/// <summary>
/// Initializes the above defined fields. For each step in assembly
/// we use a separate class for implementation. This method assigns
/// these variables to classes with desired implementation.
/// </summary>
protected void InitializeDefaultGraphModifiers()
{
// Assign uninitialized fields to default values
if (DanglingLinksPurger == null)
{
DanglingLinksPurger = new DanglingLinksPurger();
}
if (RedundantPathsPurger == null)
{
RedundantPathsPurger = new RedundantPathsPurger(RedundantPathLengthThreshold);
}
if (LowCoverageContigPurger == null)
{
LowCoverageContigPurger = new SimplePathContigBuilder();
}
}
/// <summary>
/// Initializes a new instance of the ParallelDeNovoAssembler class.
/// Sets thresholds to default values.
/// Also initializes instances implementing different steps.
/// </summary>
public ParallelDeNovoAssembler()
{
ContigCoverageThreshold = -1;
ErosionThreshold = -1;
AllowErosion = false;
// Initialize to default here.
// Values set to -1 here will be reset based on input sequences.
this.kmerLength = -1;
DanglingLinksThreshold = -1;
RedundantPathLengthThreshold = -1;
this.sequenceReads = new List <ISequence>();
// Contig and scaffold Builder are required modules. Set this to default.
ContigBuilder = new SimplePathContigBuilder();
// Default values for parameters used in building scaffolds.
ScaffoldRedundancy = 2;
Depth = 10;
AllowKmerLengthEstimation = true;
}
/// <summary>
/// Initializes a new instance of the ParallelDeNovoAssembler class.
/// Sets thresholds to default values.
/// Also initializes instances implementing different steps.
/// </summary>
public ParallelDeNovoAssembler()
{
ContigCoverageThreshold = -1;
ErosionThreshold = -1;
AllowErosion = false;
// Initialize to default here.
// Values set to -1 here will be reset based on input sequences.
this.kmerLength = -1;
DanglingLinksThreshold = -1;
RedundantPathLengthThreshold = -1;
this.sequenceReads = new List<ISequence>();
// Contig and scaffold Builder are required modules. Set this to default.
ContigBuilder = new SimplePathContigBuilder();
// Default values for parameters used in building scaffolds.
ScaffoldRedundancy = 2;
Depth = 10;
AllowKmerLengthEstimation = true;
}
/// <summary>
/// Validate the SimpleContigBuilder Build() method using step 4 graph
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
/// <param name="isChromosomeRC">Is Chromosome RC?</param>
internal void ValidateSimpleContigBuilderBuild(string nodeName, bool isChromosomeRC)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.KmerLengthNode);
string expectedContigsString = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ContigsNode);
string[] expectedContigs = expectedContigsString.Split(',');
string expectedContigsCount = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ContigsCount);
// 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 from graph in step4
this.KmerLength = int.Parse(kmerLength, (IFormatProvider)null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
this.CreateGraph();
DeBruijnGraph graph = this.Graph;
this.UnDangleGraph();
this.RemoveRedundancy();
// Validate the SimpleContigBuilder.Build() by passing graph
SimplePathContigBuilder builder = new SimplePathContigBuilder();
IList<ISequence> contigs = builder.Build(graph).ToList();
if (isChromosomeRC)
{
Assert.AreEqual(expectedContigsCount,
contigs.Count.ToString((IFormatProvider)null));
}
else
{
// Validate the contigs
for (int index = 0; index < contigs.Count; index++)
{
Assert.IsTrue(expectedContigs.Contains(new string(contigs[index].Select(a => (char)a).ToArray())));
}
}
}
ApplicationLog.WriteLine(@"Padena P1 :SimpleContigBuilder.BuildContigs() validation for Padena step5 completed successfully");
}
/// <summary>
/// Initializes the above defined fields. For each step in assembly
/// we use a separate class for implementation. This method assigns
/// these variables to classes with desired implementation.
/// </summary>
protected void InitializeDefaultGraphModifiers()
{
// Assign uninitialized fields to default values
if (DanglingLinksPurger == null)
{
DanglingLinksPurger = new DanglingLinksPurger();
}
if (RedundantPathsPurger == null)
{
RedundantPathsPurger = new RedundantPathsPurger(RedundantPathLengthThreshold);
}
if (LowCoverageContigPurger == null)
{
LowCoverageContigPurger = new SimplePathContigBuilder();
}
}
/// <summary>
/// Validate the SimpleContigBuilder Build() method using step 4 graph
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateSimpleContigBuilderBuild(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
string expectedContigsString =
utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ContigsNode);
string[] expectedContigs = expectedContigsString.Split(',');
// Get the input reads and build kmers
IEnumerable<ISequence> sequenceReads = null;
FastAParser parser = new FastAParser();
parser.Open( filePath.Replace("\\", System.IO.Path.DirectorySeparatorChar.ToString()));
sequenceReads = parser.Parse().ToList();
parser.Close();
// Build kmers from step1,graph in step2
// Remove the dangling links from graph in step3
// Remove bubbles from graph in step4
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();
// Validate the SimpleContigBuilder.Build() by passing graph
SimplePathContigBuilder builder = new SimplePathContigBuilder();
IEnumerable<ISequence> contigs = builder.Build(this.Graph);
// Validate the contigs
for (int index = 0; index < contigs.Count(); index++)
{
Assert.IsTrue(expectedContigs.Contains(
new string(contigs.ToList()[index].Select(a => (char)a).ToArray())));
}
ApplicationLog.WriteLine(
@"Padena BVT :SimpleContigBuilder.BuildContigs() validation for
Padena step5 completed successfully");
}