private void ValidateMUMmerAlignGeneralTestCases(string nodeName)
{
// Gets the reference sequence from the configuration file
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format(null, "MUMmer P2 : Successfully validated the File Path '{0}'.", filePath));
var fastaParserObj = new FastAParser();
IEnumerable<ISequence> referenceSeqs = fastaParserObj.Parse(filePath);
ISequence referenceSeq = referenceSeqs.ElementAt(0);
// Gets the reference sequence from the configuration file
string queryFilePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format(null, "MUMmer P2 : Successfully validated the Search File Path '{0}'.", queryFilePath));
var fastaParserObj1 = new FastAParser();
IEnumerable<ISequence> querySeqs = fastaParserObj1.Parse(queryFilePath);
string mumLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode);
var mum = new MUMmerAligner
{
LengthOfMUM = long.Parse(mumLength, null),
StoreMUMs = true,
PairWiseAlgorithm = new NeedlemanWunschAligner(),
GapOpenCost = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null)
};
IList<IPairwiseSequenceAlignment> align = mum.Align(referenceSeq, querySeqs);
// Validate FinalMUMs and MUMs Properties.
Assert.IsNotNull(mum.MUMs);
string expectedScore = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ScoreNodeName);
string[] expectedSequences = utilityObj.xmlUtil.GetTextValues(nodeName, Constants.ExpectedSequencesNode);
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment seqAlign = new PairwiseSequenceAlignment();
var alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(referenceSeq.Alphabet, expectedSequences[0]),
SecondSequence = new Sequence(referenceSeq.Alphabet, expectedSequences[1]),
Score = Convert.ToInt32(expectedScore, null),
FirstOffset = Int32.MinValue,
SecondOffset = Int32.MinValue,
};
seqAlign.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(seqAlign);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(align, expectedOutput));
ApplicationLog.WriteLine("MUMmer P2 : Successfully validated the aligned sequences.");
}
public void TestMUMmerAlignerSingleMum()
{
const string reference = "TTAATTTTAG";
const string search = "AGTTTAGAG";
ISequence referenceSeq = new Sequence(Alphabets.DNA, reference);
ISequence searchSeq = new Sequence(Alphabets.DNA, search);
var searchSeqs = new List<ISequence> {searchSeq};
MUMmerAligner mummer = new MUMmerAligner
{
LengthOfMUM = 3,
PairWiseAlgorithm = new NeedlemanWunschAligner(),
GapExtensionCost = -2
};
IList<IPairwiseSequenceAlignment> result = mummer.Align(referenceSeq, searchSeqs);
// Check if output is not null
Assert.AreNotEqual(null, result);
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "TTAATTTTAG--"),
SecondSequence = new Sequence(Alphabets.DNA, "---AGTTTAGAG"),
Consensus = new Sequence(AmbiguousDnaAlphabet.Instance, "TTAAKTTTAGAG"),
Score = -6,
FirstOffset = 0,
SecondOffset = 3
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
public void TestMUMmerAlignerSingleMumRNA()
{
const string reference = "AUGCUUUUCCCCCCC";
const string search = "UAUAUUUUGG";
MUMmerAligner mummer = new MUMmerAligner
{
LengthOfMUM = 3,
PairWiseAlgorithm = new NeedlemanWunschAligner(),
SimilarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna),
GapOpenCost = -8,
GapExtensionCost = -2
};
ISequence referenceSeq = new Sequence(Alphabets.RNA, reference);
List<ISequence> searchSeqs = new List<ISequence> { new Sequence(Alphabets.RNA, search) };
IList<IPairwiseSequenceAlignment> result = mummer.Align(referenceSeq, searchSeqs);
// Check if output is not null
Assert.AreNotEqual(0, result.Count);
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.RNA, "-AUGCUUUUCCCCCCC"),
SecondSequence = new Sequence(Alphabets.RNA, "UAUA-UUUUGG-----"),
Consensus = new Sequence(AmbiguousRnaAlphabet.Instance, "UAURCUUUUSSCCCCC"),
Score = -14,
FirstOffset = 1,
SecondOffset = 0
});
expectedOutput.Add(align);
AlignmentHelpers.CompareAlignment(result, expectedOutput);
}