public void PerformMUMmerPerf()
{
Stopwatch _watchObj = new Stopwatch();
IList <IPairwiseSequenceAlignment> alignment = null;
// Get Sequence file path.
string refPath =
Utility._xmlUtil.GetTextValue(Constants.MUMmerNodeName,
Constants.RefFilePathNode);
string queryPath =
Utility._xmlUtil.GetTextValue(Constants.MUMmerNodeName,
Constants.QueryFilePathNode);
string smFilePath =
Utility._xmlUtil.GetTextValue(Constants.MUMmerNodeName,
Constants.SMFilePathNode);
// Create a List for input files.
List <string> lstInputFiles = new List <string>();
lstInputFiles.Add(refPath);
lstInputFiles.Add(queryPath);
FastaParser parserObj = new FastaParser();
IList <ISequence> seqs1 = parserObj.Parse(refPath);
parserObj = new FastaParser();
IList <ISequence> seqs2 = parserObj.Parse(queryPath);
IAlphabet alphabet = Alphabets.DNA;
ISequence originalSequence1 = seqs1[0];
ISequence originalSequence2 = seqs2[0];
ISequence aInput = new Sequence(alphabet, originalSequence1.ToString());
ISequence bInput = new Sequence(alphabet, originalSequence2.ToString());
SimilarityMatrix sm = new SimilarityMatrix(smFilePath);
mummerObj = new MUMmer3();
mummerObj.GapOpenCost = -10;
mummerObj.GapExtensionCost = -10;
mummerObj.SimilarityMatrix = sm;
mummerObj.LengthOfMUM = Int32.Parse(
Utility._xmlUtil.GetTextValue(Constants.MUMmerNodeName,
Constants.MUMLengthNode));
_watchObj.Reset();
_watchObj.Start();
long memoryStart = GC.GetTotalMemory(false);
// Align sequences using MUMmer.
alignment = mummerObj.AlignSimple(aInput, seqs2);
_watchObj.Stop();
long memoryEnd = GC.GetTotalMemory(false);
string memoryUsed = (memoryEnd - memoryStart).ToString();
// Display MUMmer perf test case execution details.
DisplayTestCaseHeader(lstInputFiles, _watchObj, memoryUsed,
"MUMmer");
Console.WriteLine(string.Format(
"MUMmer AlignSimple() method, Alignment Score is : {0}",
alignment[0].PairwiseAlignedSequences[0].Score.ToString()));
// Dispose MUMmer object.
mummerObj = null;
}
/// <summary>
/// Validates the Mummer align method for several test cases for the parameters passed.
/// </summary>
/// <param name="nodeName">Node name to be read from xml</param>
/// <param name="isSeqList">Is MUMmer alignment with List of sequences</param>
static void ValidateMUMmerAlignGeneralTestCases(string nodeName, bool isFilePath,
bool isSeqList)
{
ISequence referenceSeq = null;
ISequence querySeq = null;
IList <ISequence> querySeqs = null;
string referenceSequence = string.Empty;
string querySequence = string.Empty;
IList <IPairwiseSequenceAlignment> align = null;
if (isFilePath)
{
// Gets the reference sequence from the configurtion file
string filePath = Utility._xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format(null,
"MUMmer BVT : Successfully validated the File Path '{0}'.", filePath));
FastaParser parser = new FastaParser();
IList <ISequence> referenceSeqs = parser.Parse(filePath);
referenceSeq = referenceSeqs[0];
referenceSequence = referenceSeq.ToString();
// Gets the reference sequence from the configurtion file
string queryFilePath = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format(null,
"MUMmer BVT : Successfully validated the Search File Path '{0}'.", queryFilePath));
FastaParser queryParser = new FastaParser();
querySeqs = queryParser.Parse(queryFilePath);
querySeq = querySeqs[0];
querySequence = querySeq.ToString();
}
else
{
// Gets the reference sequence from the configurtion file
referenceSequence = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SequenceNode);
string referenceSeqAlphabet = Utility._xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode);
referenceSeq = new Sequence(Utility.GetAlphabet(referenceSeqAlphabet),
referenceSequence);
querySequence = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceNode);
referenceSeqAlphabet = Utility._xmlUtil.GetTextValue(nodeName,
Constants.SearchSequenceAlphabetNode);
querySeq = new Sequence(Utility.GetAlphabet(referenceSeqAlphabet),
querySequence);
querySeqs = new List <ISequence>();
querySeqs.Add(querySeq);
}
string mumLength = Utility._xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode);
MUMmer mum = new MUMmer3();
mum.LengthOfMUM = long.Parse(mumLength, null);
mum.PairWiseAlgorithm = new NeedlemanWunschAligner();
mum.GapOpenCost = int.Parse(Utility._xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode),
(IFormatProvider)null);
if (isSeqList)
{
querySeqs.Add(referenceSeq);
align = mum.Align(querySeqs);
}
else
{
align = mum.AlignSimple(referenceSeq, querySeqs);
}
string expectedScore = Utility._xmlUtil.GetTextValue(nodeName, Constants.ScoreNodeName);
Assert.AreEqual(expectedScore,
align[0].PairwiseAlignedSequences[0].Score.ToString((IFormatProvider)null));
Console.WriteLine(string.Format(null,
"MUMmer BVT : Successfully validated the score for the sequence '{0}' and '{1}'.",
referenceSequence, querySequence));
ApplicationLog.WriteLine(string.Format(null,
"MUMmer BVT : Successfully validated the score for the sequence '{0}' and '{1}'.",
referenceSequence, querySequence));
string[] expectedSequences = Utility._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 = int.Parse(expectedScore);
seqAlign.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(seqAlign);
Assert.IsTrue(CompareAlignment(align, expectedOutput));
Console.WriteLine("MUMmer BVT : Successfully validated the aligned sequences.");
ApplicationLog.WriteLine("MUMmer BVT : Successfully validated the aligned sequences.");
}
