/// <summary>
/// Validate building Kmer using sequence and kmer length.
/// </summary>
/// <param name="nodeName">Name of the xml node for different test cases</param>
/// <param name="IsKmerBuilder">True if validating kmerbuilder or else false.</param>
private void ValidateKmer(string nodeName, bool IsKmerBuilder)
{
// Get the parameters from Xml
string Sequence = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string expectedKmerCount = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmrSeqCountNode);
string expectedKmerSeq = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerSequenceNode);
string expectedKmerPos = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.PositionsNode);
// Create a Kmer Sequence.
ISequence seq = new Sequence(Alphabets.DNA, Sequence);
KmersOfSequence kmerSeq;
if (IsKmerBuilder)
{
// Build Kmer.
var kmerBuilder = new SequenceToKmerBuilder();
KmersOfSequence kmerList = kmerBuilder.Build(seq, 2);
// Validate builder kmer.
Assert.AreEqual(expectedKmerCount, kmerList.Kmers.Count.ToString((IFormatProvider) null));
Assert.AreEqual(expectedKmerSeq, new String(kmerList.BaseSequence.Select(a => (char) a).ToArray()));
Assert.AreEqual(expectedKmerPos, kmerList.Length.ToString((IFormatProvider) null));
}
else
{
kmerSeq = new KmersOfSequence(seq, 2);
// Validate Kmer Seq.
Assert.AreEqual(expectedKmerSeq, new String(kmerSeq.BaseSequence.Select(a => (char) a).ToArray()));
Assert.AreEqual(expectedKmerPos, kmerSeq.Length.ToString((IFormatProvider) null));
}
}
/// <summary>
/// Validate KmersOfSequence ToSequences() method which returns kmers sequence
/// using its positions
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateKmersOfSequenceToSequences(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
string kmerOutputFile = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.KmersOutputFileNode);
// Get the input reads and build kmers
IEnumerable<ISequence> sequenceReads = null;
using (FastAParser parser = new FastAParser(filePath))
{
sequenceReads = parser.Parse();
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));
// Get the array of kmer sequence using ToSequence()
int index = 0;
// Validate the generated kmer sequence with the expected output
using (StreamReader kmerFile = new StreamReader(kmerOutputFile))
{
string line = string.Empty;
List<string[]> fileContent = new List<string[]>();
while (null != (line = kmerFile.ReadLine()))
{
fileContent.Add(line.Split(','));
}
foreach (ISequence sequenceRead in sequenceReads)
{
int count = 0;
KmersOfSequence kmerSequence = new KmersOfSequence(sequenceRead,
int.Parse(kmerLength, (IFormatProvider)null), lstKmers[index].Kmers);
IEnumerable<ISequence> sequences = kmerSequence.KmersToSequences();
foreach (ISequence sequence in sequences)
{
string aab = new string(sequence.Select(a => (char)a).ToArray());
Assert.AreEqual(fileContent[index][count], aab);
count++;
}
index++;
}
}
}
ApplicationLog.WriteLine(@"Padena P1 : KmersOfSequence ToSequences() method validation completed successfully");
}
/// <summary>
/// Validate KmersOfSequence ctor by passing base sequence reads, kmer length and
/// built kmers
/// </summary>
/// <param name="nodeName">xml node name.</param>
internal void ValidateKmersOfSequenceCtorWithBuildKmers(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.KmerLengthNode);
// Get the input reads
IEnumerable<ISequence> sequenceReads = null;
using (FastAParser parser = new FastAParser(filePath))
{
sequenceReads = parser.Parse();
SequenceToKmerBuilder builder = new SequenceToKmerBuilder();
IList<KmersOfSequence> lstKmers = new List<KmersOfSequence>();
// Validate KmersOfSequence ctor using build kmers
foreach (ISequence sequence in sequenceReads)
{
KmersOfSequence kmer = builder.Build(sequence, int.Parse(kmerLength, (IFormatProvider)null));
KmersOfSequence kmerSequence = new KmersOfSequence(sequence,
int.Parse(kmerLength, (IFormatProvider)null), kmer.Kmers);
lstKmers.Add(kmerSequence);
}
ValidateKmersList(lstKmers, sequenceReads.ToList(), nodeName);
}
ApplicationLog.WriteLine(@"Padena P1 : KmersOfSequence ctor with build kmers method validation completed successfully");
}
/// <summary>
/// Validate KmersOfSequence ctor by passing base sequence reads, kmer length and
/// built kmers and validate its properties.
/// </summary>
/// <param name="nodeName">xml node name.</param>
internal void ValidateKmersOfSequenceCtorProperties(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string kmerLength = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.KmerLengthNode);
string expectedSeq = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.BaseSequenceNode);
string expectedKmers = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.KmersCountNode);
// Get the input reads
IEnumerable<ISequence> sequenceReads = null;
using (FastAParser parser = new FastAParser(filePath))
{
sequenceReads = parser.Parse();
SequenceToKmerBuilder builder = new SequenceToKmerBuilder();
KmersOfSequence kmer = builder.Build(sequenceReads.ToList()[0],
int.Parse(kmerLength, (IFormatProvider)null));
KmersOfSequence kmerSequence = new KmersOfSequence(sequenceReads.ToList()[0],
int.Parse(kmerLength, (IFormatProvider)null), kmer.Kmers);
// Validate KmerOfSequence properties.
Assert.AreEqual(expectedSeq, new string(kmerSequence.BaseSequence.Select(a => (char)a).ToArray()));
Assert.AreEqual(expectedKmers, kmerSequence.Kmers.Count.ToString((IFormatProvider)null));
}
ApplicationLog.WriteLine(@"Padena P1 : KmersOfSequence ctor with build kmers method validation completed successfully");
}
/// <summary>
/// Validate kmersofsequence ctor() by passing kmers, kmer length and input reads
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidateKmersOfSequenceCtor(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;
using (FastAParser parser = new FastAParser(filePath))
{
sequenceReads = parser.Parse();
// Validate the KmersOfSequence ctor by passing build kmers
// Validate the kmersof sequence instance using GetKmerSequence()
this.KmerLength = int.Parse(kmerLength, (IFormatProvider)null);
this.SequenceReads.Clear();
this.SetSequenceReads(sequenceReads.ToList());
IEnumerable<KmersOfSequence> lstKmers =
(new SequenceToKmerBuilder()).Build(this.SequenceReads, this.KmerLength);
IList<KmersOfSequence> newKmersList = new List<KmersOfSequence>();
int index = 0;
foreach (KmersOfSequence kmer in lstKmers)
{
KmersOfSequence newkmer = new KmersOfSequence(sequenceReads.ElementAt(index),
int.Parse(kmerLength, (IFormatProvider)null), kmer.Kmers);
newKmersList.Add(newkmer);
index++;
}
ValidateKmersList(newKmersList, new List<ISequence>(sequenceReads), nodeName);
}
ApplicationLog.WriteLine(
@"Padena BVT : KmersOfSequence ctor validation for
Padena step1 completed successfully");
}