/// <summary>
/// Validate the DeBruijnNode ctor by passing the kmer and validating
/// the node object.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateDeBruijnNodeCtor(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.KmerLengthNode);
string nodeExtensionsCount = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.NodeExtensionsCountNode);
string kmersCount = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.KmersCountNode);
string leftNodeExtensionCount = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.LeftNodeExtensionsCountNode);
string rightNodeExtensionCount = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.RightNodeExtensionsCountNode);
// Get the input reads and build kmers
IEnumerable<ISequence> sequenceReads = null;
using (FastAParser parser = new FastAParser(filePath))
{
sequenceReads = parser.Parse();
// Build the kmers using this
this.KmerLength = int.Parse(kmerLength, (IFormatProvider)null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
IList<KmersOfSequence> lstKmers = new List<KmersOfSequence>(
(new SequenceToKmerBuilder()).Build(this.SequenceReads, this.KmerLength));
// Validate the node creation
// Create node and add left node.
ISequence seq = this.SequenceReads.First();
KmerData32 kmerData = new KmerData32();
kmerData.SetKmerData(seq, lstKmers[0].Kmers.First().Positions[0], this.KmerLength);
DeBruijnNode node = new DeBruijnNode(kmerData, 1);
kmerData = new KmerData32();
kmerData.SetKmerData(seq, lstKmers[1].Kmers.First().Positions[0], this.KmerLength);
DeBruijnNode leftnode = new DeBruijnNode(kmerData, 1);
DeBruijnNode rightnode = new DeBruijnNode(kmerData, 1);
node.SetExtensionNode(false, true, leftnode);
node.SetExtensionNode(true, true, rightnode);
// Validate DeBruijnNode class properties.
Assert.AreEqual(nodeExtensionsCount, node.ExtensionsCount.ToString((IFormatProvider)null));
Assert.AreEqual(kmersCount, node.KmerCount.ToString((IFormatProvider)null));
Assert.AreEqual(leftNodeExtensionCount, node.LeftExtensionNodesCount.ToString((IFormatProvider)null));
Assert.AreEqual(rightNodeExtensionCount, node.RightExtensionNodesCount.ToString((IFormatProvider)null));
Assert.AreEqual(leftNodeExtensionCount, node.LeftExtensionNodesCount.ToString((IFormatProvider)null));
Assert.AreEqual(rightNodeExtensionCount, node.RightExtensionNodesCount.ToString((IFormatProvider)null));
}
ApplicationLog.WriteLine("Padena P1 : DeBruijnNode ctor() validation for Padena step2 completed successfully");
}
/// <summary>
/// Validate AddRightEndExtension() method of DeBruijnNode
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateDeBruijnNodeAddRightExtension(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
// Get the input reads and build kmers
using (FastAParser parser = new FastAParser(filePath))
{
IEnumerable<ISequence> sequenceReads = parser.Parse();
// Build kmers from step1
this.KmerLength = int.Parse(kmerLength, null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
IList<KmersOfSequence> lstKmers = new List<KmersOfSequence>((new SequenceToKmerBuilder()).Build(this.SequenceReads, this.KmerLength));
// Validate the node creation
// Create node and add left node.
ISequence seq = this.SequenceReads.First();
KmerData32 kmerData = new KmerData32();
kmerData.SetKmerData(seq, lstKmers[0].Kmers.First().Positions[0], this.KmerLength);
DeBruijnNode node = new DeBruijnNode(kmerData, 1);
kmerData = new KmerData32();
kmerData.SetKmerData(seq, lstKmers[1].Kmers.First().Positions[0], this.KmerLength);
DeBruijnNode rightNode = new DeBruijnNode(kmerData, 1);
node.SetExtensionNode(true, true, rightNode);
Assert.AreEqual(lstKmers[1].Kmers.First().Count, node.RightExtensionNodesCount);
}
ApplicationLog.WriteLine(@"Padena BVT :DeBruijnNode AddRightExtension() validation for Padena step2 completed successfully");
}
/// <summary>
/// Validate RemoveExtension() method of DeBruijnNode
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateDeBruijnNodeRemoveExtension(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.KmerLengthNode);
// Get the input reads and build kmers
IEnumerable<ISequence> sequenceReads = null;
FastAParser parser = new FastAParser();
parser.Open(filePath);
sequenceReads = parser.Parse().ToList();
parser.Close ();
// Build kmers from step1
this.KmerLength = int.Parse(kmerLength, (IFormatProvider)null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
IList<KmersOfSequence> lstKmers = new List<KmersOfSequence>(
(new SequenceToKmerBuilder()).Build(this.SequenceReads, this.KmerLength));
// Validate the node creation
// Create node and add left node.
ISequence seq = this.SequenceReads.First();
KmerData32 kmerData = new KmerData32();
kmerData.SetKmerData(seq, lstKmers[0].Kmers.First().Positions[0], this.KmerLength);
DeBruijnNode node = new DeBruijnNode(kmerData, 1);
kmerData = new KmerData32();
kmerData.SetKmerData(seq, lstKmers[1].Kmers.First().Positions[0], this.KmerLength);
DeBruijnNode leftnode = new DeBruijnNode(kmerData, 1);
DeBruijnNode rightnode = new DeBruijnNode(kmerData, 1);
node.SetExtensionNode(false, true, leftnode);
node.SetExtensionNode(true, true, rightnode);
// Validates count before removing right and left extension nodes.
Assert.AreEqual(lstKmers[1].Kmers.First().Count,
node.RightExtensionNodesCount);
Assert.AreEqual(1, node.RightExtensionNodesCount);
Assert.AreEqual(1, node.LeftExtensionNodesCount);
// Remove right and left extension nodes.
node.RemoveExtensionThreadSafe(rightnode);
node.RemoveExtensionThreadSafe(leftnode);
// Validate node after removing right and left extensions.
Assert.AreEqual(0, node.RightExtensionNodesCount);
Assert.AreEqual(0, node.LeftExtensionNodesCount);
ApplicationLog.WriteLine(@"Padena P1 :DeBruijnNode AddRightExtension() validation for Padena step2 completed successfully");
}
/// <summary>
/// Validate the DeBruijnNode ctor by passing the kmer and validating
/// the node object.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateDeBruijnNodeCtor(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
// Get the input reads and build kmers
FastAParser parser = new FastAParser();
parser.Open( filePath.Replace("\\", System.IO.Path.DirectorySeparatorChar.ToString()));
IEnumerable<ISequence> sequenceReads = parser.Parse().ToList();
parser.Close ();
// Build the kmers using assembler
this.KmerLength = int.Parse(kmerLength, null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
IList<KmersOfSequence> lstKmers = new List<KmersOfSequence>((new SequenceToKmerBuilder()).Build(this.SequenceReads, this.KmerLength));
// Validate the node creation
// Create node and add left node.
ISequence seq = this.SequenceReads.First();
KmerData32 kmerData = new KmerData32();
kmerData.SetKmerData(seq, lstKmers[0].Kmers.First().Positions[0], this.KmerLength);
DeBruijnNode node = new DeBruijnNode(kmerData, 1);
kmerData = new KmerData32();
kmerData.SetKmerData(seq, lstKmers[1].Kmers.First().Positions[0], this.KmerLength);
DeBruijnNode leftnode = new DeBruijnNode(kmerData, 1);
node.SetExtensionNode(false, true, leftnode);
Assert.AreEqual(lstKmers[1].Kmers.First().Count, node.LeftExtensionNodesCount);
ApplicationLog.WriteLine(
"Padena BVT : DeBruijnNode ctor() validation for Padena step2 completed successfully");
}
