public void ValidateNUCmerGetClusters()
{
// NOTE: Nigel ran this test with the same data through mmummer and mgaps and got the same result.
// Gets the reference sequence from the FastA file
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeSequenceNodeName,
Constants.FilePathNode);
// Gets the query sequence from the FastA file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeSequenceNodeName,
Constants.SearchSequenceFilePathNode);
FastAParser parser = new FastAParser();
IEnumerable <ISequence> seqs1 = parser.Parse(filePath);
IEnumerable <ISequence> seqs2 = parser.Parse(queryFilePath);
var nuc = new Bio.Algorithms.Alignment.NUCmer(seqs1.First())
{
LengthOfMUM = 5,
MinimumScore = 0,
};
var clusts = nuc.GetClusters(seqs2.First());
string clustCount1 = this.utilityObj.xmlUtil.GetTextValue(
Constants.MediumSizeSequenceNodeName, Constants.ClustCount1Node);
Assert.AreEqual(clustCount1, clusts.Count.ToString(CultureInfo.InvariantCulture));
}
/// <summary>
/// Returns the cluster.
/// </summary>
/// <param name="referenceSequence">The Reference sequences.</param>
/// <param name="originalQuerySequences">The Query sequences.</param>
/// <returns>Returns list of clusters.</returns>
private IList<List<IList<Cluster>>> GetCluster(IEnumerable<ISequence> referenceSequence, IEnumerable<ISequence> originalQuerySequences)
{
var clusters = new List<List<IList<Cluster>>>();
var clusters1 = new List<IList<Cluster>>();
IEnumerable<ISequence> querySequences =
Forward ? originalQuerySequences
: (Reverse
? ReverseComplementSequenceList(originalQuerySequences)
: AddReverseComplementsToSequenceList(originalQuerySequences));
_queryCount += querySequences.Count();
foreach (var sequence in referenceSequence)
{
NUCmer nucmer = new NUCmer(sequence)
{
FixedSeparation = FixedSeparation,
BreakLength = BreakLength,
LengthOfMUM = MinMatch,
MaximumSeparation = MaxGap,
MinimumScore = MinCluster,
SeparationFactor = (float) DiagFactor
};
clusters1.AddRange(querySequences.Select(qs => nucmer.GetClusters(qs, !MaxMatch, qs.IsMarkedAsReverseComplement())));
}
clusters.Add(clusters1);
return clusters;
}
public void ValidateNUCmerGetClusters()
{
// NOTE: Nigel ran this test with the same data through mmummer and mgaps and got the same result.
// Gets the reference sequence from the FastA file
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeSequenceNodeName,
Constants.FilePathNode);
// Gets the query sequence from the FastA file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeSequenceNodeName,
Constants.SearchSequenceFilePathNode);
FastAParser parser = new FastAParser();
IEnumerable<ISequence> seqs1 = parser.Parse(filePath);
IEnumerable<ISequence> seqs2 = parser.Parse(queryFilePath);
var nuc = new Bio.Algorithms.Alignment.NUCmer(seqs1.First()) {
LengthOfMUM = 5,
MinimumScore = 0,
};
var clusts = nuc.GetClusters(seqs2.First());
string clustCount1 = this.utilityObj.xmlUtil.GetTextValue(
Constants.MediumSizeSequenceNodeName, Constants.ClustCount1Node);
Assert.AreEqual(clustCount1, clusts.Count.ToString(CultureInfo.InvariantCulture));
}
