private void ValidateMUMmerAlignGeneralTestCases(string nodeName)
{
// Gets the reference sequence from the configuration file
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode).TestDir();
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).TestDir();
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 TestMUMmerAlignerSingleMumRNA()
{
string reference = "AUGCUUUUCCCCCCC";
string search = "UAUAUUUUGG";
Sequence referenceSeq = null;
Sequence searchSeq = null;
List <ISequence> searchSeqs = null;
referenceSeq = new Sequence(Alphabets.RNA, reference);
searchSeq = new Sequence(Alphabets.RNA, search);
searchSeqs = new List <ISequence>();
searchSeqs.Add(searchSeq);
MUMmerAligner mummer = new MUMmerAligner();
mummer.LengthOfMUM = 3;
mummer.PairWiseAlgorithm = new NeedlemanWunschAligner();
mummer.SimilarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna);
mummer.GapOpenCost = -8;
mummer.GapExtensionCost = -2;
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();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.RNA, "-AUGCUUUUCCCCCCC");
alignedSeq.SecondSequence = new Sequence(Alphabets.RNA, "UAU-AUUUU-----GG");
alignedSeq.Consensus = new Sequence(AmbiguousRnaAlphabet.Instance, "UAUGMUUUUCCCCCSS");
alignedSeq.Score = -14;
alignedSeq.FirstOffset = 1;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
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 = 5,
FirstOffset = 0,
SecondOffset = 3
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
public void TestMUMmerAlignerMultipleMum()
{
string reference = "ATGCGCATCCCCTT";
string search = "GCGCCCCCTA";
Sequence referenceSeq = null;
Sequence searchSeq = null;
referenceSeq = new Sequence(Alphabets.DNA, reference);
searchSeq = new Sequence(Alphabets.DNA, search);
List <ISequence> searchSeqs = new List <ISequence>();
searchSeqs.Add(searchSeq);
MUMmerAligner mummer = new MUMmerAligner();
mummer.LengthOfMUM = 4;
mummer.PairWiseAlgorithm = new NeedlemanWunschAligner();
IList <IPairwiseSequenceAlignment> result = mummer.AlignSimple(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();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "ATGCGCATCCCCTT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "--GCGC--CCCCTA");
alignedSeq.Consensus = new Sequence(AmbiguousDnaAlphabet.Instance, "ATGCGCATCCCCTW");
alignedSeq.Score = -11;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 2;
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-UUUU-------GG"),
Consensus = new Sequence(AmbiguousRnaAlphabet.Instance, "UAURCUUUUCCCCCCCGG"),
Score = -2,
FirstOffset = 1,
SecondOffset = 0
});
expectedOutput.Add(align);
AlignmentHelpers.CompareAlignment(result, expectedOutput);
}
/// <summary>
/// Initializes static members of the SequenceAligners class.
/// Static constructor
/// </summary>
static SequenceAligners()
{
NUCmer = new NucmerPairwiseAligner();
MUMmer = new MUMmerAligner();
NeedlemanWunsch = new NeedlemanWunschAligner();
SmithWaterman = new SmithWatermanAligner();
var knownAligners = new List <ISequenceAligner> {
SmithWaterman, NeedlemanWunsch, MUMmer, NUCmer
};
// Get the registered aligners
IEnumerable <ISequenceAligner> registeredAligners = GetAligners();
if (null != registeredAligners)
{
knownAligners.AddRange(registeredAligners
.Where(aligner => aligner != null &&
knownAligners.All(sa => string.Compare(sa.Name, aligner.Name, StringComparison.OrdinalIgnoreCase) != 0)));
}
All = knownAligners;
}
public void TestMUMmer3MultipleMumWithCustomMatrix()
{
string reference = "ATGCGCATCCCCTT";
string search = "GCGCCCCCTA";
Sequence referenceSeq = null;
Sequence searchSeq = null;
referenceSeq = new Sequence(Alphabets.DNA, reference);
searchSeq = new Sequence(Alphabets.DNA, search);
List <ISequence> searchSeqs = new List <ISequence>();
searchSeqs.Add(searchSeq);
int[,] customMatrix = new int[256, 256];
customMatrix[(byte)'A', (byte)'A'] = 3;
customMatrix[(byte)'A', (byte)'T'] = -2;
customMatrix[(byte)'A', (byte)'G'] = -2;
customMatrix[(byte)'A', (byte)'c'] = -2;
customMatrix[(byte)'G', (byte)'G'] = 3;
customMatrix[(byte)'G', (byte)'A'] = -2;
customMatrix[(byte)'G', (byte)'T'] = -2;
customMatrix[(byte)'G', (byte)'C'] = -2;
customMatrix[(byte)'T', (byte)'T'] = 3;
customMatrix[(byte)'T', (byte)'A'] = -2;
customMatrix[(byte)'T', (byte)'G'] = -2;
customMatrix[(byte)'T', (byte)'C'] = -2;
customMatrix[(byte)'C', (byte)'C'] = 3;
customMatrix[(byte)'C', (byte)'T'] = -2;
customMatrix[(byte)'C', (byte)'A'] = -2;
customMatrix[(byte)'C', (byte)'G'] = -2;
DiagonalSimilarityMatrix matrix = new DiagonalSimilarityMatrix(3, -2);
int gapOpenCost = -6;
MUMmerAligner mummer = new MUMmerAligner();
mummer.LengthOfMUM = 4;
mummer.PairWiseAlgorithm = new NeedlemanWunschAligner();
mummer.SimilarityMatrix = matrix;
mummer.GapOpenCost = gapOpenCost;
mummer.GapExtensionCost = -2;
IList <IPairwiseSequenceAlignment> result = mummer.AlignSimple(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();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "ATGCGCATCCCCTT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "--GCGC--CCCCTA");
alignedSeq.Consensus = new Sequence(AmbiguousDnaAlphabet.Instance, "ATGCGCATCCCCTW");
alignedSeq.Score = 1;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 2;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}