public void TestKimuraDistanceMatrixGenerator()
{
List <ISequence> sequences = new List <ISequence>();
sequences.Add(new Sequence(Alphabets.DNA, "ACGTAA"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCTTATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGACAAAATCAG"));
int kmerLength = 3;
// test of kmer counting
KmerDistanceScoreCalculator kmerDistanceScoreCalculator = new KmerDistanceScoreCalculator(kmerLength, MoleculeType.DNA);
Dictionary <String, float> countDictionaryA = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[0], kmerLength);
Dictionary <String, float> countDictionaryB = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[1], kmerLength);
Dictionary <String, float> expectedCountDictionaryA = new Dictionary <String, float>();
expectedCountDictionaryA.Add("ACG", 1);
expectedCountDictionaryA.Add("CGT", 1);
expectedCountDictionaryA.Add("GTA", 1);
expectedCountDictionaryA.Add("TAA", 1);
Assert.AreEqual(countDictionaryA, expectedCountDictionaryA);
foreach (var pair in countDictionaryA)
{
foreach (char s in pair.Key)
{
Console.Write(s + " ");
}
Console.WriteLine(pair.Value);
}
foreach (var pair in countDictionaryB)
{
foreach (char s in pair.Key)
{
Console.Write(s + " ");
}
Console.WriteLine(pair.Value);
}
float distanceScore = kmerDistanceScoreCalculator.CalculateDistanceScore(countDictionaryA, countDictionaryB);
Console.WriteLine(distanceScore);
KmerDistanceMatrixGenerator kmerDistanceMatrixGenerator = new KmerDistanceMatrixGenerator(sequences, kmerLength, MoleculeType.DNA);
for (int i = 0; i < sequences.Count - 1; ++i)
{
for (int j = i + 1; j < sequences.Count; ++j)
{
Console.WriteLine("Kmer Distance of sequence {0}, and {1} is: {2}", i, j, kmerDistanceMatrixGenerator.DistanceMatrix[i, j]);
}
}
}
public void TestKimuraDistanceMatrixGenerator()
{
List <ISequence> sequences = new List <ISequence>();
sequences.Add(new Sequence(Alphabets.DNA, "ACGTAA"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCAATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAATCTTATCAG"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGACAAAATCAG"));
int kmerLength = 3;
// test kmer counting
KmerDistanceScoreCalculator kmerDistanceScoreCalculator =
new KmerDistanceScoreCalculator(kmerLength, MoleculeType.DNA);
Dictionary <String, float> countDictionaryA =
KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[0], kmerLength);
Dictionary <String, float> countDictionaryB =
KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[1], kmerLength);
Dictionary <String, float> expectedCountDictionaryA = new Dictionary <String, float>();
expectedCountDictionaryA.Add("ACG", 1);
expectedCountDictionaryA.Add("CGT", 1);
expectedCountDictionaryA.Add("GTA", 1);
expectedCountDictionaryA.Add("TAA", 1);
Assert.AreEqual(countDictionaryA["ACG"], expectedCountDictionaryA["ACG"]);
Assert.AreEqual(countDictionaryA["CGT"], expectedCountDictionaryA["CGT"]);
Assert.AreEqual(countDictionaryA["GTA"], expectedCountDictionaryA["GTA"]);
Assert.AreEqual(countDictionaryA["TAA"], expectedCountDictionaryA["TAA"]);
Dictionary <String, float> expectedCountDictionaryB = new Dictionary <String, float>();
expectedCountDictionaryB.Add("GGG", 1);
expectedCountDictionaryB.Add("GGA", 1);
expectedCountDictionaryB.Add("GAA", 1);
expectedCountDictionaryB.Add("AAT", 2);
expectedCountDictionaryB.Add("ATC", 2);
expectedCountDictionaryB.Add("TCA", 2);
expectedCountDictionaryB.Add("CAA", 1);
expectedCountDictionaryB.Add("CAG", 1);
Assert.AreEqual(countDictionaryB["GGG"], expectedCountDictionaryB["GGG"]);
Assert.AreEqual(countDictionaryB["GGA"], expectedCountDictionaryB["GGA"]);
Assert.AreEqual(countDictionaryB["GAA"], expectedCountDictionaryB["GAA"]);
Assert.AreEqual(countDictionaryB["AAT"], expectedCountDictionaryB["AAT"]);
Assert.AreEqual(countDictionaryB["ATC"], expectedCountDictionaryB["ATC"]);
Assert.AreEqual(countDictionaryB["TCA"], expectedCountDictionaryB["TCA"]);
Assert.AreEqual(countDictionaryB["CAA"], expectedCountDictionaryB["CAA"]);
Assert.AreEqual(countDictionaryB["CAG"], expectedCountDictionaryB["CAG"]);
foreach (var pair in countDictionaryA)
{
foreach (char s in pair.Key)
{
Console.Write(s + " ");
}
Console.WriteLine(pair.Value);
}
foreach (var pair in countDictionaryB)
{
foreach (char s in pair.Key)
{
Console.Write(s + " ");
}
Console.WriteLine(pair.Value);
}
float distanceScore = kmerDistanceScoreCalculator.CalculateDistanceScore(countDictionaryA, countDictionaryB);
Console.WriteLine(distanceScore);
PAMSAMMultipleSequenceAligner.parallelOption = new ParallelOptions {
MaxDegreeOfParallelism = 2
};
KmerDistanceMatrixGenerator kmerDistanceMatrixGenerator = new KmerDistanceMatrixGenerator(sequences, kmerLength, MoleculeType.DNA);
for (int i = 0; i < sequences.Count - 1; ++i)
{
for (int j = i + 1; j < sequences.Count; ++j)
{
Console.WriteLine("Kmer Distance of sequence {0}, and {1} is: {2}", i, j, kmerDistanceMatrixGenerator.DistanceMatrix[i, j]);
}
}
// test kmer counting CoVariance
KmerDistanceScoreCalculator kmerDistanceScoreCalculatorB = new KmerDistanceScoreCalculator(kmerLength, MoleculeType.DNA, DistanceFunctionTypes.CoVariance);
countDictionaryA = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[0], kmerLength);
countDictionaryB = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[1], kmerLength);
distanceScore = kmerDistanceScoreCalculatorB.CalculateDistanceScore(countDictionaryA, countDictionaryB);
Console.WriteLine(distanceScore);
KmerDistanceMatrixGenerator kmerDistanceMatrixGeneratorB = new KmerDistanceMatrixGenerator(sequences, kmerLength, MoleculeType.DNA, DistanceFunctionTypes.CoVariance);
for (int i = 0; i < sequences.Count - 1; ++i)
{
for (int j = i + 1; j < sequences.Count; ++j)
{
Console.WriteLine("Kmer Distance of sequence {0}, and {1} is: {2}", i, j, kmerDistanceMatrixGeneratorB.DistanceMatrix[i, j]);
}
}
// test kmer counting ModifiedMUSCLE
KmerDistanceScoreCalculator kmerDistanceScoreCalculatorC = new KmerDistanceScoreCalculator(kmerLength, MoleculeType.DNA, DistanceFunctionTypes.ModifiedMUSCLE);
countDictionaryA = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[0], kmerLength);
countDictionaryB = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[1], kmerLength);
distanceScore = kmerDistanceScoreCalculatorC.CalculateDistanceScore(countDictionaryA, countDictionaryB);
Console.WriteLine(distanceScore);
KmerDistanceMatrixGenerator kmerDistanceMatrixGeneratorC = new KmerDistanceMatrixGenerator(sequences, kmerLength, MoleculeType.DNA, DistanceFunctionTypes.ModifiedMUSCLE);
for (int i = 0; i < sequences.Count - 1; ++i)
{
for (int j = i + 1; j < sequences.Count; ++j)
{
Console.WriteLine("Kmer Distance of sequence {0}, and {1} is: {2}", i, j, kmerDistanceMatrixGeneratorC.DistanceMatrix[i, j]);
}
}
// test kmer counting PearsonCorrelation
KmerDistanceScoreCalculator kmerDistanceScoreCalculatorD = new KmerDistanceScoreCalculator(kmerLength, MoleculeType.DNA, DistanceFunctionTypes.PearsonCorrelation);
countDictionaryA = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[0], kmerLength);
countDictionaryB = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[1], kmerLength);
distanceScore = kmerDistanceScoreCalculatorD.CalculateDistanceScore(countDictionaryA, countDictionaryB);
Console.WriteLine(distanceScore);
KmerDistanceMatrixGenerator kmerDistanceMatrixGeneratorD = new KmerDistanceMatrixGenerator(sequences, kmerLength, MoleculeType.DNA, DistanceFunctionTypes.PearsonCorrelation);
for (int i = 0; i < sequences.Count - 1; ++i)
{
for (int j = i + 1; j < sequences.Count; ++j)
{
Console.WriteLine("Kmer Distance of sequence {0}, and {1} is: {2}", i, j, kmerDistanceMatrixGeneratorD.DistanceMatrix[i, j]);
}
}
// Test for case 2
sequences.Clear();
sequences.Add(new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGAAAAATCAGATT"));
sequences.Add(new Sequence(Alphabets.DNA, "GGGACAAAATCAG"));
// test kmer counting
countDictionaryA = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[0], kmerLength);
countDictionaryB = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[1], kmerLength);
foreach (var pair in countDictionaryA)
{
foreach (char s in pair.Key)
{
Console.Write(s + " ");
}
Console.WriteLine(pair.Value);
}
foreach (var pair in countDictionaryB)
{
foreach (char s in pair.Key)
{
Console.Write(s + " ");
}
Console.WriteLine(pair.Value);
}
distanceScore = kmerDistanceScoreCalculator.CalculateDistanceScore(countDictionaryA, countDictionaryB);
Console.WriteLine(distanceScore);
kmerDistanceMatrixGenerator = new KmerDistanceMatrixGenerator(sequences, kmerLength, MoleculeType.DNA);
for (int i = 0; i < sequences.Count - 1; ++i)
{
for (int j = i + 1; j < sequences.Count; ++j)
{
Console.WriteLine("Kmer Distance of sequence {0}, and {1} is: {2}", i, j, kmerDistanceMatrixGenerator.DistanceMatrix[i, j]);
}
}
// Test on larger dataset
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"));
kmerLength = 4;
kmerDistanceMatrixGenerator =
new KmerDistanceMatrixGenerator(sequences, kmerLength, MoleculeType.DNA, DistanceFunctionTypes.EuclideanDistance);
kmerDistanceScoreCalculator = new KmerDistanceScoreCalculator(kmerLength, MoleculeType.DNA, DistanceFunctionTypes.EuclideanDistance);
for (int i = 0; i < kmerDistanceMatrixGenerator.DistanceMatrix.Dimension - 1; ++i)
{
for (int j = i + 1; j < kmerDistanceMatrixGenerator.DistanceMatrix.Dimension; ++j)
{
countDictionaryA = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[i], kmerLength);
countDictionaryB = KmerDistanceScoreCalculator.CalculateKmerCounting(sequences[j], kmerLength);
MsaUtils.Normalize(countDictionaryA);
MsaUtils.Normalize(countDictionaryB);
float score = kmerDistanceScoreCalculator.CalculateDistanceScore(countDictionaryA, countDictionaryB);
Console.WriteLine("{0}-{1}: {2}", i, j, score);
Console.WriteLine("{0}-{1}: {2}", i, j, kmerDistanceMatrixGenerator.DistanceMatrix[i, j]);
// Assert.AreEqual(score, kmerDistanceMatrixGenerator.DistanceMatrix[i, j]);
}
}
}
public float DistanceScore(int kmerLength, IAlphabet alphabet, DistanceFunctionTypes distanceFunctionType, Dictionary <string, float> countsDA, Dictionary <string, float> countsDB)
{
_indexer = new KmerDistanceScoreCalculator(kmerLength, alphabet, distanceFunctionType);
return(_indexer.CalculateDistanceScore(countsDA, countsDB));
}
