public void SmithWatermanProteinSeqAffineGap()
{
IPairwiseSequenceAligner sw = new SmithWatermanAligner
{
SimilarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62),
GapOpenCost = -8,
GapExtensionCost = -1,
};
ISequence sequence1 = new Sequence(Alphabets.Protein, "HEAGAWGHEE");
ISequence sequence2 = new Sequence(Alphabets.Protein, "PAWHEAE");
IList<IPairwiseSequenceAlignment> result = sw.Align(sequence1, sequence2);
AlignmentHelpers.LogResult(sw, result);
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.Protein, "AWGHE"),
SecondSequence = new Sequence(Alphabets.Protein, "AW-HE"),
Consensus = new Sequence(Alphabets.AmbiguousProtein, "AWGHE"),
Score = 20,
FirstOffset = 0,
SecondOffset = 3
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
}
public void PairwiseOverlapProteinSeqSimpleGap()
{
string sequenceString1 = "HEAGAWGHEE";
string sequenceString2 = "PAWHEAE";
Sequence sequence1 = new Sequence(Alphabets.Protein, sequenceString1);
Sequence sequence2 = new Sequence(Alphabets.Protein, sequenceString2);
SimilarityMatrix sm = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
int gapPenalty = -8;
PairwiseOverlapAligner overlap = new PairwiseOverlapAligner();
overlap.SimilarityMatrix = sm;
overlap.GapOpenCost = gapPenalty;
IList<IPairwiseSequenceAlignment> result = overlap.AlignSimple(sequence1, sequence2);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"{0}, Simple; Matrix {1}; GapOpenCost {2}", overlap.Name, overlap.SimilarityMatrix.Name, overlap.GapOpenCost));
foreach (IPairwiseSequenceAlignment sequenceResult in result)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"score {0}", sequenceResult.PairwiseAlignedSequences[0].Score));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 0 {0}", sequenceResult.FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 1 {0}", sequenceResult.SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 0 {0}", sequenceResult.PairwiseAlignedSequences[0].FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 1 {0}", sequenceResult.PairwiseAlignedSequences[0].SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"consesus {0}", sequenceResult.PairwiseAlignedSequences[0].Consensus.ToString()));
}
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.Protein, "GAWGHEE");
alignedSeq.SecondSequence = new Sequence(Alphabets.Protein, "PAW-HEA");
alignedSeq.Consensus = new Sequence(Alphabets.AmbiguousProtein, "XAWGHEX");
alignedSeq.Score = 25;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 3;
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 = -6,
FirstOffset = 0,
SecondOffset = 3
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
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 NeedlemanWunschProteinSeqAffineGap()
{
IPairwiseSequenceAligner nw = new NeedlemanWunschAligner
{
SimilarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62),
GapOpenCost = -8,
GapExtensionCost = -1
};
ISequence sequence1 = new Sequence(Alphabets.Protein, "HEAGAWGHEE");
ISequence sequence2 = new Sequence(Alphabets.Protein, "PAWHEAE");
IList<IPairwiseSequenceAlignment> result = nw.Align(sequence1, sequence2);
AlignmentHelpers.LogResult(nw, result);
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.Protein, "HEAGAWGHE-E"),
SecondSequence = new Sequence(Alphabets.Protein, "P---AW-HEAE"),
Consensus = new Sequence(AmbiguousProteinAlphabet.Instance, "XEAGAWGHEAE"),
Score = 5,
FirstOffset = 0,
SecondOffset = 0
});
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput));
}
/// <summary>
/// Given two byte arrays representing a pairwise alignment, shift them so
/// that all deletions start as early as possible. For example:
///
/// <code>
/// TTTTAAAATTTT -> Converts to -> TTTTAAAATTTT
/// TTTTAA--TTTT TTTT--AATTTT
/// </code>
///
/// This function takes a IPairwiseSequenceAlignment and assumes that the first sequence is the reference and second
/// sequence is the query. It returns a new Pairwise sequence alignment with all of the indels left aligned as well as a list of variants.
/// </summary>
/// <param name="aln">Aln. The second sequence should be of type QualitativeSequence or Sequence</param>
/// <param name="callVariants">callVariants. If true, it will call variants, otherwise the second half of tuple will be null. </param>
public static Tuple<IPairwiseSequenceAlignment, List<Variant>> LeftAlignIndelsAndCallVariants(IPairwiseSequenceAlignment aln, bool callVariants = true) {
if (aln == null) {
throw new NullReferenceException ("aln");
}
if (aln.PairwiseAlignedSequences == null || aln.PairwiseAlignedSequences.Count != 1) {
throw new ArgumentException ("The pairwise aligned sequence should only have one alignment");
}
var frstAln = aln.PairwiseAlignedSequences.First ();
var seq1 = frstAln.FirstSequence;
var seq2 = frstAln.SecondSequence;
if (seq1 == null) {
throw new NullReferenceException ("seq1");
} else if (seq2 == null) {
throw new NullReferenceException ("seq2");
}
//TODO: Might implement an ambiguity check later.
#if FALSE
if (seq1.Alphabet.HasAmbiguity || seq2.Alphabet.HasAmbiguity) {
throw new ArgumentException ("Cannot left align sequences with ambiguous symbols.");
}
#endif
// Note we have to copy unless we can guarantee the array will not be mutated.
byte[] refseq = seq1.ToArray ();
ISequence newQuery;
List<Variant> variants = null;
// Call variants for a qualitative sequence
if (seq2 is QualitativeSequence) {
var qs = seq2 as QualitativeSequence;
var query = Enumerable.Zip (qs, qs.GetQualityScores (), (bp, qv) => new BPandQV (bp, (byte)qv, false)).ToArray ();
AlignmentUtils.LeftAlignIndels (refseq, query);
AlignmentUtils.VerifyNoGapsOnEnds (refseq, query);
if (callVariants) {
variants = VariantCaller.CallVariants (refseq, query, seq2.IsMarkedAsReverseComplement());
}
var newQueryQS = new QualitativeSequence (qs.Alphabet,
qs.FormatType,
query.Select (z => z.BP).ToArray (),
query.Select (p => p.QV).ToArray (),
false);
newQueryQS.Metadata = seq2.Metadata;
newQuery = newQueryQS;
} else if (seq2 is Sequence) { // For a sequence with no QV values.
var qs = seq2 as Sequence;
var query = qs.Select (v => new BPandQV (v, 0, false)).ToArray();
AlignmentUtils.LeftAlignIndels (refseq, query);
AlignmentUtils.VerifyNoGapsOnEnds (refseq, query);
// ISequence does not have a setable metadata
var newQueryS = new Sequence(qs.Alphabet, query.Select(z=>z.BP).ToArray(), false);
newQueryS.Metadata = seq2.Metadata;
if (callVariants) {
variants = VariantCaller.CallVariants (refseq, query, seq2.IsMarkedAsReverseComplement());
}
newQuery = newQueryS;
} else {
throw new ArgumentException ("Can only left align indels if the query sequence is of type Sequence or QualitativeSequence.");
}
if (aln.FirstSequence != null && aln.FirstSequence.ID != null) {
foreach (var v in variants) {
v.RefName = aln.FirstSequence.ID;
}
}
var newRef = new Sequence (seq1.Alphabet, refseq, false);
newRef.ID = seq1.ID;
newRef.Metadata = seq1.Metadata;
newQuery.ID = seq2.ID;
var newaln = new PairwiseSequenceAlignment (aln.FirstSequence, aln.SecondSequence);
var pas = new PairwiseAlignedSequence ();
pas.FirstSequence = newRef;
pas.SecondSequence = newQuery;
newaln.Add (pas);
return new Tuple<IPairwiseSequenceAlignment, List<Variant>> (newaln, variants);
}
/// <summary>
/// This method is considered as main execute method which defines the
/// step by step algorithm. Derived class flows the defined flow by this
/// method. Store generated MUMs in properties MUMs, SortedMUMs.
/// Alignment first finds MUMs for all the query sequence, and then
/// runs pairwise algorithm on gaps to produce alignments.
/// </summary>
/// <param name="referenceSequence">Reference sequence.</param>
/// <param name="querySequenceList">List of input sequences.</param>
/// <returns>A list of sequence alignments.</returns>
private IList<IPairwiseSequenceAlignment> AlignmentWithAccumulatedMUMs(
ISequence referenceSequence,
IEnumerable<ISequence> querySequenceList)
{
// Get MUMs
this.mums = new Dictionary<ISequence, IEnumerable<Match>>();
IList<IPairwiseSequenceAlignment> results = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment alignment = null;
IEnumerable<Match> mum;
if (this.Validate(referenceSequence, querySequenceList))
{
// Safety check for public methods to ensure that null
// inputs are handled.
if (referenceSequence == null || querySequenceList == null)
{
return null;
}
Sequence seq = referenceSequence as Sequence;
if (seq == null)
{
throw new ArgumentException(Properties.Resource.OnlySequenceClassSupported);
}
MUMmer mummer = new MUMmer(seq);
mummer.LengthOfMUM = this.LengthOfMUM;
mummer.NoAmbiguity = this.AmbigiousMatchesAllowed;
foreach (ISequence sequence in querySequenceList)
{
if (sequence.Equals(referenceSequence))
{
continue;
}
alignment = new PairwiseSequenceAlignment(referenceSequence, sequence);
// Step2 : streaming process is performed with the query sequence
if (this.MaximumMatchEnabled)
{
mum = mummer.GetMatches(sequence);
}
else
{
mum = mummer.GetMatchesUniqueInReference(sequence);
}
this.mums.Add(sequence, mum);
// Step3(a) : sorted mum list based on reference sequence
LongestIncreasingSubsequence lis = new LongestIncreasingSubsequence();
IList<Match> sortedMumList = lis.SortMum(GetMumsForLIS(mum));
if (sortedMumList.Count > 0)
{
// Step3(b) : LIS using greedy cover algorithm
IList<Match> finalMumList = lis.GetLongestSequence(sortedMumList);
if (finalMumList.Count > 0)
{
// Step 4 : get all the gaps in each sequence and call
// pairwise alignment
alignment.PairwiseAlignedSequences.Add(
this.ProcessGaps(referenceSequence, sequence, finalMumList));
}
results.Add(alignment);
}
else
{
IList<IPairwiseSequenceAlignment> sequenceAlignment = this.RunPairWise(
referenceSequence,
sequence);
foreach (IPairwiseSequenceAlignment pairwiseAlignment in sequenceAlignment)
{
results.Add(pairwiseAlignment);
}
}
}
}
return results;
}
public void ValidatePairwiseSequenceAlignmentToString()
{
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
var alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.Protein, "AWGHE");
alignedSeq.SecondSequence = new Sequence(Alphabets.Protein, "AW-HE");
alignedSeq.Consensus = new Sequence(Alphabets.Protein, "AWGHE");
alignedSeq.Score = 28;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 3;
align.PairwiseAlignedSequences.Add(alignedSeq);
string actualString = align.ToString();
string expectedString = "AWGHE\r\nAWGHE\r\nAW-HE\r\n\r\n".Replace("\r\n", System.Environment.NewLine);
Assert.AreEqual(actualString, expectedString);
}
/// <summary>
/// This method is considered as main execute method which defines the
/// step by step algorithm. Derived class flows the defined flow by this
/// method.
/// </summary>
/// <param name="referenceSequenceList">Reference sequence.</param>
/// <param name="originalQuerySequences">List of input sequences.</param>
/// <returns>A list of sequence alignment.</returns>
private IEnumerable <IPairwiseSequenceAlignment> Alignment(IEnumerable <ISequence> referenceSequenceList, IEnumerable <ISequence> originalQuerySequences)
{
ConsensusResolver = new SimpleConsensusResolver(referenceSequenceList.ElementAt(0).Alphabet);
IEnumerable <ISequence> querySequenceList =
ForwardOnly ? originalQuerySequences
: (ReverseOnly
? ReverseComplementSequenceList(originalQuerySequences)
: AddReverseComplementsToSequenceList(originalQuerySequences));
IList <IPairwiseSequenceAlignment> results = new List <IPairwiseSequenceAlignment>();
var deltas = new List <DeltaAlignment>();
foreach (ISequence refSequence in referenceSequenceList)
{
this.nucmerAlgo = new NUCmer(refSequence);
if (GapOpenCost != DefaultGapOpenCost)
{
this.nucmerAlgo.GapOpenCost = GapOpenCost;
}
if (GapExtensionCost != DefaultGapExtensionCost)
{
this.nucmerAlgo.GapExtensionCost = GapExtensionCost;
}
if (LengthOfMUM != DefaultLengthOfMUM)
{
this.nucmerAlgo.LengthOfMUM = LengthOfMUM;
}
// Set the ClusterBuilder properties to defaults
if (FixedSeparation != ClusterBuilder.DefaultFixedSeparation)
{
this.nucmerAlgo.FixedSeparation = FixedSeparation;
}
if (MaximumSeparation != ClusterBuilder.DefaultMaximumSeparation)
{
this.nucmerAlgo.MaximumSeparation = MaximumSeparation;
}
if (MinimumScore != ClusterBuilder.DefaultMinimumScore)
{
this.nucmerAlgo.MinimumScore = MinimumScore;
}
if (SeparationFactor != ClusterBuilder.DefaultSeparationFactor)
{
this.nucmerAlgo.SeparationFactor = SeparationFactor;
}
if (BreakLength != ModifiedSmithWaterman.DefaultBreakLength)
{
this.nucmerAlgo.BreakLength = BreakLength;
}
this.nucmerAlgo.ConsensusResolver = ConsensusResolver;
if (SimilarityMatrix != null)
{
this.nucmerAlgo.SimilarityMatrix = SimilarityMatrix;
}
foreach (ISequence querySequence in querySequenceList)
{
// Check for parameters that would prevent an alignment from being returned.
if (Math.Min(querySequence.Count, refSequence.Count) < MinimumScore)
{
var msg = "Bad parameter settings for NucmerPairwiseAligner. " +
"Tried to align a reference of length " + refSequence.Count.ToString() +
" to a sequence of length " + querySequence.Count.ToString() +
" while requiring a minimum score of MinimumScore = " + MinimumScore +
". This will prevent any alignments from being returned.";
throw new ArgumentException(msg);
}
IEnumerable <DeltaAlignment> deltaAlignment = this.nucmerAlgo.GetDeltaAlignments(querySequence, !MaxMatch, querySequence.IsMarkedAsReverseComplement());
deltas.AddRange(deltaAlignment);
}
}
if (deltas.Count > 0)
{
ISequence concatReference = referenceSequenceList.ElementAt(0);
//// concat all the sequences into one sequence
if (referenceSequenceList.Count() > 1)
{
concatReference = ConcatSequence(referenceSequenceList);
}
foreach (ISequence querySequence in querySequenceList)
{
List <DeltaAlignment> qDelta = deltas.Where(d => d.QuerySequence.Equals(querySequence)).ToList();
IPairwiseSequenceAlignment sequenceAlignment = new PairwiseSequenceAlignment(concatReference, querySequence);
// Convert delta alignments to sequence alignments
IList <PairwiseAlignedSequence> alignments = ConvertDeltaToAlignment(qDelta);
if (alignments.Count > 0)
{
foreach (PairwiseAlignedSequence align in alignments)
{
// Calculate the score of alignment
align.Score = CalculateScore(
align.FirstSequence,
align.SecondSequence);
// Make Consensus
align.Consensus = MakeConsensus(
align.FirstSequence,
align.SecondSequence);
sequenceAlignment.PairwiseAlignedSequences.Add(align);
}
}
results.Add(sequenceAlignment);
}
}
return(results);
}
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 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.");
}
public static void TestExceptionThrownForUnclippedAlignment() {
var refseq = "ACAATATA";
var queryseq = "ACAATAT-";
var r = new Sequence (DnaAlphabet.Instance, refseq);
var q = new Sequence (DnaAlphabet.Instance, queryseq);
var aln = new PairwiseSequenceAlignment (r, q);
var pas = new PairwiseAlignedSequence ();
pas.FirstSequence = r;
pas.SecondSequence = q;
aln.Add (pas);
Assert.Throws<FormatException> (() => VariantCaller.LeftAlignIndelsAndCallVariants (aln, true));
refseq = "AAACAATATA";
queryseq = "AA-CAATATA";
r = new Sequence (DnaAlphabet.Instance, refseq);
q = new Sequence (DnaAlphabet.Instance, queryseq);
aln = new PairwiseSequenceAlignment (r, q);
pas = new PairwiseAlignedSequence ();
pas.FirstSequence = r;
pas.SecondSequence = q;
aln.Add (pas);
Assert.Throws<FormatException> (() => VariantCaller.LeftAlignIndelsAndCallVariants (aln, true));
}
public static void TestLeftAlignmentStep() {
var refseq = "ACAATAAAAGCGCGCGCGCGTTACGTATAT--ATGGATAT";
var queryseq = "ACAATAA-AGC--GCGC--GTTACGTATATATATGGATAT";
var r = new Sequence (DnaAlphabet.Instance, refseq);
var q = new Sequence (DnaAlphabet.Instance, queryseq);
var aln = new PairwiseSequenceAlignment (r, q);
var pas = new PairwiseAlignedSequence ();
pas.FirstSequence = r;
pas.SecondSequence = q;
aln.Add (pas);
var tpl = VariantCaller.LeftAlignIndelsAndCallVariants (aln, true);
// Check the left alignment
aln = tpl.Item1 as PairwiseSequenceAlignment;
var lar = aln.PairwiseAlignedSequences [0].FirstSequence.ConvertToString();
var laq = aln.PairwiseAlignedSequences [0].SecondSequence.ConvertToString();
var exprefseq = "ACAATAAAAGCGCGCGCGCGTTACG--TATATATGGATAT";
var expqueryseq = "ACAAT-AAA----GCGCGCGTTACGTATATATATGGATAT";
Assert.AreEqual (exprefseq, lar);
Assert.AreEqual (expqueryseq, laq);
// And it's hard, so we might as well check the variants
var variants = tpl.Item2;
Assert.AreEqual (3, variants.Count);
string[] bases = new string[] { "A", "GCGC", "TA" };
char[] hpbases = new char[] { 'A', 'G', 'T' };
bool[] inHp = new bool[] { true, false, false };
int[] lengths = new int[] { 1, 4, 2 };
int[] starts = new int[] { 4, 8, 24 };
IndelType[] types = new IndelType[] { IndelType.Deletion, IndelType.Deletion, IndelType.Insertion };
for (int i = 0; i < 3; i++) {
Assert.AreEqual (VariantType.INDEL, variants [i].Type);
var vi = variants [i] as IndelVariant;
Assert.AreEqual (hpbases[i], vi.HomopolymerBase);
Assert.AreEqual (starts [i], vi.StartPosition);
Assert.AreEqual (lengths [i], vi.Length);
Assert.AreEqual (bases [i], vi.InsertedOrDeletedBases);
Assert.AreEqual (inHp [i], vi.InHomopolymer);
Assert.AreEqual (types [i], vi.InsertionOrDeletion);
}
}
private void ValidateGeneralSequenceAlignment(string nodeName, bool validateProperty)
{
// Read the xml file for getting both the files for aligning.
string origSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string origSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
IAlphabet alphabet =
Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
ApplicationLog.WriteLine(string.Format("SequenceAlignment P1 : First sequence used is '{0}'.",
origSequence1));
ApplicationLog.WriteLine(string.Format("SequenceAlignment P1 : Second sequence used is '{0}'.",
origSequence2));
// Create two sequences
ISequence aInput = new Sequence(alphabet, origSequence1);
ISequence bInput = new Sequence(alphabet, origSequence2);
// Add the sequences to the Sequence alignment object using AddSequence() method.
IList<IPairwiseSequenceAlignment> sequenceAlignmentObj = new List<IPairwiseSequenceAlignment>();
var alignSeq = new PairwiseAlignedSequence {FirstSequence = aInput, SecondSequence = bInput};
IPairwiseSequenceAlignment seqAlignObj = new PairwiseSequenceAlignment();
seqAlignObj.Add(alignSeq);
sequenceAlignmentObj.Add(seqAlignObj);
// Read the output back and validate the same.
IList<PairwiseAlignedSequence> newAlignedSequences =
sequenceAlignmentObj[0].PairwiseAlignedSequences;
ApplicationLog.WriteLine(string.Format("SequenceAlignment P1 : First sequence read is '{0}'.",
origSequence1));
ApplicationLog.WriteLine(string.Format("SequenceAlignment P1 : Second sequence read is '{0}'.",
origSequence2));
if (validateProperty)
{
string score = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MatchScoreNode);
string seqCount = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceCountNode);
Assert.IsFalse(sequenceAlignmentObj.IsReadOnly);
Assert.AreEqual(sequenceAlignmentObj.Count.ToString((IFormatProvider) null), seqCount);
Assert.AreEqual(
sequenceAlignmentObj[0].PairwiseAlignedSequences[0].Score.ToString((IFormatProvider) null), score);
Assert.AreEqual(sequenceAlignmentObj.Count.ToString((IFormatProvider) null), seqCount);
ApplicationLog.WriteLine("SequenceAlignment P1 : Successfully validated the IsRead Property");
ApplicationLog.WriteLine("SequenceAlignment P1 : Successfully validated the Count Property");
ApplicationLog.WriteLine("SequenceAlignment P1 : Successfully validated the Sequences Property");
}
else
{
Assert.AreEqual(new String(newAlignedSequences[0].FirstSequence.Select(a => (char) a).ToArray()),
origSequence1);
Assert.AreEqual(new String(newAlignedSequences[0].SecondSequence.Select(a => (char) a).ToArray()),
origSequence2);
}
}
private void ValidateNeedlemanWunschAlignment(string nodeName, AlignParameters alignParam,
SimilarityMatrixParameters similarityMatrixParam,
AlignmentType alignType)
{
ISequence aInput, bInput;
IAlphabet alphabet =
Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
// Parse the files and get the sequence.
if (alignParam.ToString().Contains("Code"))
{
string sequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string sequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
aInput = new Sequence(alphabet, sequence1);
bInput = new Sequence(alphabet, sequence2);
}
else
{
// Read the xml file for getting both the files for aligning.
string filePath1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode1);
string filePath2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode2);
var parseObjectForFile1 = new FastAParser { Alphabet = alphabet };
ISequence originalSequence1 = parseObjectForFile1.Parse(filePath1).FirstOrDefault();
Assert.IsNotNull(originalSequence1);
aInput = new Sequence(alphabet, originalSequence1.ConvertToString());
var parseObjectForFile2 = new FastAParser { Alphabet = alphabet };
ISequence originalSequence2 = parseObjectForFile2.Parse(filePath2).FirstOrDefault();
Assert.IsNotNull(originalSequence2);
bInput = new Sequence(alphabet, originalSequence2.ConvertToString());
}
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
SimilarityMatrix sm;
switch (similarityMatrixParam)
{
case SimilarityMatrixParameters.TextReader:
using (TextReader reader = new StreamReader(blosumFilePath))
sm = new SimilarityMatrix(reader);
break;
case SimilarityMatrixParameters.DiagonalMatrix:
string matchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MatchScoreNode);
string misMatchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MisMatchScoreNode);
sm = new DiagonalSimilarityMatrix(int.Parse(matchValue, null),
int.Parse(misMatchValue, null));
break;
default:
sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
break;
}
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapExtensionCostNode),
null);
var needlemanWunschObj = new NeedlemanWunschAligner();
if (AlignParameters.AllParam != alignParam)
{
needlemanWunschObj.SimilarityMatrix = sm;
needlemanWunschObj.GapOpenCost = gapOpenCost;
}
IList<IPairwiseSequenceAlignment> result = null;
switch (alignParam)
{
case AlignParameters.AlignList:
case AlignParameters.AlignListCode:
var sequences = new List<ISequence> {aInput, bInput};
switch (alignType)
{
case AlignmentType.Align:
needlemanWunschObj.GapExtensionCost = gapExtensionCost;
result = needlemanWunschObj.Align(sequences);
break;
default:
result = needlemanWunschObj.AlignSimple(sequences);
break;
}
break;
case AlignParameters.AllParam:
case AlignParameters.AllParamCode:
switch (alignType)
{
case AlignmentType.Align:
needlemanWunschObj.GapExtensionCost = gapExtensionCost;
result = needlemanWunschObj.Align(sm,
gapOpenCost, gapExtensionCost, aInput, bInput);
break;
default:
result = needlemanWunschObj.AlignSimple(sm, gapOpenCost, aInput, bInput);
break;
}
break;
case AlignParameters.AlignTwo:
case AlignParameters.AlignTwoCode:
switch (alignType)
{
case AlignmentType.Align:
needlemanWunschObj.GapExtensionCost = gapExtensionCost;
result = needlemanWunschObj.Align(aInput, bInput);
break;
default:
result = needlemanWunschObj.AlignSimple(aInput, bInput);
break;
}
break;
default:
break;
}
// Read the xml file for getting both the files for aligning.
string expectedSequence1, expectedSequence2, expectedScore;
switch (alignType)
{
case AlignmentType.Align:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedGapExtensionScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionSequence1Node);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionSequence2Node);
break;
default:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode1);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode2);
break;
}
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment(aInput, bInput);
var alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(alphabet, expectedSequence1),
SecondSequence = new Sequence(alphabet, expectedSequence2),
Score = Convert.ToInt32(expectedScore, null)
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
ApplicationLog.WriteLine(string.Format("NeedlemanWunschAligner P1 : Final Score '{0}'.", expectedScore));
ApplicationLog.WriteLine(string.Format("NeedlemanWunschAligner P1 : Aligned First Sequence is '{0}'.", expectedSequence1));
ApplicationLog.WriteLine(string.Format("NeedlemanWunschAligner P1 : Aligned Second Sequence is '{0}'.", expectedSequence2));
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
public void ValidateSequenceAlignmentProperties()
{
// Read the xml file for getting both the files for aligning.
string origSequence1 = this.utilityObj.xmlUtil.GetTextValue(Constants.AlignDnaAlgorithmNodeName,
Constants.SequenceNode1);
string origSequence2 = this.utilityObj.xmlUtil.GetTextValue(Constants.AlignDnaAlgorithmNodeName,
Constants.SequenceNode2);
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(
Constants.AlignDnaAlgorithmNodeName,
Constants.AlphabetNameNode));
string seqCount = this.utilityObj.xmlUtil.GetTextValue(
Constants.AlignDnaAlgorithmNodeName,
Constants.SequenceCountNode);
// Create two sequences
ISequence aInput = new Sequence(alphabet, origSequence1);
ISequence bInput = new Sequence(alphabet, origSequence2);
// Add the sequences to the Sequence alignment object using AddSequence() method.
IList<IPairwiseSequenceAlignment> sequenceAlignmentObj = new List<IPairwiseSequenceAlignment>();
var alignSeq = new PairwiseAlignedSequence();
alignSeq.FirstSequence = aInput;
alignSeq.SecondSequence = bInput;
IPairwiseSequenceAlignment seqAlignObj = new PairwiseSequenceAlignment(aInput, bInput);
seqAlignObj.Add(alignSeq);
sequenceAlignmentObj.Add(seqAlignObj);
// Validate all properties of sequence alignment class.
Assert.AreEqual(seqCount, seqAlignObj.Count.ToString((IFormatProvider) null));
Assert.AreEqual(origSequence1, new string(seqAlignObj.FirstSequence.Select(a => (char) a).ToArray()));
Assert.AreEqual(origSequence2, new string(seqAlignObj.SecondSequence.Select(a => (char) a).ToArray()));
Assert.IsFalse(seqAlignObj.IsReadOnly);
Assert.IsNull(seqAlignObj.Documentation);
Assert.AreEqual(seqCount, seqAlignObj.PairwiseAlignedSequences.Count.ToString((IFormatProvider) null));
ApplicationLog.WriteLine("SequenceAlignment P1 : Successfully validated the IsRead Property");
ApplicationLog.WriteLine("SequenceAlignment P1 : Successfully validated the Count Property");
ApplicationLog.WriteLine("SequenceAlignment P1 : Successfully validated the Sequences Property");
}
/// <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="isFilePath">Is Sequence saved in File</param>
/// <param name="isAlignList">Is align method to take list?</param>
/// <param name="addParam">Additional parameter</param>
/// Suppress the ParserParam variable CA1801 as this would be reused later.
void ValidateMUMmerAlignGeneralTestCases(string nodeName, bool isFilePath, bool isAlignList, AdditionalParameters addParam)
{
ISequence referenceSeq;
IList<ISequence> querySeqs;
List<ISequence> alignList = null;
if (isFilePath)
{
// Gets the reference sequence from the configuration file
string filePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
Assert.IsNotNull(filePath);
Assert.IsTrue(File.Exists(filePath));
IEnumerable<ISequence> referenceSeqs;
FastAParser fastaParserObj = new FastAParser();
referenceSeqs = fastaParserObj.Parse(filePath);
referenceSeq = referenceSeqs.FirstOrDefault();
Assert.IsNotNull(referenceSeq);
// Gets the query sequence from the configuration file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
Assert.IsTrue(File.Exists(queryFilePath));
querySeqs = fastaParserObj.Parse(queryFilePath).ToList();
ISequence querySeq = querySeqs.First();
if (isAlignList)
{
alignList = new List<ISequence> {referenceSeq, querySeq};
}
}
else
{
// Gets the reference sequence from the configuration file
string referenceSequence = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode);
string referenceSeqAlphabet = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode);
referenceSeq = new Sequence(Utility.GetAlphabet(referenceSeqAlphabet), referenceSequence);
string querySequence = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceNode);
referenceSeqAlphabet = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceAlphabetNode);
ISequence querySeq = new Sequence(Utility.GetAlphabet(referenceSeqAlphabet), querySequence);
querySeqs = new List<ISequence>();
if (isAlignList)
{
alignList = new List<ISequence> {referenceSeq, querySeq};
}
else
querySeqs.Add(querySeq);
}
// Setup the algorithm
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode);
MUMmerAligner mumAlignObj = new MUMmerAligner {LengthOfMUM = long.Parse(mumLength, null), StoreMUMs = true};
switch (addParam)
{
case AdditionalParameters.PerformSimilarityMatrixChange:
mumAlignObj.SimilarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
mumAlignObj.GapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null);
break;
default:
mumAlignObj.GapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null);
break;
}
IEnumerable<ISequence> alignEnumSeqs = alignList;
IList<IPairwiseSequenceAlignment> align = isAlignList
? mumAlignObj.AlignSimple(alignEnumSeqs)
: mumAlignObj.AlignSimple(referenceSeq, querySeqs);
// Validate MUMs Properties
Assert.IsNotNull(mumAlignObj.MUMs);
string expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ScoreNodeName);
string[] expectedSequences = this.utilityObj.xmlUtil.GetTextValues(nodeName, Constants.ExpectedSequencesNode);
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
// Validate for two aligned sequences and single aligned sequences appropriately
if (querySeqs.Count <= 1)
{
IPairwiseSequenceAlignment seqAlign = new PairwiseSequenceAlignment();
PairwiseAlignedSequence 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(CompareAlignment(align, expectedOutput));
}
else
{
string[] expectedScores = expectedScore.Split(',');
IPairwiseSequenceAlignment seq1Align = new PairwiseSequenceAlignment();
IPairwiseSequenceAlignment seq2Align = new PairwiseSequenceAlignment();
// Get the first sequence for validation
PairwiseAlignedSequence alignedSeq1 = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(referenceSeq.Alphabet, expectedSequences[0]),
SecondSequence = new Sequence(referenceSeq.Alphabet, expectedSequences[1]),
Score = int.Parse(expectedScores[0], null),
FirstOffset = Int32.MinValue,
SecondOffset = Int32.MinValue,
};
seq1Align.PairwiseAlignedSequences.Add(alignedSeq1);
expectedOutput.Add(seq1Align);
// Get the second sequence for validation
PairwiseAlignedSequence alignedSeq2 = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(referenceSeq.Alphabet, expectedSequences[2]),
SecondSequence = new Sequence(referenceSeq.Alphabet, expectedSequences[3]),
Score = int.Parse(expectedScores[1], null),
FirstOffset = Int32.MinValue,
SecondOffset = Int32.MinValue,
};
seq2Align.PairwiseAlignedSequences.Add(alignedSeq2);
expectedOutput.Add(seq2Align);
Assert.IsTrue(CompareAlignment(align, expectedOutput));
}
}
/// <summary>
/// This method is considered as main execute method which defines the
/// step by step algorithm. Drived class flows the defined flow by this
/// method. Does not store MUMs, processes MUMs and gaps to find
/// alignment directly.
/// </summary>
/// <param name="referenceSequence">reference sequence</param>
/// <param name="querySequenceList">list of input sequences</param>
/// <returns>A list of sequence alignments</returns>
private IList <IPairwiseSequenceAlignment> AlignmentWithoutAccumulatedMUMs(
ISequence referenceSequence,
IList <ISequence> querySequenceList)
{
IList <IPairwiseSequenceAlignment> results = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment alignment = null;
if (Validate(referenceSequence, querySequenceList))
{
// Safety check for public methods to ensure that null
// inputs are handled.
if (referenceSequence == null || querySequenceList == null)
{
return(null);
}
// Getting refernce sequence
_referenceSequence = referenceSequence;
// Step1 : building suffix trees using reference sequence
_suffixTree = BuildSuffixTree(_referenceSequence);
// On each query sequence aligned with reference sequence
foreach (ISequence sequence in querySequenceList)
{
if (sequence.Equals(referenceSequence))
{
continue;
}
alignment = new PairwiseSequenceAlignment(referenceSequence, sequence);
// Step2 : streaming process is performed with the query sequence
_mumList = Streaming(_suffixTree, sequence, LengthOfMUM);
// Step3(a) : sorted mum list based on reference sequence
_sortedMumList = SortMum(_mumList);
if (_sortedMumList.Count > 0)
{
// Step3(b) : LIS using greedy cover algorithm
_finalMumList = CollectLongestIncreasingSubsequence(_sortedMumList);
if (_finalMumList.Count > 0)
{
// Step 4 : get all the gaps in each sequence and call
// pairwise alignment
alignment.PairwiseAlignedSequences.Add(ProcessGaps(referenceSequence, sequence));
}
results.Add(alignment);
}
else
{
IList <IPairwiseSequenceAlignment> sequenceAlignment = RunPairWise(
referenceSequence,
sequence);
foreach (IPairwiseSequenceAlignment pairwiseAlignment in sequenceAlignment)
{
results.Add(pairwiseAlignment);
}
}
}
}
return(results);
}
/// <summary>
/// This is step (3) in the dynamic programming model - to walk the traceback/scoring
/// matrix and generate the alignment.
/// </summary>
private PairwiseSequenceAlignment CreateAlignment(IEnumerable<OptScoreMatrixCell> startingCells)
{
// Generate each alignment.
var alignment = new PairwiseSequenceAlignment(_sequence1, _sequence2);
foreach (var startingCell in startingCells)
alignment.PairwiseAlignedSequences.Add(CreateAlignmentFromCell(startingCell));
// Include the scoring table if requested.
if (IncludeScoreTable)
alignment.Metadata["ScoreTable"] = GetScoreTable();
return alignment;
}
/// <summary>
/// This method is considered as main execute method which defines the
/// step by step algorithm. Drived class flows the defined flow by this
/// method. Store generated MUMs in properties MUMs, SortedMUMs.
/// Alignment first finds MUMs for all the query sequence, and then
/// runs pairwise algorithm on gaps to produce alignments.
/// </summary>
/// <param name="referenceSequence">reference sequence</param>
/// <param name="querySequenceList">list of input sequences</param>
/// <returns>A list of sequence alignments</returns>
private IList <IPairwiseSequenceAlignment> AlignmentWithAccumulatedMUMs(
ISequence referenceSequence,
IList <ISequence> querySequenceList)
{
// Get MUMs
IDictionary <ISequence, IList <MaxUniqueMatch> > queryMums = new Dictionary <ISequence, IList <MaxUniqueMatch> >();
_mums = new Dictionary <ISequence, IList <MaxUniqueMatch> >();
_finalMums = new Dictionary <ISequence, IList <MaxUniqueMatch> >();
if (Validate(referenceSequence, querySequenceList))
{
IList <MaxUniqueMatch> mumList;
// Step1 : building suffix trees using reference sequence
SequenceSuffixTree suffixTree = BuildSuffixTree(referenceSequence);
// On each query sequence aligned with reference sequence
foreach (ISequence sequence in querySequenceList)
{
if (sequence.Equals(referenceSequence))
{
continue;
}
// Step2 : streaming process is performed with the query sequence
mumList = Streaming(suffixTree, sequence, LengthOfMUM);
_mums.Add(sequence, mumList);
// Step3(a) : sorted mum list based on reference sequence
mumList = SortMum(mumList);
if (mumList.Count > 0)
{
// Step3(b) : LIS using greedy cover algorithm
mumList = CollectLongestIncreasingSubsequence(mumList);
}
else
{
mumList = null;
}
_finalMums.Add(sequence, mumList);
}
}
IList <IPairwiseSequenceAlignment> results = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment alignment = null;
if (MUMs != null && FinalMUMs != null)
{
// Getting refernce sequence
_referenceSequence = referenceSequence;
// On each query sequence aligned with reference sequence
foreach (var finalMum in FinalMUMs)
{
var sequence = finalMum.Key;
_mumList = MUMs[sequence];
_finalMumList = finalMum.Value;
alignment = new PairwiseSequenceAlignment(referenceSequence, sequence);
if (_mumList.Count > 0)
{
if (_finalMumList.Count > 0)
{
// Step 4 : get all the gaps in each sequence and call
// pairwise alignment
alignment.PairwiseAlignedSequences.Add(ProcessGaps(referenceSequence, sequence));
}
results.Add(alignment);
}
else
{
IList <IPairwiseSequenceAlignment> sequenceAlignment = RunPairWise(
referenceSequence,
sequence);
foreach (IPairwiseSequenceAlignment pairwiseAlignment in sequenceAlignment)
{
results.Add(pairwiseAlignment);
}
}
}
}
return(results);
}
/// <summary>
/// Validates PairwiseOverlapAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Xml node name</param>
/// <param name="isTextFile">Is text file an input.</param>
/// <param name="caseType">Case Type</param>
/// <param name="additionalParameter">parameter based on which certain validations are done.</param>
/// <param name="alignType">Is the Align type Simple or Align with Gap Extension cost?</param>
/// <param name="similarityMatrixParam">Similarity Matrix</param>
private void ValidatePairwiseOverlapAlignment(string nodeName, bool isTextFile,
SequenceCaseType caseType, AlignParameters additionalParameter,
AlignmentType alignType,
SimilarityMatrixParameters similarityMatrixParam)
{
Sequence aInput = null;
Sequence bInput = null;
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
if (isTextFile)
{
// Read the xml file for getting both the files for aligning.
string filePath1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode1);
string filePath2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode2);
var parser1 = new FastAParser();
ISequence originalSequence1 = parser1.Parse(filePath1).ElementAt(0);
ISequence originalSequence2 = parser1.Parse(filePath2).ElementAt(0);
// Create input sequence for sequence string in different cases.
GetSequenceWithCaseType(new string(originalSequence1.Select(a => (char) a).ToArray()),
new string(originalSequence2.Select(a => (char) a).ToArray()), alphabet,
caseType, out aInput, out bInput);
}
else
{
string originalSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string originalSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
// Create input sequence for sequence string in different cases.
GetSequenceWithCaseType(
originalSequence1,
originalSequence2,
alphabet,
caseType,
out aInput,
out bInput);
}
var aInputString = new string(aInput.Select(a => (char) a).ToArray());
var bInputString = new string(bInput.Select(a => (char) a).ToArray());
ApplicationLog.WriteLine(string.Format(null,
"PairwiseOverlapAligner P2 : First sequence used is '{0}'.",
aInputString));
ApplicationLog.WriteLine(string.Format(null,
"PairwiseOverlapAligner P2 : Second sequence used is '{0}'.",
bInputString));
// Create similarity matrix object for a given file.
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
SimilarityMatrix sm = null;
switch (similarityMatrixParam)
{
case SimilarityMatrixParameters.TextReader:
using (TextReader reader = new StreamReader(blosumFilePath))
sm = new SimilarityMatrix(reader);
break;
case SimilarityMatrixParameters.DiagonalMatrix:
string matchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MatchScoreNode);
string misMatchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MisMatchScoreNode);
sm = new DiagonalSimilarityMatrix(int.Parse(matchValue, null),
int.Parse(misMatchValue, null));
break;
default:
sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
break;
}
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.GapExtensionCostNode), null);
// Create PairwiseOverlapAligner instance and set its values.
var pairwiseOverlapObj = new PairwiseOverlapAligner();
if (additionalParameter != AlignParameters.AllParam)
{
pairwiseOverlapObj.SimilarityMatrix = sm;
pairwiseOverlapObj.GapOpenCost = gapOpenCost;
pairwiseOverlapObj.GapExtensionCost = gapExtensionCost;
}
IList<IPairwiseSequenceAlignment> result = null;
// Align the input sequences.
switch (additionalParameter)
{
case AlignParameters.AlignList:
var sequences = new List<ISequence>();
sequences.Add(aInput);
sequences.Add(bInput);
switch (alignType)
{
case AlignmentType.Align:
result = pairwiseOverlapObj.Align(sequences);
break;
default:
result = pairwiseOverlapObj.AlignSimple(sequences);
break;
}
break;
case AlignParameters.AlignTwo:
switch (alignType)
{
case AlignmentType.Align:
result = pairwiseOverlapObj.Align(aInput, bInput);
break;
default:
result = pairwiseOverlapObj.AlignSimple(aInput, bInput);
break;
}
break;
case AlignParameters.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;
}
aInput = null;
bInput = null;
sm = null;
// Get the expected sequence and scorde from xml config.
string expectedSequence1 = string.Empty;
string expectedSequence2 = string.Empty;
string expectedScore = string.Empty;
switch (alignType)
{
case AlignmentType.Align:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionSequence1Node);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionSequence2Node);
break;
default:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode1);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode2);
break;
}
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
string[] expectedSequences1, expectedSequences2;
var seperators = new char[1] {';'};
expectedSequences1 = expectedSequence1.Split(seperators);
expectedSequences2 = expectedSequence2.Split(seperators);
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
PairwiseAlignedSequence alignedSeq;
for (int i = 0; i < expectedSequences1.Length; i++)
{
alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(alphabet, expectedSequences1[i]),
SecondSequence = new Sequence(alphabet, expectedSequences2[i]),
Score = Convert.ToInt32(expectedScore, null),
FirstOffset = Int32.MinValue,
SecondOffset = Int32.MinValue,
};
align.PairwiseAlignedSequences.Add(alignedSeq);
}
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput,true));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P2 : Final Score '{0}'.", expectedScore));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P2 : Aligned First Sequence is '{0}'.", expectedSequence1));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P2 : Aligned Second Sequence is '{0}'.", expectedSequence2));
}
/// <summary>
/// Launches the alignment algorithm
/// </summary>
public virtual List<IPairwiseSequenceAlignment> Align()
{
InitializeCache();
// Grid
for (int diagonal = 0; diagonal < gridCols + gridRows - 2; diagonal++)
{
for (int blockRow = 0; blockRow < gridRows; blockRow++)
{
int blockCol = diagonal - blockRow;
if ((blockCol >= 0) && (blockCol < gridCols))
{
int lastRow = (blockRow == gridRows - 1) ? (int)(colHeight - Helper.BigMul(blockRow, gridStride) - 1) : gridStride;
int lastCol = (blockCol == gridCols - 1) ? (int)(rowWidth - Helper.BigMul(blockCol, gridStride) - 1) : gridStride;
ComputeIntermediateBlock(blockRow, blockCol, lastRow, lastCol);
}
}
}
sbyte[][] trace = new sbyte[gridStride + 1][];
for (int i = 0; i <= gridStride; i++)
{
trace[i] = new sbyte[gridStride + 1];
}
// Last Block - grid calculation and Traceback combined
int completeTraceRow = gridRows - 1;
int completeTraceCol = gridCols - 1;
int completeLastRow = (int)(colHeight - Helper.BigMul(completeTraceRow, gridStride) - 1);
int completeLastCol = (int)(rowWidth - Helper.BigMul(completeTraceCol, gridStride) - 1);
ComputeCornerBlock(completeTraceRow, completeTraceCol, completeLastRow, completeLastCol, trace);
//Traceback
if (optScoreCells.Count == 0)
{
return new List<IPairwiseSequenceAlignment>();
}
else
{
PairwiseSequenceAlignment alignment = new PairwiseSequenceAlignment(sequenceI, sequenceJ);
for (int alignmentCount = 0; alignmentCount < optScoreCells.Count; alignmentCount++)
{
PairwiseAlignedSequence result = new PairwiseAlignedSequence();
result.Score = optScore;
long alignmentRow = optScoreCells[alignmentCount].Item1;
long alignmentCol = optScoreCells[alignmentCount].Item2;
int blockRow = (int)(alignmentRow / gridStride);
int blockCol = (int)(alignmentCol / gridStride);
int lastRow = (int)(alignmentRow - Helper.BigMul(blockRow, gridStride));
int lastCol = (int)(alignmentCol - Helper.BigMul(blockCol, gridStride));
result.Metadata["EndOffsets"] = new List<long> { alignmentRow - 1, alignmentCol - 1 };
long alignmentLength = 0;
byte[] sequence1 = new byte[colHeight + rowWidth];
byte[] sequence2 = new byte[colHeight + rowWidth];
int colGaps = 0;
int rowGaps = 0;
while ((blockRow >= 0) && (blockCol >= 0))
{
if ((blockRow != completeTraceRow) || (blockCol != completeTraceCol) || (lastRow > completeLastRow) || (lastCol > completeLastCol))
{
ComputeTraceBlock(blockRow, blockCol, lastRow, lastCol, trace);
completeTraceRow = blockRow;
completeTraceCol = blockCol;
completeLastRow = lastRow;
completeLastCol = lastCol;
}
long startPositionI = blockRow * gridStride - 1;
long startPositionJ = blockCol * gridStride - 1;
while ((trace[lastRow][lastCol] != SourceDirection.Stop) && (trace[lastRow][lastCol] != SourceDirection.Block))
{
switch (trace[lastRow][lastCol])
{
case SourceDirection.Diagonal:
// diagonal, no gap, use both sequence residues
sequence1[alignmentLength] = sequenceI[startPositionI + lastRow];
sequence2[alignmentLength] = sequenceJ[startPositionJ + lastCol];
alignmentLength++;
lastRow--;
lastCol--;
break;
case SourceDirection.Up:
// up, gap in J
sequence1[alignmentLength] = sequenceI[startPositionI + lastRow];
sequence2[alignmentLength] = this.gapCode;
alignmentLength++;
lastRow--;
colGaps++;
break;
case SourceDirection.Left:
// left, gap in I
sequence1[alignmentLength] = this.gapCode;
sequence2[alignmentLength] = sequenceJ[startPositionJ + lastCol];
alignmentLength++;
lastCol--;
rowGaps++;
break;
}
}
if (trace[lastRow][lastCol] == SourceDirection.Stop)
{
// Be nice, turn aligned solutions around so that they match the input sequences
byte[] alignedA = new byte[alignmentLength];
byte[] alignedB = new byte[alignmentLength];
for (long i = 0, j = alignmentLength - 1; i < alignmentLength; i++, j--)
{
alignedA[i] = sequence1[j];
alignedB[i] = sequence2[j];
}
// If alphabet of inputA is DnaAlphabet then alphabet of alignedA may be Dna or AmbiguousDna.
IAlphabet alphabet = Alphabets.AutoDetectAlphabet(alignedA, 0, alignedA.GetLongLength(), sequenceI.Alphabet);
Sequence seq = new Sequence(alphabet, alignedA, false);
seq.ID = sequenceI.ID;
// seq.DisplayID = aInput.DisplayID;
result.FirstSequence = seq;
alphabet = Alphabets.AutoDetectAlphabet(alignedB, 0, alignedB.GetLongLength(), sequenceJ.Alphabet);
seq = new Sequence(alphabet, alignedB, false);
seq.ID = sequenceJ.ID;
// seq.DisplayID = bInput.DisplayID;
result.SecondSequence = seq;
// Offset is start of alignment in input sequence with respect to other sequence.
if (lastCol >= lastRow)
{
result.FirstOffset = lastCol - lastRow;
result.SecondOffset = 0;
}
else
{
result.FirstOffset = 0;
result.SecondOffset = lastRow - lastCol;
}
result.Metadata["StartOffsets"] = new List<long> { lastRow, lastCol };
result.Metadata["Insertions"] = new List<long> { rowGaps, colGaps };
alignment.PairwiseAlignedSequences.Add(result);
break;
}
else
{
if (lastRow == 0 && lastCol == 0)
{
blockRow--;
blockCol--;
lastRow = gridStride;
lastCol = gridStride;
}
else
{
if (lastRow == 0)
{
blockRow--;
lastRow = gridStride;
}
else
{
blockCol--;
lastCol = gridStride;
}
}
}
}
}
return new List<IPairwiseSequenceAlignment>() { alignment };
}
}
public void PairwiseOverlapMultipleAlignments()
{
Sequence sequence1 = new Sequence(Alphabets.DNA, "CCCAACCC");
Sequence sequence2 = new Sequence(Alphabets.DNA, "CCC");
SimilarityMatrix sm = new DiagonalSimilarityMatrix(5, -20);
int gapPenalty = -10;
PairwiseOverlapAligner overlap = new PairwiseOverlapAligner();
overlap.SimilarityMatrix = sm;
overlap.GapOpenCost = gapPenalty;
IList<IPairwiseSequenceAlignment> result = overlap.AlignSimple(sequence1, sequence2);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"{0}, Simple; Matrix {1}; GapOpenCost {2}", overlap.Name, overlap.SimilarityMatrix.Name, overlap.GapOpenCost));
foreach (IPairwiseSequenceAlignment sequenceResult in result)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"score {0}", sequenceResult.PairwiseAlignedSequences[0].Score));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 0 {0}", sequenceResult.FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"input 1 {0}", sequenceResult.SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 0 {0}", sequenceResult.PairwiseAlignedSequences[0].FirstSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"result 1 {0}", sequenceResult.PairwiseAlignedSequences[0].SecondSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"consesus {0}", sequenceResult.PairwiseAlignedSequences[0].Consensus.ToString()));
}
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
// First alignment
PairwiseAlignedSequence alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "CCC");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "CCC");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "CCC");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 0;
align.PairwiseAlignedSequences.Add(alignedSeq);
// Second alignment
alignedSeq = new PairwiseAlignedSequence();
alignedSeq.FirstSequence = new Sequence(Alphabets.DNA, "CCC");
alignedSeq.SecondSequence = new Sequence(Alphabets.DNA, "CCC");
alignedSeq.Consensus = new Sequence(Alphabets.DNA, "CCC");
alignedSeq.Score = 15;
alignedSeq.FirstOffset = 0;
alignedSeq.SecondOffset = 5;
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
/// <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="isFilePath"></param>
/// <param name="isSeqList">Is MUMmer alignment with List of sequences</param>
void ValidateMUMmerAlignGeneralTestCases(string nodeName, bool isFilePath, bool isSeqList)
{
ISequence referenceSeq;
ISequence querySeq;
IList<ISequence> querySeqs = new List<ISequence>();
string referenceSequence;
string querySequence;
IList<IPairwiseSequenceAlignment> align;
if (isFilePath)
{
// Gets the reference sequence from the configuration file
string filePath = this.utilityObj.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();
IEnumerable<ISequence> referenceSeqs = parser.Parse(filePath);
referenceSeq = referenceSeqs.FirstOrDefault();
Assert.IsNotNull(referenceSeq);
referenceSequence = referenceSeq.ConvertToString();
parser.Close();
// Gets the reference sequence from the configuration file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceFilePathNode);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format(null, "MUMmer BVT : Successfully validated the Search File Path '{0}'.", queryFilePath));
FastAParser queryParserObj = new FastAParser();
querySeqs = queryParserObj.Parse(queryFilePath).ToList();
querySeq = querySeqs.FirstOrDefault();
Assert.IsNotNull(querySeq);
querySequence = querySeq.ConvertToString();
queryParserObj.Close();
}
else
{
// Gets the reference sequence from the configuration file
referenceSequence = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode);
string referenceSeqAlphabet = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode);
referenceSeq = new Sequence(Utility.GetAlphabet(referenceSeqAlphabet), referenceSequence);
querySequence = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceNode);
referenceSeqAlphabet = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceAlphabetNode);
querySeq = new Sequence(Utility.GetAlphabet(referenceSeqAlphabet), querySequence);
querySeqs = new List<ISequence> {querySeq};
}
string mumLength = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode);
var mumAlignObj = new Bio.Algorithms.MUMmer.MUMmerAligner
{
LengthOfMUM = long.Parse(mumLength, null),
GapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null)
};
if (isSeqList)
{
querySeqs.Add(referenceSeq);
align = mumAlignObj.Align(querySeqs);
}
else
{
align = mumAlignObj.AlignSimple(referenceSeq, querySeqs);
}
string expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ScoreNodeName);
Assert.AreEqual(expectedScore, align[0].PairwiseAlignedSequences[0].Score.ToString((IFormatProvider)null));
ApplicationLog.WriteLine(string.Format(null, "MUMmer BVT : Successfully validated the score for the sequence '{0}' and '{1}'.", referenceSequence, querySequence));
string[] expectedSequences = this.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(CompareAlignment(align, expectedOutput));
ApplicationLog.WriteLine("MUMmer BVT : Successfully validated the aligned sequences.");
}
/// <summary>
/// Validates PairwiseOverlapAlignment algorithm for the parameters passed.
/// </summary>
/// <param name="nodeName">Node Name in the xml.</param>
/// <param name="alignParam">parameter based on which certain validations are done.</param>
/// <param name="similarityMatrixParam">Similarity Matrix Parameter.</param>
/// <param name="alignType">Alignment Type</param>
private void ValidatePairwiseOverlapAlignment(string nodeName, AlignParameters alignParam,
SimilarityMatrixParameters similarityMatrixParam,
AlignmentType alignType)
{
ISequence aInput;
ISequence bInput;
IAlphabet alphabet = Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
if (alignParam.ToString().Contains("Code"))
{
string sequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string sequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
aInput = new Sequence(alphabet, sequence1);
bInput = new Sequence(alphabet, sequence2);
}
else
{
// Read the xml file for getting both the files for aligning.
string filePath1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode1);
string filePath2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode2);
var parser1 = new FastAParser { Alphabet = alphabet };
aInput = parser1.Parse(filePath1).ElementAt(0);
bInput = parser1.Parse(filePath2).ElementAt(0);
}
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
SimilarityMatrix sm;
switch (similarityMatrixParam)
{
case SimilarityMatrixParameters.TextReader:
using (TextReader reader = new StreamReader(blosumFilePath))
sm = new SimilarityMatrix(reader);
break;
case SimilarityMatrixParameters.DiagonalMatrix:
string matchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MatchScoreNode);
string misMatchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MisMatchScoreNode);
sm = new DiagonalSimilarityMatrix(int.Parse(matchValue, null), int.Parse(misMatchValue, null));
break;
default:
sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
break;
}
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapExtensionCostNode), null);
var pairwiseOverlapObj = new PairwiseOverlapAligner();
if (AlignParameters.AllParam != alignParam)
{
pairwiseOverlapObj.SimilarityMatrix = sm;
pairwiseOverlapObj.GapOpenCost = gapOpenCost;
}
IList<IPairwiseSequenceAlignment> result = null;
switch (alignParam)
{
case AlignParameters.AlignList:
case AlignParameters.AlignListCode:
var sequences = new List<ISequence> {aInput, bInput};
switch (alignType)
{
case AlignmentType.Align:
pairwiseOverlapObj.GapExtensionCost = gapExtensionCost;
result = pairwiseOverlapObj.Align(sequences);
break;
default:
result = pairwiseOverlapObj.AlignSimple(sequences);
break;
}
break;
case AlignParameters.AllParam:
case AlignParameters.AllParamCode:
switch (alignType)
{
case AlignmentType.Align:
pairwiseOverlapObj.GapExtensionCost = gapExtensionCost;
result = pairwiseOverlapObj.Align(sm, gapOpenCost, gapExtensionCost, aInput, bInput);
break;
default:
result = pairwiseOverlapObj.AlignSimple(sm, gapOpenCost, aInput, bInput);
break;
}
break;
case AlignParameters.AlignTwo:
case AlignParameters.AlignTwoCode:
switch (alignType)
{
case AlignmentType.Align:
pairwiseOverlapObj.GapExtensionCost = gapExtensionCost;
result = pairwiseOverlapObj.Align(aInput, bInput);
break;
default:
result = pairwiseOverlapObj.AlignSimple(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(nodeName, Constants.ExpectedGapExtensionScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedGapExtensionSequence1Node);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedGapExtensionSequence2Node);
break;
default:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedScoreNode);
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode1);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, 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),
FirstOffset = Int32.MinValue,
SecondOffset = Int32.MinValue,
};
align.PairwiseAlignedSequences.Add(alignedSeq);
}
expectedOutput.Add(align);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(result, expectedOutput, true));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P1 : Final Score '{0}'.", expectedScore));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P1 : Aligned First Sequence is '{0}'.", expectedSequence1));
ApplicationLog.WriteLine(string.Format(null, "PairwiseOverlapAligner P1 : Aligned Second Sequence is '{0}'.", expectedSequence2));
}
/// <summary>
/// Launches the alignment algorithm
/// </summary>
public virtual List <IPairwiseSequenceAlignment> Align()
{
InitializeCache();
// Grid
for (int diagonal = 0; diagonal < gridCols + gridRows - 2; diagonal++)
{
for (int blockRow = 0; blockRow < gridRows; blockRow++)
{
int blockCol = diagonal - blockRow;
if ((blockCol >= 0) && (blockCol < gridCols))
{
int lastRow = (blockRow == gridRows - 1) ? (int)(colHeight - Math.BigMul(blockRow, gridStride) - 1) : gridStride;
int lastCol = (blockCol == gridCols - 1) ? (int)(rowWidth - Math.BigMul(blockCol, gridStride) - 1) : gridStride;
ComputeIntermediateBlock(blockRow, blockCol, lastRow, lastCol);
}
}
}
sbyte[][] trace = new sbyte[gridStride + 1][];
for (int i = 0; i <= gridStride; i++)
{
trace[i] = new sbyte[gridStride + 1];
}
// Last Block - grid calculation and Traceback combined
int completeTraceRow = gridRows - 1;
int completeTraceCol = gridCols - 1;
int completeLastRow = (int)(colHeight - Math.BigMul(completeTraceRow, gridStride) - 1);
int completeLastCol = (int)(rowWidth - Math.BigMul(completeTraceCol, gridStride) - 1);
ComputeCornerBlock(completeTraceRow, completeTraceCol, completeLastRow, completeLastCol, trace);
//Traceback
if (optScoreCells.Count == 0)
{
return(new List <IPairwiseSequenceAlignment>());
}
else
{
PairwiseSequenceAlignment alignment = new PairwiseSequenceAlignment(sequenceI, sequenceJ);
for (int alignmentCount = 0; alignmentCount < optScoreCells.Count; alignmentCount++)
{
PairwiseAlignedSequence result = new PairwiseAlignedSequence();
result.Score = optScore;
long alignmentRow = optScoreCells[alignmentCount].Item1;
long alignmentCol = optScoreCells[alignmentCount].Item2;
int blockRow = (int)(alignmentRow / gridStride);
int blockCol = (int)(alignmentCol / gridStride);
int lastRow = (int)(alignmentRow - Math.BigMul(blockRow, gridStride));
int lastCol = (int)(alignmentCol - Math.BigMul(blockCol, gridStride));
result.Metadata["EndOffsets"] = new List <long> {
alignmentRow - 1, alignmentCol - 1
};
long alignmentLength = 0;
byte[] sequence1 = new byte[colHeight + rowWidth];
byte[] sequence2 = new byte[colHeight + rowWidth];
int colGaps = 0;
int rowGaps = 0;
while ((blockRow >= 0) && (blockCol >= 0))
{
if ((blockRow != completeTraceRow) || (blockCol != completeTraceCol) || (lastRow > completeLastRow) || (lastCol > completeLastCol))
{
ComputeTraceBlock(blockRow, blockCol, lastRow, lastCol, trace);
completeTraceRow = blockRow;
completeTraceCol = blockCol;
completeLastRow = lastRow;
completeLastCol = lastCol;
}
long startPositionI = blockRow * gridStride - 1;
long startPositionJ = blockCol * gridStride - 1;
while ((trace[lastRow][lastCol] != SourceDirection.Stop) && (trace[lastRow][lastCol] != SourceDirection.Block))
{
switch (trace[lastRow][lastCol])
{
case SourceDirection.Diagonal:
// diagonal, no gap, use both sequence residues
sequence1[alignmentLength] = sequenceI[startPositionI + lastRow];
sequence2[alignmentLength] = sequenceJ[startPositionJ + lastCol];
alignmentLength++;
lastRow--;
lastCol--;
break;
case SourceDirection.Up:
// up, gap in J
sequence1[alignmentLength] = sequenceI[startPositionI + lastRow];
sequence2[alignmentLength] = this.gapCode;
alignmentLength++;
lastRow--;
colGaps++;
break;
case SourceDirection.Left:
// left, gap in I
sequence1[alignmentLength] = this.gapCode;
sequence2[alignmentLength] = sequenceJ[startPositionJ + lastCol];
alignmentLength++;
lastCol--;
rowGaps++;
break;
}
}
if (trace[lastRow][lastCol] == SourceDirection.Stop)
{
// Be nice, turn aligned solutions around so that they match the input sequences
byte[] alignedA = new byte[alignmentLength];
byte[] alignedB = new byte[alignmentLength];
for (long i = 0, j = alignmentLength - 1; i < alignmentLength; i++, j--)
{
alignedA[i] = sequence1[j];
alignedB[i] = sequence2[j];
}
// If alphabet of inputA is DnaAlphabet then alphabet of alignedA may be Dna or AmbiguousDna.
IAlphabet alphabet = Alphabets.AutoDetectAlphabet(alignedA, 0, alignedA.LongLength, sequenceI.Alphabet);
Sequence seq = new Sequence(alphabet, alignedA, false);
seq.ID = sequenceI.ID;
// seq.DisplayID = aInput.DisplayID;
result.FirstSequence = seq;
alphabet = Alphabets.AutoDetectAlphabet(alignedB, 0, alignedB.LongLength, sequenceJ.Alphabet);
seq = new Sequence(alphabet, alignedB, false);
seq.ID = sequenceJ.ID;
// seq.DisplayID = bInput.DisplayID;
result.SecondSequence = seq;
// Offset is start of alignment in input sequence with respect to other sequence.
if (lastCol >= lastRow)
{
result.FirstOffset = lastCol - lastRow;
result.SecondOffset = 0;
}
else
{
result.FirstOffset = 0;
result.SecondOffset = lastRow - lastCol;
}
result.Metadata["StartOffsets"] = new List <long> {
lastRow, lastCol
};
result.Metadata["Insertions"] = new List <long> {
rowGaps, colGaps
};
alignment.PairwiseAlignedSequences.Add(result);
break;
}
else
{
if (lastRow == 0 && lastCol == 0)
{
blockRow--;
blockCol--;
lastRow = gridStride;
lastCol = gridStride;
}
else
{
if (lastRow == 0)
{
blockRow--;
lastRow = gridStride;
}
else
{
blockCol--;
lastCol = gridStride;
}
}
}
}
}
return(new List <IPairwiseSequenceAlignment>()
{
alignment
});
}
}
private void ValidateSmithWatermanAlignment(string nodeName, bool isTextFile,
SequenceCaseType caseType, AlignParameters additionalParameter,
AlignmentType alignType,
SimilarityMatrixParameters similarityMatrixParam)
{
Sequence aInput, bInput;
IAlphabet alphabet =
Utility.GetAlphabet(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
if (isTextFile)
{
// Read the xml file for getting both the files for aligning.
string filePath1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode1);
string filePath2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode2);
// Parse the files and get the sequence.
ISequence originalSequence1 = null;
ISequence originalSequence2 = null;
var parseObjectForFile1 = new FastAParser { Alphabet = alphabet };
originalSequence1 = parseObjectForFile1.Parse(filePath1).ElementAt(0);
originalSequence2 = parseObjectForFile1.Parse(filePath2).ElementAt(0);
// Create input sequence for sequence string in different cases.
GetSequenceWithCaseType(originalSequence1.ConvertToString(), originalSequence2.ConvertToString(),
alphabet, caseType, out aInput, out bInput);
}
else
{
string originalSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode1);
string originalSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceNode2);
// Create input sequence for sequence string in different cases.
GetSequenceWithCaseType(
originalSequence1,
originalSequence2,
alphabet,
caseType,
out aInput,
out bInput);
}
ApplicationLog.WriteLine(string.Format("SmithWatermanAligner P2 : First sequence used is '{0}'.",
aInput.ConvertToString()));
ApplicationLog.WriteLine(string.Format("SmithWatermanAligner P2 : Second sequence used is '{0}'.",
bInput.ConvertToString()));
// Create similarity matrix object for a given file.
string blosumFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.BlosumFilePathNode);
SimilarityMatrix sm;
switch (similarityMatrixParam)
{
case SimilarityMatrixParameters.TextReader:
using (TextReader reader = new StreamReader(blosumFilePath))
sm = new SimilarityMatrix(reader);
break;
case SimilarityMatrixParameters.DiagonalMatrix:
string matchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MatchScoreNode);
string misMatchValue = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MisMatchScoreNode);
sm = new DiagonalSimilarityMatrix(int.Parse(matchValue, null),
int.Parse(misMatchValue, null));
break;
default:
sm = new SimilarityMatrix(new StreamReader(blosumFilePath));
break;
}
int gapOpenCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null);
int gapExtensionCost = int.Parse(this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapExtensionCostNode),
null);
// Create SmithWatermanAligner instance and set its values.
var smithWatermanObj = new SmithWatermanAligner();
if (additionalParameter != AlignParameters.AllParam)
{
smithWatermanObj.SimilarityMatrix = sm;
smithWatermanObj.GapOpenCost = gapOpenCost;
smithWatermanObj.GapExtensionCost = gapExtensionCost;
}
IList<IPairwiseSequenceAlignment> result = null;
// Align the input sequences.
switch (additionalParameter)
{
case AlignParameters.AlignList:
switch (alignType)
{
case AlignmentType.Align:
result = smithWatermanObj.Align(new List<ISequence> {aInput, bInput});
break;
default:
result = smithWatermanObj.AlignSimple(new List<ISequence> {aInput, bInput});
break;
}
break;
case AlignParameters.AlignTwo:
switch (alignType)
{
case AlignmentType.Align:
result = smithWatermanObj.Align(aInput, bInput);
break;
default:
result = smithWatermanObj.AlignSimple(aInput, bInput);
break;
}
break;
case AlignParameters.AllParam:
switch (alignType)
{
case AlignmentType.Align:
result = smithWatermanObj.Align(sm, gapOpenCost,
gapExtensionCost, aInput, bInput);
break;
default:
result = smithWatermanObj.AlignSimple(sm, gapOpenCost, aInput, bInput);
break;
}
break;
default:
break;
}
// Get the expected sequence and scorde from xml config.
string expectedSequence1, expectedSequence2, expectedScore;
switch (alignType)
{
case AlignmentType.Align:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedGapExtensionScoreNode);
switch (caseType)
{
case SequenceCaseType.LowerCase:
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants
.ExpectedGapExtensionSequence1InLower);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants
.ExpectedGapExtensionSequence2InLower);
break;
default:
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants
.ExpectedGapExtensionSequence1Node);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants
.ExpectedGapExtensionSequence2Node);
break;
}
break;
default:
expectedScore = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedScoreNode);
switch (caseType)
{
case SequenceCaseType.LowerCase:
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequence1inLowerNode);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequence2inLowerNode);
break;
case SequenceCaseType.LowerUpperCase:
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequence1inLowerNode);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode2);
break;
default:
expectedSequence1 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode1);
expectedSequence2 = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedSequenceNode2);
break;
}
break;
}
// Match the alignment result with expected result.
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
var alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(alphabet, expectedSequence1),
SecondSequence = new Sequence(alphabet, expectedSequence2),
Score = Convert.ToInt32(expectedScore, null),
FirstOffset = Int32.MinValue,
SecondOffset = Int32.MinValue,
};
align.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(align);
ApplicationLog.WriteLine(string.Format(null, "SmithWatermanAligner P2 : Final Score '{0}'.", expectedScore));
ApplicationLog.WriteLine(string.Format(null, "SmithWatermanAligner P2 : Aligned First Sequence is '{0}'.",
expectedSequence1));
ApplicationLog.WriteLine(string.Format(null, "SmithWatermanAligner P2 : Aligned Second Sequence is '{0}'.",
expectedSequence2));
Assert.IsTrue(CompareAlignment(result, expectedOutput));
}
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));
}
public void NeedlemanWunschDnaSeqSimpleGap()
{
IPairwiseSequenceAligner nw = new NeedlemanWunschAligner
{
SimilarityMatrix = new DiagonalSimilarityMatrix(2, -1),
GapOpenCost = -2
};
ISequence sequence1 = new Sequence(Alphabets.DNA, "GAATTCAGTTA");
ISequence sequence2 = new Sequence(Alphabets.DNA, "GGATCGA");
IList<IPairwiseSequenceAlignment> result = nw.AlignSimple(sequence1, sequence2);
AlignmentHelpers.LogResult(nw, result);
IList<IPairwiseSequenceAlignment> expectedOutput = new List<IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment align = new PairwiseSequenceAlignment();
align.PairwiseAlignedSequences.Add(new PairwiseAlignedSequence
{
FirstSequence = new Sequence(Alphabets.DNA, "GAATTCAGTTA"),
SecondSequence = new Sequence(Alphabets.DNA, "GGAT-C-G--A"),
Consensus = new Sequence(AmbiguousDnaAlphabet.Instance, "GRATTCAGTTA"),
Score = 3,
FirstOffset = 0,
SecondOffset = 0
});
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-UUUUGG-----"),
Consensus = new Sequence(AmbiguousRnaAlphabet.Instance, "UAURCUUUUSSCCCCC"),
Score = -14,
FirstOffset = 1,
SecondOffset = 0
});
expectedOutput.Add(align);
AlignmentHelpers.CompareAlignment(result, expectedOutput);
}
public void TestNUCmer3CustomBreakLength()
{
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" },
};
NucmerPairwiseAligner 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.IsNotNull(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));
}
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 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));
}
/// <summary>
/// This method is considered as main execute method which defines the
/// step by step algorithm. Derived class flows the defined flow by this
/// method.
/// </summary>
/// <param name="referenceSequenceList">Reference sequence.</param>
/// <param name="originalQuerySequences">List of input sequences.</param>
/// <returns>A list of sequence alignment.</returns>
private IEnumerable<IPairwiseSequenceAlignment> Alignment(IEnumerable<ISequence> referenceSequenceList, IEnumerable<ISequence> originalQuerySequences)
{
ConsensusResolver = new SimpleConsensusResolver(referenceSequenceList.ElementAt(0).Alphabet);
IEnumerable<ISequence> querySequenceList =
ForwardOnly ? originalQuerySequences
: (ReverseOnly
? ReverseComplementSequenceList(originalQuerySequences)
: AddReverseComplementsToSequenceList(originalQuerySequences));
IList<IPairwiseSequenceAlignment> results = new List<IPairwiseSequenceAlignment>();
var deltas = new List<DeltaAlignment>();
foreach (ISequence refSequence in referenceSequenceList)
{
this.nucmerAlgo = new NUCmer(refSequence);
if (GapOpenCost != DefaultGapOpenCost) this.nucmerAlgo.GapOpenCost = GapOpenCost;
if (GapExtensionCost != DefaultGapExtensionCost) this.nucmerAlgo.GapExtensionCost = GapExtensionCost;
if (LengthOfMUM != DefaultLengthOfMUM) this.nucmerAlgo.LengthOfMUM = LengthOfMUM;
// Set the ClusterBuilder properties to defaults
if (FixedSeparation != ClusterBuilder.DefaultFixedSeparation) this.nucmerAlgo.FixedSeparation = FixedSeparation;
if (MaximumSeparation != ClusterBuilder.DefaultMaximumSeparation) this.nucmerAlgo.MaximumSeparation = MaximumSeparation;
if (MinimumScore != ClusterBuilder.DefaultMinimumScore) this.nucmerAlgo.MinimumScore = MinimumScore;
if (SeparationFactor != ClusterBuilder.DefaultSeparationFactor) this.nucmerAlgo.SeparationFactor = SeparationFactor;
if (BreakLength != ModifiedSmithWaterman.DefaultBreakLength) this.nucmerAlgo.BreakLength = BreakLength;
this.nucmerAlgo.ConsensusResolver = ConsensusResolver;
if (SimilarityMatrix != null) this.nucmerAlgo.SimilarityMatrix = SimilarityMatrix;
foreach (ISequence querySequence in querySequenceList)
{
// Check for parameters that would prevent an alignment from being returned.
if (Math.Min(querySequence.Count, refSequence.Count) < MinimumScore)
{
var msg = "Bad parameter settings for NucmerPairwiseAligner. " +
"Tried to align a reference of length " + refSequence.Count.ToString() +
" to a sequence of length " + querySequence.Count.ToString() +
" while requiring a minimum score of MinimumScore = " + MinimumScore +
". This will prevent any alignments from being returned.";
throw new ArgumentException(msg);
}
IEnumerable<DeltaAlignment> deltaAlignment = this.nucmerAlgo.GetDeltaAlignments(querySequence, !MaxMatch, querySequence.IsMarkedAsReverseComplement());
deltas.AddRange(deltaAlignment);
}
}
if (deltas.Count > 0)
{
ISequence concatReference = referenceSequenceList.ElementAt(0);
//// concat all the sequences into one sequence
if (referenceSequenceList.Count() > 1)
{
concatReference = ConcatSequence(referenceSequenceList);
}
foreach (ISequence querySequence in querySequenceList)
{
List<DeltaAlignment> qDelta = deltas.Where(d => d.QuerySequence.Equals(querySequence)).ToList();
IPairwiseSequenceAlignment sequenceAlignment = new PairwiseSequenceAlignment(concatReference, querySequence);
// Convert delta alignments to sequence alignments
IList<PairwiseAlignedSequence> alignments = ConvertDeltaToAlignment(qDelta);
if (alignments.Count > 0)
{
foreach (PairwiseAlignedSequence align in alignments)
{
// Calculate the score of alignment
align.Score = CalculateScore(
align.FirstSequence,
align.SecondSequence);
// Make Consensus
align.Consensus = MakeConsensus(
align.FirstSequence,
align.SecondSequence);
sequenceAlignment.PairwiseAlignedSequences.Add(align);
}
}
results.Add(sequenceAlignment);
}
}
return results;
}