stopwatch.StartNew();
this.UndangleGraphStarted();
this.UnDangleGraph();
sw.Stop();
this.UndangleGraphEnded();
this.TaskTimeSpanReport(sw.Elapsed);
this.NodeCountReport();
// Step 4: Remove redundant paths from graph
sw = Stopwatch.StartNew();
this.RemoveRedundancyStarted();
this.RemoveRedundancy();
this.NodeCountReport();
// Perform dangling link purger step once more.
// This is done to remove any links created by redundant paths purger.
this._statusMessage = string.Format(CultureInfo.CurrentCulture, Properties.Resource.SecondaryUndangleGraphStarted, DateTime.Now);
this.RaiseStatusEvent();
this.UnDangleGraph();
this._statusMessage = string.Format(CultureInfo.CurrentCulture, Properties.Resource.SecondaryUndangleGraphEnded, DateTime.Now);
this.RaiseStatusEvent();
// Report end after undangle
sw.Stop();
this.RemoveRedundancyEnded();
this.TaskTimeSpanReport(sw.Elapsed);
this.NodeCountReport();
// Step 5: Build Contigs
sw = Stopwatch.StartNew();
this.BuildContigsStarted();
IEnumerable <ISequence> contigSequences = this.BuildContigs();
sw.Stop();
this.BuildContigsEnded();
this.TaskTimeSpanReport(sw.Elapsed);
PadenaAssembly result = new PadenaAssembly();
result.AddContigs(contigSequences);
return(result);
}
/// <summary>
/// Assemble the list of sequence reads.
/// </summary>
/// <param name="inputSequences">List of input sequences.</param>
/// <returns>Assembled output.</returns>
public virtual IDeNovoAssembly Assemble(IEnumerable<ISequence> inputSequences)
{
if (inputSequences == null)
{
throw new ArgumentNullException("inputSequences");
}
this.sequenceReads = inputSequences;
CancellationTokenSource cts = new CancellationTokenSource();
ReportIntermediateProgress(cts.Token);
try
{
// Remove ambiguous reads and set up fields for assembler process
Initialize();
// Step 1, 2: Create k-mers from reads and build de bruijn graph
Stopwatch sw = Stopwatch.StartNew();
CreateGraphStarted();
CreateGraph();
sw.Stop();
CreateGraphEnded();
TaskTimeSpanReport(sw.Elapsed);
NodeCountReport();
// Estimate and set default value for erosion and coverage thresholds
sw = Stopwatch.StartNew();
EstimateDefaultValuesStarted();
EstimateDefaultThresholds();
sw.Stop();
EstimateDefaultValuesEnded();
TaskTimeSpanReport(sw.Elapsed);
// Step 3: Remove dangling links from graph
sw = Stopwatch.StartNew();
UndangleGraphStarted();
UnDangleGraph();
sw.Stop();
UndangleGraphEnded();
TaskTimeSpanReport(sw.Elapsed);
NodeCountReport();
// Step 4: Remove redundant paths from graph
sw = Stopwatch.StartNew();
RemoveRedundancyStarted();
RemoveRedundancy();
NodeCountReport();
// Perform dangling link purger step once more.
// This is done to remove any links created by redundant paths purger.
StatusMessage = string.Format(CultureInfo.CurrentCulture, Properties.Resource.SecondaryUndangleGraphStarted, DateTime.Now);
UnDangleGraph();
StatusMessage = string.Format(CultureInfo.CurrentCulture, Properties.Resource.SecondaryUndangleGraphEnded, DateTime.Now);
// Report end after undangle
sw.Stop();
RemoveRedundancyEnded();
TaskTimeSpanReport(sw.Elapsed);
NodeCountReport();
// Step 5: Build Contigs
sw = Stopwatch.StartNew();
BuildContigsStarted();
IEnumerable<ISequence> contigSequences = BuildContigs();
sw.Stop();
BuildContigsEnded();
TaskTimeSpanReport(sw.Elapsed);
PadenaAssembly result = new PadenaAssembly();
result.AddContigs(contigSequences);
return result;
}
finally
{
cts.Cancel();
}
}
/// <summary>
/// Validate ParallelDenovoAssembler class properties.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ParallelDenovoAssemblyProperties(string nodeName)
{
// Get values from XML node.
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
string library = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.LibraryName);
string StdDeviation = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.StdDeviation);
string mean = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Mean);
// Get the input reads and build kmers
IEnumerable<ISequence> sequenceReads = null;
using (FastAParser parser = new FastAParser(filePath))
{
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 the contigs
this.KmerLength = int.Parse(kmerLength, (IFormatProvider)null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
this.CreateGraph();
this.UnDangleGraph();
this.RedundantPathsPurger =
new RedundantPathsPurger(int.Parse(kmerLength, (IFormatProvider)null) + 1);
this.RemoveRedundancy();
this.ContigBuilder = new SimplePathContigBuilder();
// Build contigs
IEnumerable<ISequence> contigs = this.BuildContigs();
CloneLibraryInformation cloneLibInfoObj = new CloneLibraryInformation();
cloneLibInfoObj.LibraryName = library;
cloneLibInfoObj.MeanLengthOfInsert = float.Parse(mean, (IFormatProvider)null);
cloneLibInfoObj.StandardDeviationOfInsert = float.Parse(StdDeviation, (IFormatProvider)null);
// Build scaffolds.
CloneLibrary.Instance.AddLibrary(library, float.Parse(mean, (IFormatProvider)null),
float.Parse(StdDeviation, (IFormatProvider)null));
IEnumerable<ISequence> scaffolds = BuildScaffolds(contigs.ToList());
PadenaAssembly denovoAssembly = new PadenaAssembly();
denovoAssembly.AddContigs(contigs);
denovoAssembly.AddScaffolds(scaffolds);
Assert.AreEqual(denovoAssembly.ContigSequences.Count(),
contigs.Count());
Assert.AreEqual(denovoAssembly.Scaffolds.Count(), scaffolds.Count());
Assert.IsNull(denovoAssembly.Documentation);
// Validates the Clone Library for the existing clone
CloneLibraryInformation actualObj = CloneLibrary.Instance.GetLibraryInformation(library);
Assert.IsTrue(actualObj.Equals(cloneLibInfoObj));
ApplicationLog.WriteLine("CloneLibraryInformation Equals() is successfully validated");
}
// Validate ParallelDenovoAssembler properties.
ApplicationLog.WriteLine(
@"Padena BVT : Validated ParallelDenovo Assembly properties");
}