public void SmithWatermanAlignerMultipleAlignments1()
{
IPairwiseSequenceAligner sw = new SmithWatermanAligner
{
SimilarityMatrix = new DiagonalSimilarityMatrix(5, -20),
GapOpenCost = -5
};
ISequence sequence1 = new Sequence(Alphabets.DNA, "AAATTCCCAG");
ISequence sequence2 = new Sequence(Alphabets.DNA, "AAAGCCC");
IList <IPairwiseSequenceAlignment> result = sw.AlignSimple(sequence1, sequence2);
AlignmentHelpers.LogResult(sw, result);
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment(sequence1, sequence2);
// First alignment
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "AAA"),
SecondSequence = new Sequence(Alphabets.DNA, "AAA"),
Consensus = new Sequence(Alphabets.DNA, "AAA"),
Score = 15,
FirstOffset = 0,
SecondOffset = 0
});
// Second alignment
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "CCC"),
SecondSequence = new Sequence(Alphabets.DNA, "CCC"),
Consensus = new Sequence(Alphabets.DNA, "CCC"),
Score = 15,
FirstOffset = 0,
SecondOffset = 1
});
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.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);
}
public void TestDanglingLinksPurger()
{
const int KmerLength = 11;
const int DangleThreshold = 3;
List <ISequence> readSeqs = TestInputs.GetDanglingReads();
SequenceReads.Clear();
this.SetSequenceReads(readSeqs);
this.KmerLength = KmerLength;
DanglingLinksThreshold = DangleThreshold;
DanglingLinksPurger = new DanglingLinksPurger(DangleThreshold);
CreateGraph();
long graphCount = Graph.NodeCount;
long graphEdges = Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
var graphNodes = Graph.GetNodes().Select(n => Graph.GetNodeSequence(n)).ToList();
DanglingLinksThreshold = DangleThreshold;
UnDangleGraph();
long dangleRemovedGraphCount = Graph.NodeCount;
long dangleRemovedGraphEdge = Graph.GetNodes().Select(n => n.ExtensionsCount).Sum();
var dangleRemovedGraphNodes = Graph.GetNodes().Select(n => Graph.GetNodeSequence(n)).ToList();
// Compare the two graphs
Assert.AreEqual(2, graphCount - dangleRemovedGraphCount);
Assert.AreEqual(4, graphEdges - dangleRemovedGraphEdge);
var checkList = graphNodes.Except(dangleRemovedGraphNodes, new SequenceEqualityComparer());
HashSet <string> expected = new HashSet <string> {
"ATCGAACGATG", "TCGAACGATGA"
};
AlignmentHelpers.CompareSequenceLists(expected, checkList);
}
public void ValidatePairwiseAlignedSequenceCustomBreakLength()
{
var referenceSeqs = new List <ISequence>()
{
new Sequence(Alphabets.DNA, "CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGT")
{
ID = "R1"
},
new Sequence(Alphabets.DNA, "CCCCCCCCC")
{
ID = "R2"
},
new Sequence(Alphabets.DNA, "TTTTT")
{
ID = "R3"
}
};
var searchSeqs = new List <ISequence>()
{
new Sequence(Alphabets.DNA, "CATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAA")
{
ID = "Q1"
},
new Sequence(Alphabets.DNA, "CAAAGTCTCTATCAGAATGCAGATGCAGATGTTTTTGTGGGGTCATCAAGATATAGCAAGAAGTTCAAGC")
{
ID = "Q2"
},
new Sequence(Alphabets.DNA, "AAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGC")
{
ID = "Q3"
},
};
var nucmer = new NucmerPairwiseAligner
{
MaximumSeparation = 0,
MinimumScore = 2,
SeparationFactor = 0.12F,
LengthOfMUM = 5,
BreakLength = 2,
ForwardOnly = true,
};
var result = nucmer.Align(referenceSeqs, searchSeqs).Select(a => a as IPairwiseSequenceAlignment).ToList();
// Check if output is not null
Assert.AreNotEqual(null, result);
var expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "AAAGGGA"),
SecondSequence = new Sequence(Alphabets.DNA, "AAAGGGA"),
Consensus = new Sequence(Alphabets.DNA, "AAAGGGA"),
Score = 21,
FirstOffset = 8,
SecondOffset = 0
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "CATTA"),
SecondSequence = new Sequence(Alphabets.DNA, "CATTA"),
Consensus = new Sequence(Alphabets.DNA, "CATTA"),
Score = 15,
FirstOffset = 0,
SecondOffset = 31
});
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "ATGTT"),
SecondSequence = new Sequence(Alphabets.DNA, "ATGTT"),
Consensus = new Sequence(Alphabets.DNA, "ATGTT"),
Score = 15,
FirstOffset = 13,
SecondOffset = 0
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "GAATGC"),
SecondSequence = new Sequence(Alphabets.DNA, "GAATGC"),
Consensus = new Sequence(Alphabets.DNA, "GAATGC"),
Score = 18,
FirstOffset = 0,
SecondOffset = 11
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "TTTTT"),
SecondSequence = new Sequence(Alphabets.DNA, "TTTTT"),
Consensus = new Sequence(Alphabets.DNA, "TTTTT"),
Score = 15,
FirstOffset = 31,
SecondOffset = 0
});
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "CAAAA"),
SecondSequence = new Sequence(Alphabets.DNA, "CAAAA"),
Consensus = new Sequence(Alphabets.DNA, "CAAAA"),
Score = 15,
FirstOffset = 3,
SecondOffset = 0
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "GGATT"),
SecondSequence = new Sequence(Alphabets.DNA, "GGATT"),
Consensus = new Sequence(Alphabets.DNA, "GGATT"),
Score = 15,
FirstOffset = 45,
SecondOffset = 0
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "GCAAA"),
SecondSequence = new Sequence(Alphabets.DNA, "GCAAA"),
Consensus = new Sequence(Alphabets.DNA, "GCAAA"),
Score = 15,
FirstOffset = 0,
SecondOffset = 9
});
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "TTACC"),
SecondSequence = new Sequence(Alphabets.DNA, "TTACC"),
Consensus = new Sequence(Alphabets.DNA, "TTACC"),
Score = 15,
FirstOffset = 22,
SecondOffset = 0
});
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
ApplicationLog.WriteLine("PairwiseAlignedSequence P1: Successfully validated Sequence with Custom Break Length.");
}
public void ValidatePairwiseAlignedSequenceMultipleRefQuery()
{
var referenceSeqs = new List <ISequence>()
{
new Sequence(Alphabets.DNA, "ATGCGCATCCCC")
{
ID = "R1"
},
new Sequence(Alphabets.DNA, "TAGCT")
{
ID = "R2"
}
};
var searchSeqs = new List <ISequence>()
{
new Sequence(Alphabets.DNA, "CCGCGCCCCCTC")
{
ID = "Q1"
},
new Sequence(Alphabets.DNA, "AGCT")
{
ID = "Q2"
}
};
var nucmer = new NucmerPairwiseAligner
{
FixedSeparation = 0,
MinimumScore = 2,
SeparationFactor = -1,
LengthOfMUM = 3,
ForwardOnly = true,
};
IList <IPairwiseSequenceAlignment> result = nucmer.Align(referenceSeqs, searchSeqs).Select(a => a as IPairwiseSequenceAlignment).ToList();
// Check if output is not null
Assert.AreNotEqual(null, result);
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
var alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "GCGCATCCCC"),
SecondSequence = new Sequence(Alphabets.DNA, "GCGC--CCCC"),
Consensus = new Sequence(Alphabets.DNA, "GCGCATCCCC"),
Score = -5,
FirstOffset = 0,
SecondOffset = 0
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "AGCT"),
SecondSequence = new Sequence(Alphabets.DNA, "AGCT"),
Consensus = new Sequence(Alphabets.DNA, "AGCT"),
Score = 12,
FirstOffset = 0,
SecondOffset = 1
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
ApplicationLog.WriteLine("PairwiseAlignedSequence P1: Successfully validated Sequence with Multiple Reference.");
}
/// <summary>
/// Validates PairwiseOverlapAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="isTextFile">Is text file an input.</param>
/// <param name="alignParam">parameter based on which certain validations are done.</param>
/// <param name="alignType">Is the Align type Simple or Align with Gap Extension cost?</param>
private void ValidatePairwiseOverlapAlignment(bool isTextFile, AlignmentParamType alignParam, AlignmentType alignType)
{
ISequence aInput;
ISequence bInput;
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.AlphabetNameNode));
if (isTextFile)
{
// Read the xml file for getting both the files for aligning.
string filePath1 = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.FilePathNode1).TestDir();
string filePath2 = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.FilePathNode2).TestDir();
//Parse the files and get the sequence.
var parser = new FastAParser {
Alphabet = alphabet
};
aInput = parser.Parse(filePath1).ElementAt(0);
bInput = parser.Parse(filePath2).ElementAt(0);
}
else
{
// Read the xml file for getting both the files for aligning.
string origSequence1 = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.SequenceNode1);
string origSequence2 = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.SequenceNode2);
aInput = new Sequence(alphabet, origSequence1);
bInput = new Sequence(alphabet, origSequence2);
}
var aInputString = aInput.ConvertToString();
var bInputString = bInput.ConvertToString();
ApplicationLog.WriteLine($"PairwiseOverlapAligner BVT : First sequence used is '{aInputString}'.");
ApplicationLog.WriteLine($"PairwiseOverlapAligner BVT : Second sequence used is '{bInputString}'.");
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.BlosumFilePathNode).TestDir();
var sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.GapExtensionCostNode), null);
var pairwiseOverlapObj = new PairwiseOverlapAligner();
if (AlignmentParamType.AllParam != alignParam)
{
pairwiseOverlapObj.SimilarityMatrix = sm;
pairwiseOverlapObj.GapOpenCost = gapOpenCost;
}
IList <IPairwiseSequenceAlignment> result = null;
switch (alignParam)
{
case AlignmentParamType.AlignList:
var sequences = new List <ISequence> {
aInput, bInput
};
switch (alignType)
{
case AlignmentType.Align:
result = pairwiseOverlapObj.Align(sequences);
break;
default:
result = pairwiseOverlapObj.AlignSimple(sequences);
break;
}
break;
case AlignmentParamType.AlignTwo:
switch (alignType)
{
case AlignmentType.Align:
result = pairwiseOverlapObj.Align(aInput, bInput);
break;
default:
result = pairwiseOverlapObj.AlignSimple(aInput, bInput);
break;
}
break;
case AlignmentParamType.AllParam:
switch (alignType)
{
case AlignmentType.Align:
result = pairwiseOverlapObj.Align(sm, gapOpenCost,
gapExtensionCost, aInput, bInput);
break;
default:
result = pairwiseOverlapObj.AlignSimple(sm, gapOpenCost, aInput, bInput);
break;
}
break;
default:
break;
}
// Read the xml file for getting both the files for aligning.
string expectedSequence1;
string expectedSequence2;
string expectedScore;
switch (alignType)
{
case AlignmentType.Align:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.ExpectedGapExtensionScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.ExpectedGapExtensionSequence1Node);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.ExpectedGapExtensionSequence2Node);
break;
default:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.ExpectedScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.ExpectedSequenceNode1);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(Constants.PairwiseOverlapAlignAlgorithmNodeName, Constants.ExpectedSequenceNode2);
break;
}
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
var seperators = new[] { ';' };
string[] expectedSequences1 = expectedSequence1.Split(seperators);
string[] expectedSequences2 = expectedSequence2.Split(seperators);
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
for (int i = 0; i < expectedSequences1.Length; i++)
{
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(alphabet, expectedSequences1[i]),
SecondSequence = new Sequence(alphabet, expectedSequences2[i]),
Score = Convert.ToInt32(expectedScore, null)
};
align.PairwiseAlignedSequences.Add(alignedSeq);
}
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner BVT : Final Score '{0}'.", expectedScore));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner BVT : Aligned First Sequence is '{0}'.", expectedSequence1));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner BVT : Aligned Second Sequence is '{0}'.", expectedSequence2));
}
/// <summary>
/// Compare the alignment of mummer and defined alignment
/// </summary>
/// <param name="actualAlignment"></param>
/// <param name="expectedAlignment">expected output</param>
/// <returns>Compare result of alignments</returns>
private static bool CompareAlignment(IList <IPairwiseSequenceAlignment> actualAlignment,
IList <IPairwiseSequenceAlignment> expectedAlignment)
{
return(AlignmentHelpers.CompareAlignment(actualAlignment, expectedAlignment));
}
public void TestNUCmer3MultipleReferencesAndQueries()
{
Sequence referenceSeq = null;
Sequence searchSeq = null;
List <ISequence> referenceSeqs = null;
List <ISequence> searchSeqs = null;
referenceSeqs = new List <ISequence>();
string reference = "ATGCGCATCCCC";
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R1";
referenceSeqs.Add(referenceSeq);
reference = "TAGCT";
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R11";
referenceSeqs.Add(referenceSeq);
searchSeqs = new List <ISequence>();
string search = "CCGCGCCCCCTC";
searchSeq = new Sequence(Alphabets.DNA, search);
searchSeq.ID = "Q1";
searchSeqs.Add(searchSeq);
search = "AGCT";
searchSeq = new Sequence(Alphabets.DNA, search);
searchSeq.ID = "Q11";
searchSeqs.Add(searchSeq);
NucmerPairwiseAligner nucmer = new NucmerPairwiseAligner();
nucmer.FixedSeparation = 0;
nucmer.MinimumScore = 2;
nucmer.SeparationFactor = -1;
nucmer.LengthOfMUM = 3;
nucmer.ForwardOnly = true;
IList <IPairwiseSequenceAlignment> result = nucmer.Align(referenceSeqs, searchSeqs).Select(a => a as IPairwiseSequenceAlignment).ToList();
// 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, "GCGCATCCCC");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "GCGC--CCCC");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "GCGCATCCCC");
alignedSeq.Score = -5;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "AGCT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "AGCT");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "AGCT");
alignedSeq.Score = 12;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 1;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
}
public void TestNUCmer3CustomBreakLength()
{
Sequence referenceSeq = null;
Sequence searchSeq = null;
List <ISequence> referenceSeqs = null;
List <ISequence> searchSeqs = null;
referenceSeqs = new List <ISequence>();
string reference = "CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGT";
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R1";
referenceSeqs.Add(referenceSeq);
reference = "CCCCCCCCC";
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R2";
referenceSeqs.Add(referenceSeq);
reference = "TTTTT";
referenceSeq = new Sequence(Alphabets.DNA, reference);
referenceSeq.ID = "R3";
referenceSeqs.Add(referenceSeq);
searchSeqs = new List <ISequence>();
string search = "CATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAA";
searchSeq = new Sequence(Alphabets.DNA, search);
searchSeq.ID = "Q1";
searchSeqs.Add(searchSeq);
search = "CAAAGTCTCTATCAGAATGCAGATGCAGATGTTTTTGTGGGGTCATCAAGATATAGCAAGAAGTTCAAGC";
searchSeq = new Sequence(Alphabets.DNA, search);
searchSeq.ID = "Q2";
searchSeqs.Add(searchSeq);
search = "AAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGC";
searchSeq = new Sequence(Alphabets.DNA, search);
searchSeq.ID = "Q3";
searchSeqs.Add(searchSeq);
NucmerPairwiseAligner nucmer = new NucmerPairwiseAligner();
nucmer.MaximumSeparation = 0;
nucmer.MinimumScore = 2;
nucmer.SeparationFactor = 0.12F;
nucmer.LengthOfMUM = 5;
nucmer.BreakLength = 2;
nucmer.ForwardOnly = true;
IList <IPairwiseSequenceAlignment> result = nucmer.Align(referenceSeqs, searchSeqs).Select(a => a as IPairwiseSequenceAlignment).ToList();
// Check if output is not null
Assert.AreNotEqual(null, result);
List <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "AAAGGGA");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "AAAGGGA");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "AAAGGGA");
alignedSeq.Score = 21;
alignedSeq.FirstOffset = 8;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "CATTA");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "CATTA");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "CATTA");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 31;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "ATGTT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "ATGTT");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "ATGTT");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 13;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "GAATGC");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "GAATGC");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "GAATGC");
alignedSeq.Score = 18;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 11;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "TTTTT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "TTTTT");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "TTTTT");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 31;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
align = new PairwiseSequenceAlignment();
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "CAAAA");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "CAAAA");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "CAAAA");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 3;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "GGATT");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "GGATT");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "GGATT");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 45;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "GCAAA");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "GCAAA");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "GCAAA");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 9;
align.PairwiseAlignedSequences.Add(alignedSeq);
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "TTACC");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "TTACC");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "TTACC");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 22;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
}