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-UUUU-------GG"),
Consensus = new Sequence(AmbiguousRnaAlphabet.Instance, "UAURCUUUUCCCCCCCGG"),
Score = -2,
FirstOffset = 1,
SecondOffset = 0
});
expectedOutput.Add(align);
AlignmentHelpers.CompareAlignment(result, expectedOutput);
}
void ValidateMUMmerAlignGeneralTestCases(string nodeName)
{
ISequence referenceSeq = null;
IEnumerable <ISequence> querySeqs = null;
IEnumerable <ISequence> referenceSeqs = null;
// Gets the reference sequence from the configurtion file
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"MUMmer P2 : Successfully validated the File Path '{0}'.",
filePath));
FastAParser fastaParserObj = new FastAParser(filePath);
referenceSeqs = fastaParserObj.Parse();
referenceSeq = referenceSeqs.ElementAt(0);
// Gets the reference sequence from the configurtion file
string queryFilePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"MUMmer P2 : Successfully validated the Search File Path '{0}'.",
queryFilePath));
FastAParser fastaParserObj1 = new FastAParser(queryFilePath);
querySeqs = fastaParserObj1.Parse();
string mumLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode);
MUMmerAligner mum = new MUMmerAligner();
mum.LengthOfMUM = long.Parse(mumLength, null);
mum.StoreMUMs = true;
mum.PairWiseAlgorithm = new NeedlemanWunschAligner();
mum.GapOpenCost =
int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode),
(IFormatProvider)null);
IList <IPairwiseSequenceAlignment> align = null;
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();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(referenceSeq.Alphabet, expectedSequences[0]);
alignedSeq.SecondSequence = new Sequence(referenceSeq.Alphabet, expectedSequences[1]);
alignedSeq.Score = Convert.ToInt32(expectedScore, (IFormatProvider)null);
seqAlign.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(seqAlign);
Assert.IsTrue(CompareAlignment(align, expectedOutput));
Console.WriteLine("MUMmer P2 : Successfully validated the aligned sequences.");
ApplicationLog.WriteLine("MUMmer P2 : Successfully validated the aligned sequences.");
}