public void testBug3()
{
//Test on DNA benchmark dataset
ISequenceParser parser = new FastaParser();
string filepath = @"TestUtils\122_raw.afa";
MoleculeType mt = MoleculeType.DNA;
IList <ISequence> orgSequences = parser.Parse(filepath);
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = false;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 2;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.InnerProductFast;
SimilarityMatrix similarityMatrix = null;
switch (mt)
{
case (MoleculeType.DNA):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
break;
case (MoleculeType.RNA):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna);
break;
case (MoleculeType.Protein):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
break;
default:
throw new InvalidDataException("Invalid molecular type");
}
//DateTime startTime = DateTime.Now;
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, mt, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Assert.IsNotNull(msa.AlignedSequences);
((FastaParser)parser).Dispose();
}
public void testBug()
{
List <ISequence> sequences = new List <ISequence>();
ISequence seq1 = new Sequence(Alphabets.Protein, "MQEPQSELNIDPPLSQETFSELWNLLPENNVLSSELCPAVDELLLPESVVNWLDEDSDDAPRMPATSAP");
ISequence seq2 = new Sequence(Alphabets.Protein, "PLSQETFSDLWNLLPENNLLSSELSAPVDDLLPYTDVATWLDECPNEAPQMPEPSAPAAPPPATPAPATSWPLSSFVPSQKTYPGNYGFRLGF");
ISequence seq3 = new Sequence(Alphabets.Protein, "MEPSSETGMDPPLSQETFEDLWSLLPDPLQTVTCRLDNLSEFPDYPLAADMSVLQEGLMGNAVPTVTSCAPSTDDYAGKYGLQLDFQQNGTAKS");
ISequence seq4 = new Sequence(Alphabets.Protein, "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPRVAPAPAAPTPAAPAPAPSWPLS");
ISequence seq5 = new Sequence(Alphabets.Protein, "MEESQAELGVEPPLSQETFSDLWKLLPENNLLSSELSPAVDDLLLSPEDVANWLDERPDEAPQMPEPPAPAAPTPAAPAPATSWPLSSFVPSQK");
ISequence seq6 = new Sequence(Alphabets.Protein, "MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDLLLPQDVEEFFEGPSEALRVSGAPAAQDPVTETPGPVAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQ");
ISequence seq7 = new Sequence(Alphabets.Protein, "FRLGFLHSGTAKSVTWTYSPLLNKLFCQLAKTCPVQLWVSSPPPPNTCVRAMAIYKKSEFVTEVVRRCPHHERCSDSSDGLAPPQHLIRVEGNLRAKYLDDRNTFRHSVV");
sequences.Add(seq1);
sequences.Add(seq2);
sequences.Add(seq3);
sequences.Add(seq4);
sequences.Add(seq5);
sequences.Add(seq6);
sequences.Add(seq7);
SimilarityMatrix sm = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner(sequences,
2, DistanceFunctionTypes.EuclideanDistance, UpdateDistanceMethodsTypes.Average, ProfileAlignerNames.NeedlemanWunschProfileAligner,
ProfileScoreFunctionNames.WeightedEuclideanDistance, sm, -8, -1, 2, 16);
Assert.IsNotNull(msa.AlignedSequences);
}
public void testBug2()
{
//Test on DNA benchmark dataset
string filepath = @"TestUtils\122_raw.afa".TestDir();
FastAParser parser = new FastAParser();
IList <ISequence> orgSequences = parser.Parse(filepath).ToList();
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = false;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 2;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.InnerProductFast;
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Assert.IsNotNull(msa.AlignedSequences);
}
// $TODO: Change the above namespace after PhaseOne changes
/// <summary>
/// Aligns multiple sequences using a multiple sequence aligner.
/// This sample uses PAMSAM with a set of default parameters.
/// </summary>
/// <param name="sequences">List of sequences to align.</param>
/// <returns>List of ISequenceAlignment</returns>
static IList <ISequence> DoMultipleSequenceAlignment(List <ISequence> sequences)
{
// $TODO: Change the signature after PAMSAM PhaseOne is checked in
// Initialise objects for constructor
// $TODO: Change this after PAMSAM PhaseOne is checked in
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
int gapOpenPenalty = -4;
int gapExtendPenalty = -1;
int kmerLength = 3;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.WeightedInnerProduct;
// Call aligner
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
Environment.ProcessorCount * 2, Environment.ProcessorCount);
return(msa.AlignedSequences);
}
public void TestMuscleMultipleSequenceAlignment()
{
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
int gapOpenPenalty = -4;
int gapExtendPenalty = -1;
int kmerLength = 3;
ISequence seqA = new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT");
ISequence seqB = new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG");
ISequence seqC = new Sequence(Alphabets.DNA, "GGGACAAAATCAG");
List <ISequence> sequences = new List <ISequence>();
sequences.Add(seqA);
sequences.Add(seqB);
sequences.Add(seqC);
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.WeightedInnerProduct;
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
Environment.ProcessorCount * 2, Environment.ProcessorCount);
Console.WriteLine("Aligned sequences in stage 1: {0}", msa.AlignmentScoreA);
for (int i = 0; i < msa.AlignedSequencesA.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesA[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Aligned sequences in stage 3: {0}", msa.AlignmentScoreC);
for (int i = 0; i < msa.AlignedSequencesC.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesC[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequences[i].Select(a => (char)a).ToArray()));
}
// Test case 2
Console.WriteLine("Example 2");
sequences = new List <ISequence>();
sequences.Add(new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAAATCG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCTTATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGACAAAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGACAAAATCAG"));
msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
Environment.ProcessorCount * 2, Environment.ProcessorCount);
Console.WriteLine("Aligned sequences in stage 1: {0}", msa.AlignmentScoreA);
for (int i = 0; i < msa.AlignedSequencesA.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesA[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Aligned sequences in stage 3: {0}", msa.AlignmentScoreC);
for (int i = 0; i < msa.AlignedSequencesC.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesC[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequences[i].Select(a => (char)a).ToArray()));
}
// Test case e
Console.WriteLine("Example 2");
sequences = new List <ISequence>();
sequences.Add(new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAAAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAAATCG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGACAAAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCTTATCAG"));
msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
Environment.ProcessorCount * 2, Environment.ProcessorCount);
Console.WriteLine("Aligned sequences in stage 1: {0}", msa.AlignmentScoreA);
for (int i = 0; i < msa.AlignedSequencesA.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesA[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Aligned sequences in stage 3: {0}", msa.AlignmentScoreC);
for (int i = 0; i < msa.AlignedSequencesC.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesC[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequences[i].Select(a => (char)a).ToArray()));
}
}
public void TestMuscleMultipleSequenceAlignmentRunningTime()
{
string filepath = @"TestUtils\FASTA\RunningTime\BOX246.xml.afa";
// Test on DNA benchmark dataset
FastAParser parser = new FastAParser(filepath);
IList <ISequence> orgSequences = parser.Parse().ToList();
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
//filepath = @"TestUtils\FASTA\RunningTime\12_raw.afa";
//List<ISequence> sequences = parser.Parse(filepath);
int numberOfSequences = orgSequences.Count;
Console.WriteLine("Original sequences are:");
for (int i = 0; i < numberOfSequences; ++i)
{
Console.WriteLine(new string(sequences[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Benchmark sequences are:");
for (int i = 0; i < numberOfSequences; ++i)
{
Console.WriteLine(new string(orgSequences[i].Select(a => (char)a).ToArray()));
}
PAMSAMMultipleSequenceAligner.FasterVersion = true;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = false;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 2;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.InnerProductFast;
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Console.WriteLine("The number of partitions is: {0}", numberOfPartitions);
Console.WriteLine("The number of degrees is: {0}", numberOfDegrees);
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences));
Console.WriteLine("Benchmark SPS score is: {0}", MsaUtils.MultipleAlignmentScoreFunction(orgSequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty));
Console.WriteLine("Aligned sequences in stage 1: {0}", msa.AlignmentScoreA);
for (int i = 0; i < msa.AlignedSequencesA.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesA[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesA, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesA, orgSequences));
Console.WriteLine("Aligned sequences in stage 2: {0}", msa.AlignmentScoreB);
for (int i = 0; i < msa.AlignedSequencesB.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesB[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesB, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesB, orgSequences));
Console.WriteLine("Aligned sequences in stage 3: {0}", msa.AlignmentScoreC);
for (int i = 0; i < msa.AlignedSequencesC.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesC[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesC, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesC, orgSequences));
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequences[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences));
((FastAParser)parser).Dispose();
}
public void TestMsaBenchMarkOnBralibase()
{
List <float> allQ = new List <float>();
List <float> allTC = new List <float>();
string fileDirectory = @"testData\FASTA\RNA\k10";
DirectoryInfo iD = new DirectoryInfo(fileDirectory);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = false;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
MoleculeType mt = MoleculeType.RNA;
SimilarityMatrix similarityMatrix;
int gapOpenPenalty = -20;
int gapExtendPenalty = -5;
int kmerLength = 4;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.WeightedInnerProductCached;
switch (mt)
{
case (MoleculeType.DNA):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
break;
case (MoleculeType.RNA):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna);
break;
case (MoleculeType.Protein):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
break;
default:
throw new Exception("Invalid molecular type");
}
foreach (DirectoryInfo fi in iD.GetDirectories())
{
foreach (FileInfo fiii in fi.GetFiles())
{
String filePath = fiii.FullName;
Console.WriteLine(filePath);
ISequenceParser parser = new FastaParser();
IList <ISequence> orgSequences = parser.Parse(filePath);
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
int numberOfSequences = orgSequences.Count;
Console.WriteLine("The number of sequences is: {0}", numberOfSequences);
Console.WriteLine("Original unaligned sequences are:");
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, mt, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
//Console.WriteLine(msa.AlignedSequences[i].ToString());
}
float scoreQ = MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences);
float scoreTC = MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences);
allQ.Add(scoreQ);
allTC.Add(scoreTC);
Console.WriteLine("Alignment score Q is: {0}", scoreQ);
Console.WriteLine("Alignment score TC is: {0}", scoreTC);
if (allQ.Count % 1000 == 0)
{
Console.WriteLine(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>");
Console.WriteLine("average Q score is: {0}", MsaUtils.Mean(allQ.ToArray()));
Console.WriteLine("average TC score is: {0}", MsaUtils.Mean(allTC.ToArray()));
}
}
}
Console.WriteLine("number of datasets is: {0}", allQ.Count);
Console.WriteLine("average Q score is: {0}", MsaUtils.Mean(allQ.ToArray()));
Console.WriteLine("average TC score is: {0}", MsaUtils.Mean(allTC.ToArray()));
}
public void TestMsaBenchMarkLargeDataset()
{
// Test on DNA benchmark dataset
ISequenceParser parser = new FastaParser();
string filepath = @"testdata\FASTA\Protein\Balibase\RV913\BOX032.xml.afa";
IList <ISequence> orgSequences = parser.Parse(filepath);
IList <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
int numberOfSequences = orgSequences.Count;
String outputFilePath = @"tempBOX032.xml.afa";
StreamWriter writer = new StreamWriter(outputFilePath, true);
foreach (ISequence sequence in sequences)
{
writer.WriteLine(">" + sequence.ID);
// write sequence
BasicDerivedSequence derivedSeq = new BasicDerivedSequence(sequence, false, false, 0, 0);
for (int lineStart = 0; lineStart < sequence.Count; lineStart += 60)
{
derivedSeq.RangeStart = lineStart;
derivedSeq.RangeLength = Math.Min(60, sequence.Count - lineStart);
writer.WriteLine(derivedSeq.ToString());
}
writer.Flush();
}
writer.Close();
sequences.Clear();
sequences = parser.Parse(outputFilePath);
Console.WriteLine("Original sequences are:");
for (int i = 0; i < numberOfSequences; ++i)
{
Console.WriteLine(sequences[i].ToString());
}
Console.WriteLine("Benchmark sequences are:");
for (int i = 0; i < numberOfSequences; ++i)
{
Console.WriteLine(orgSequences[i].ToString());
}
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = true;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 3;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.WeightedInnerProduct;
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, MoleculeType.Protein, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Console.WriteLine("Benchmark SPS score is: {0}", MsaUtils.MultipleAlignmentScoreFunction(orgSequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty));
Console.WriteLine("Aligned sequences in stage 1: {0}", msa.AlignmentScoreA);
for (int i = 0; i < msa.AlignedSequencesA.Count; ++i)
{
Console.WriteLine(msa.AlignedSequencesA[i].ToString());
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesA, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesA, orgSequences));
Console.WriteLine("Aligned sequences in stage 2: {0}", msa.AlignmentScoreB);
for (int i = 0; i < msa.AlignedSequencesB.Count; ++i)
{
Console.WriteLine(msa.AlignedSequencesB[i].ToString());
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesB, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesB, orgSequences));
Console.WriteLine("Aligned sequences in stage 3: {0}", msa.AlignmentScoreC);
for (int i = 0; i < msa.AlignedSequencesC.Count; ++i)
{
Console.WriteLine(msa.AlignedSequencesC[i].ToString());
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesC, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesC, orgSequences));
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
Console.WriteLine(msa.AlignedSequences[i].ToString());
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences));
if (File.Exists(outputFilePath))
{
File.Delete(outputFilePath);
}
}
public void PerformPAMSAMPerf()
{
Stopwatch _watchObj = new Stopwatch();
// Get input values from XML.
string refPath =
Utility._xmlUtil.GetTextValue(Constants.PamsamNode,
Constants.RefFilePathNode);
string queryPath =
Utility._xmlUtil.GetTextValue(Constants.PamsamNode,
Constants.QueryFilePathNode);
// Create a List for input files.
List <string> lstInputFiles = new List <string>();
lstInputFiles.Add(refPath);
lstInputFiles.Add(queryPath);
// Parse a Reference and query sequence file.
ISequenceParser parser = new FastaParser();
IList <ISequence> refsequences = parser.Parse(queryPath);
IList <ISequence> orgSequences = parser.Parse(refPath);
// Execute UnAlign method to verify that it does not contains gap
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
// Set static properties
PAMSAMMultipleSequenceAligner.FasterVersion = true;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = false;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
// Set Alignment parameters.
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 2;
int numberOfDegrees = 2;
int numberOfPartitions = 4;
// Profile Distance function name
DistanceFunctionTypes distanceFunctionName =
DistanceFunctionTypes.EuclideanDistance;
// Set Hierarchical clustering.
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName =
UpdateDistanceMethodsTypes.Average;
// Set NeedlemanWunschProfileAligner
ProfileAlignerNames profileAlignerName =
ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName =
ProfileScoreFunctionNames.InnerProduct;
// Create similarity matrix instance.
SimilarityMatrix similarityMatrix =
new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
// Reset stop watch and start timer.
_watchObj.Reset();
_watchObj.Start();
long memoryStart = GC.GetTotalMemory(true);
// Parallel Option will only get set if the PAMSAMMultipleSequenceAligner is getting called
// To test separately distance matrix, binary tree etc..
// Set the parallel option using below ctor.
msa = new PAMSAMMultipleSequenceAligner
(sequences, MoleculeType.DNA, kmerLength, distanceFunctionName,
hierarchicalClusteringMethodName, profileAlignerName,
profileProfileFunctionName, similarityMatrix, gapOpenPenalty,
gapExtendPenalty, numberOfPartitions, numberOfDegrees);
// Stop watchclock.
_watchObj.Stop();
long memoryEnd = GC.GetTotalMemory(true);
string memoryUsed = (memoryEnd - memoryStart).ToString();
// Display all aligned sequence, performance and memory optimization nos.
DisplayTestCaseHeader(lstInputFiles, _watchObj,
memoryUsed, "PAMSAM");
Console.WriteLine(string.Format(
"PAMSAM SequenceAligner method, Alignment Score is : {0}",
msa.AlignmentScore.ToString()));
int index = 0;
foreach (ISequence seq in msa.AlignedSequences)
{
Console.WriteLine(string.Format(
"PAMSAM Aligned Seq {0}:{1}", index, seq.ToString()));
index++;
}
}
public void TestMsaBenchMark()
{
string fileDirectory = @"TestUtils\FASTA\Protein\Balibase\RV911\";
DirectoryInfo iD = new DirectoryInfo(fileDirectory);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = true;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
SimilarityMatrix similarityMatrix;
int gapOpenPenalty = -20;
int gapExtendPenalty = -5;
int kmerLength = 4;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.WeightedInnerProductCached;
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
List <float> allQ = new List <float>();
List <float> allTC = new List <float>();
foreach (FileInfo fi in iD.GetFiles())
{
String filePath = fi.FullName;
Console.WriteLine(filePath);
FastAParser parser = new FastAParser(filePath);
parser.Alphabet = AmbiguousProteinAlphabet.Instance;
IList <ISequence> orgSequences = parser.Parse().ToList();
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
int numberOfSequences = orgSequences.Count;
Console.WriteLine("The number of sequences is: {0}", numberOfSequences);
Console.WriteLine("Original unaligned sequences are:");
for (int i = 0; i < numberOfSequences; ++i)
{
//Console.WriteLine(sequences[i].ToString());
}
Console.WriteLine("Original aligned sequences are:");
for (int i = 0; i < numberOfSequences; ++i)
{
//Console.WriteLine(orgSequences[i].ToString());
}
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Console.WriteLine("Aligned sequences in stage 1: {0}", msa.AlignmentScoreA);
for (int i = 0; i < msa.AlignedSequencesA.Count; ++i)
{
//Console.WriteLine(msa.AlignedSequencesA[i].ToString());
}
Console.WriteLine("Aligned sequences in stage 2: {0}", msa.AlignmentScoreB);
for (int i = 0; i < msa.AlignedSequencesB.Count; ++i)
{
//Console.WriteLine(msa.AlignedSequencesB[i].ToString());
}
Console.WriteLine("Aligned sequences in stage 3: {0}", msa.AlignmentScoreC);
for (int i = 0; i < msa.AlignedSequencesC.Count; ++i)
{
//Console.WriteLine(msa.AlignedSequencesC[i].ToString());
}
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
//Console.WriteLine(msa.AlignedSequences[i].ToString());
}
float scoreQ = MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences);
float scoreTC = MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences);
allQ.Add(scoreQ);
allTC.Add(scoreTC);
Console.WriteLine("Alignment score Q is: {0}", scoreQ);
Console.WriteLine("Alignment score TC is: {0}", scoreTC);
((FastAParser)parser).Dispose();
}
Console.WriteLine("Number of datasets is: {0}", allQ.Count);
Console.WriteLine("average Q score is: {0}", MsaUtils.Mean(allQ.ToArray()));
Console.WriteLine("average TC score is: {0}", MsaUtils.Mean(allTC.ToArray()));
}
public void TestMsaBenchMarkLargeDataset()
{
string filepath = @"\TestUtils\BOX032Small.xml.afa";
string filePathObj = Directory.GetCurrentDirectory() + filepath;
// Test on DNA benchmark dataset
FastAParser parser = new FastAParser(filePathObj);
IList <ISequence> orgSequences = parser.Parse().ToList();
IList <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
int numberOfSequences = orgSequences.Count;
String outputFilePath = @"tempBOX032.xml.afa";
using (StreamWriter writer = new StreamWriter(outputFilePath, true))
{
foreach (ISequence sequence in sequences)
{
writer.WriteLine(">" + sequence.ID);
// write sequence
for (int lineStart = 0; lineStart < sequence.Count; lineStart += 60)
{
writer.WriteLine(new String(sequence.Skip(lineStart).Take((int)Math.Min(60, sequence.Count - lineStart)).Select(a => (char)a).ToArray()));
}
writer.Flush();
}
}
sequences.Clear();
parser = new FastAParser(outputFilePath);
sequences = parser.Parse().ToList();
Console.WriteLine("Original sequences are:");
for (int i = 0; i < numberOfSequences; ++i)
{
Console.WriteLine(new string(sequences[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Benchmark sequences are:");
for (int i = 0; i < numberOfSequences; ++i)
{
Console.WriteLine(new string(orgSequences[i].Select(a => (char)a).ToArray()));
}
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = true;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 3;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.WeightedInnerProduct;
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Console.WriteLine("Benchmark SPS score is: {0}", MsaUtils.MultipleAlignmentScoreFunction(orgSequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty));
Console.WriteLine("Aligned sequences in stage 1: {0}", msa.AlignmentScoreA);
for (int i = 0; i < msa.AlignedSequencesA.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesA[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesA, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesA, orgSequences));
Console.WriteLine("Aligned sequences in stage 2: {0}", msa.AlignmentScoreB);
for (int i = 0; i < msa.AlignedSequencesB.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesB[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesB, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesB, orgSequences));
Console.WriteLine("Aligned sequences in stage 3: {0}", msa.AlignmentScoreC);
for (int i = 0; i < msa.AlignedSequencesC.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequencesC[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesC, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesC, orgSequences));
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
Console.WriteLine(new string(msa.AlignedSequences[i].Select(a => (char)a).ToArray()));
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences));
((FastAParser)parser).Dispose();
if (File.Exists(outputFilePath))
{
File.Delete(outputFilePath);
}
}
public void TestName()
{
PAMSAMMultipleSequenceAligner aligner = new PAMSAMMultipleSequenceAligner();
Assert.AreEqual("PAMSAM (MUSCLE)", aligner.Name);
}
public void TestMuscleMultipleSequenceAlignmentRunningTime()
{
// Test on DNA benchmark dataset
ISequenceParser parser = new FastaParser();
//string filepath = @"testdata\FASTA\RunningTime\122.afa";
string filepath = @"testdata\FASTA\RunningTime\BOX246.xml.afa";
MoleculeType mt = MoleculeType.Protein;
IList <ISequence> orgSequences = parser.Parse(filepath);
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
//filepath = @"testdata\FASTA\RunningTime\12_raw.afa";
//List<ISequence> sequences = parser.Parse(filepath);
int numberOfSequences = orgSequences.Count;
Console.WriteLine("Original sequences are:");
for (int i = 0; i < numberOfSequences; ++i)
{
Console.WriteLine(sequences[i].ToString());
}
Console.WriteLine("Benchmark sequences are:");
for (int i = 0; i < numberOfSequences; ++i)
{
Console.WriteLine(orgSequences[i].ToString());
}
PAMSAMMultipleSequenceAligner.FasterVersion = true;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = false;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 2;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.InnerProductFast;
SimilarityMatrix similarityMatrix = null;
switch (mt)
{
case (MoleculeType.DNA):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
break;
case (MoleculeType.RNA):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna);
break;
case (MoleculeType.Protein):
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
break;
default:
throw new Exception("Invalid molecular type");
}
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, mt, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Console.WriteLine("The number of partitions is: {0}", numberOfPartitions);
Console.WriteLine("The number of degrees is: {0}", numberOfDegrees);
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences));
Console.WriteLine("Benchmark SPS score is: {0}", MsaUtils.MultipleAlignmentScoreFunction(orgSequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty));
Console.WriteLine("Aligned sequences in stage 1: {0}", msa.AlignmentScoreA);
for (int i = 0; i < msa.AlignedSequencesA.Count; ++i)
{
Console.WriteLine(msa.AlignedSequencesA[i].ToString());
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesA, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesA, orgSequences));
Console.WriteLine("Aligned sequences in stage 2: {0}", msa.AlignmentScoreB);
for (int i = 0; i < msa.AlignedSequencesB.Count; ++i)
{
Console.WriteLine(msa.AlignedSequencesB[i].ToString());
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesB, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesB, orgSequences));
Console.WriteLine("Aligned sequences in stage 3: {0}", msa.AlignmentScoreC);
for (int i = 0; i < msa.AlignedSequencesC.Count; ++i)
{
Console.WriteLine(msa.AlignedSequencesC[i].ToString());
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesC, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesC, orgSequences));
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
Console.WriteLine(msa.AlignedSequences[i].ToString());
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences));
}
public void TestMsaBenchMarkOnBralibase()
{
var allQ = new List <float>();
var allTC = new List <float>();
string fileDirectory = @"TestUtils\Fasta\RNA\k10".TestDir();
DirectoryInfo iD = new DirectoryInfo(fileDirectory);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = false;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
var similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousRna);;
int gapOpenPenalty = -20;
int gapExtendPenalty = -5;
int kmerLength = 4;
int numberOfDegrees = 2;
int numberOfPartitions = 16;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.WeightedInnerProductCached;
foreach (DirectoryInfo fi in iD.GetDirectories())
{
foreach (FileInfo fiii in fi.GetFiles())
{
String filePath = fiii.FullName;
Console.WriteLine($"Loading: {filePath}");
var orgSequences = new FastAParser()
{
Alphabet = AmbiguousRnaAlphabet.Instance
}.Parse(filePath).ToList();
var sequences = MsaUtils.UnAlign(orgSequences);
int numberOfSequences = orgSequences.Count;
Console.WriteLine("The number of sequences is: {0}", numberOfSequences);
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
float scoreQ = MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences);
float scoreTC = MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences);
Console.WriteLine("Alignment score Q is: {0}", scoreQ);
Console.WriteLine("Alignment score TC is: {0}", scoreTC);
allQ.Add(scoreQ);
allTC.Add(scoreTC);
if (allQ.Count % 1000 == 0)
{
Console.WriteLine(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>");
Console.WriteLine("average Q score is: {0}", MsaUtils.Mean(allQ.ToArray()));
Console.WriteLine("average TC score is: {0}", MsaUtils.Mean(allTC.ToArray()));
}
}
}
Console.WriteLine("number of datasets is: {0}", allQ.Count);
Console.WriteLine("average Q score is: {0}", MsaUtils.Mean(allQ.ToArray()));
Console.WriteLine("average TC score is: {0}", MsaUtils.Mean(allTC.ToArray()));
}
public void TestMsaBenchMarkOnSABmark()
{
List <float> allQ = new List <float>();
List <float> allTC = new List <float>();
string fileDirectory = @"TestUtils\Fasta\Protein\SABmark".TestDir();
DirectoryInfo iD = new DirectoryInfo(fileDirectory);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = true;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
SimilarityMatrix similarityMatrix;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 3;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.WeightedInnerProduct;
similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
foreach (DirectoryInfo fi in iD.GetDirectories())
{
foreach (DirectoryInfo fii in fi.GetDirectories())
{
foreach (FileInfo fiii in fii.GetFiles())
{
String filePath = fiii.FullName;
Console.WriteLine(filePath);
FastAParser parser = new FastAParser();
IList <ISequence> orgSequences = parser.Parse(filePath).ToList();
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
int numberOfSequences = orgSequences.Count;
Console.WriteLine("The number of sequences is: {0}", numberOfSequences);
Console.WriteLine("Original unaligned sequences are:");
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
//Console.WriteLine(msa.AlignedSequences[i].ToString());
}
float scoreQ = MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences);
float scoreTC = MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences);
allQ.Add(scoreQ);
allTC.Add(scoreTC);
Console.WriteLine("Alignment score Q is: {0}", scoreQ);
Console.WriteLine("Alignment score TC is: {0}", scoreTC);
if (allQ.Count % 1000 == 0)
{
Console.WriteLine(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>");
Console.WriteLine("average Q score is: {0}", MsaUtils.Mean(allQ.ToArray()));
Console.WriteLine("average TC score is: {0}", MsaUtils.Mean(allTC.ToArray()));
}
}
}
}
Console.WriteLine("average Q score is: {0}", MsaUtils.Mean(allQ.ToArray()));
Console.WriteLine("average TC score is: {0}", MsaUtils.Mean(allTC.ToArray()));
}
public void TestMsaBenchMarkLargeDataset()
{
// Test on DNA benchmark dataset
string filePathObj = @"TestUtils\BOX032Small.xml.afa".TestDir();
var orgSequences = new FastAParser().Parse(filePathObj).ToList();
var sequences = MsaUtils.UnAlign(orgSequences);
int numberOfSequences = orgSequences.Count;
Assert.AreEqual(numberOfSequences, sequences.Count);
string outputFilePath = Path.GetTempFileName();
try
{
using (StreamWriter writer = new StreamWriter(outputFilePath, true))
{
foreach (ISequence sequence in sequences)
{
// write sequence
writer.WriteLine(">" + sequence.ID);
for (int lineStart = 0; lineStart < sequence.Count; lineStart += 60)
{
writer.WriteLine(new String(sequence.Skip(lineStart).Take((int)Math.Min(60, sequence.Count - lineStart)).Select(a => (char)a).ToArray()));
}
writer.Flush();
}
}
sequences = new FastAParser().Parse(outputFilePath).ToList();
}
finally
{
File.Delete(outputFilePath);
}
Console.WriteLine("Original sequences are:");
sequences.ForEach(Console.WriteLine);
Console.WriteLine("Benchmark sequences are:");
orgSequences.ForEach(Console.WriteLine);
// Begin alignment
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = true;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 3;
int numberOfDegrees = 2;
int numberOfPartitions = 16;
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum62);
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.WeightedInnerProduct;
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Console.WriteLine("Benchmark SPS score is: {0}", MsaUtils.MultipleAlignmentScoreFunction(orgSequences, similarityMatrix, gapOpenPenalty, gapExtendPenalty));
Console.WriteLine("Aligned sequences in stage 1: {0}", msa.AlignmentScoreA);
for (int i = 0; i < msa.AlignedSequencesA.Count; ++i)
{
Console.WriteLine(msa.AlignedSequencesA[i]);
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesA, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesA, orgSequences));
Console.WriteLine("Aligned sequences in stage 2: {0}", msa.AlignmentScoreB);
for (int i = 0; i < msa.AlignedSequencesB.Count; ++i)
{
Console.WriteLine(msa.AlignedSequencesB[i]);
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesB, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesB, orgSequences));
Console.WriteLine("Aligned sequences in stage 3: {0}", msa.AlignmentScoreC);
for (int i = 0; i < msa.AlignedSequencesC.Count; ++i)
{
Console.WriteLine(msa.AlignedSequencesC[i]);
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequencesC, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequencesC, orgSequences));
Console.WriteLine("Aligned sequences final: {0}", msa.AlignmentScore);
for (int i = 0; i < msa.AlignedSequences.Count; ++i)
{
Console.WriteLine(msa.AlignedSequences[i]);
}
Console.WriteLine("Alignment score Q is: {0}", MsaUtils.CalculateAlignmentScoreQ(msa.AlignedSequences, orgSequences));
Console.WriteLine("Alignment score TC is: {0}", MsaUtils.CalculateAlignmentScoreTC(msa.AlignedSequences, orgSequences));
}