public async Task PValueMainline()
{
SequenceMetadata item1 = await
FastALookupCient.LookupByAccessionIdAsync("Q10574");
SequenceMetadata item2 = await
FastALookupCient.LookupByAccessionIdAsync("P15172");
var localAlignmentImpl = new SmithWatermanImplementation(
sequenceTomatch: item1,
targetSequence: item2,
scoreProvider: new SimpleScoreProvider(),
gapOpenPenality: 1);
var pvalueCalculator = new PValueCalculator <SmithWatermanImplementation>
(
alignmentImpl: localAlignmentImpl,
permutationLimit: 10
);
string result = await pvalueCalculator.CalculatePValueAsync();
Assert.IsNotNull(result);
Console.WriteLine("--Calculated P value--");
Console.WriteLine(result);
}
public async Task SmithWatermanP15172ToP17542WithBlosum62ScoringScheme()
{
SequenceMetadata item1 = await
FastALookupCient.LookupByAccessionIdAsync("P10085");
SequenceMetadata item2 = await
FastALookupCient.LookupByAccessionIdAsync("P15172");
var localAlignmentImpl = new SmithWatermanImplementation(
sequenceTomatch: item1,
targetSequence: item2,
scoreProvider: new Blosum62ScoreProvider(),
gapOpenPenality: 4);
//var localAlignmentImpl = new SmithWatermanImplementation(
// sequenceTomatch: "KEVLAR",
// targetSequence: "KNIEVIL",
// scoreProvider: new Blosum62ScoreProvider(),
// gapOpenPenality: 4);
AlignmentImplementationResults result
= localAlignmentImpl.FindOptimalAlignment();
Console.WriteLine("--Optimal Alignment--");
Console.WriteLine(result.TargetSequenceAlignment);
Console.WriteLine(result.SearchSequenceAlignment);
Console.WriteLine("--Optimal Score--");
Console.WriteLine(result.AlignmentScore);
var pvalueCalculator = new PValueCalculator <SmithWatermanImplementation>
(
alignmentImpl: localAlignmentImpl,
permutationLimit: 1
);
string pValue = await pvalueCalculator.CalculatePValueAsync();
Assert.IsNotNull(result);
Console.WriteLine("--Calculated P value--");
Console.WriteLine(pValue);
Console.WriteLine(result.PrettyPrint());
Console.WriteLine(result.PrettyPrintScoreMatrix());
}
public async Task ViterbiGCPatchTenRuns()
{
var gcPatchParameters = new GCPatchParameters();
SequenceMetadata item1 = await
FastALookupCient.LookupByAccessionIdAsync("GCF_000091665.1_ASM9166v1_genomic");
var viterbigcPatch = new ViterbiImpl(gcPatchParameters, input: item1.Sequence);
List <ViterbiResult> results = viterbigcPatch.ExecuteViterbiAndTrain(executionCount: 10);
for (int i = 0; i < 9; i++)
{
Console.WriteLine("Iteration {0}", i + 1);
Console.WriteLine("---------------------------------------------------------------------------");
Console.WriteLine(results[i].PrettyPrint(interestedStateIndex: 1, numberOfHits: 5));
}
Console.WriteLine("Iteration {0}", 10);
Console.WriteLine("---------------------------------------------------------------------------");
Console.WriteLine(results[9].PrettyPrintAllHits(interestedStateIndex: 1));
Assert.IsNotNull(results);
}
public async Task SmithWatermanImplementationMainlineWithSimpleScoringScheme()
{
SequenceMetadata item1 = await
FastALookupCient.LookupByAccessionIdAsync("Q10574");
SequenceMetadata item2 = await
FastALookupCient.LookupByAccessionIdAsync("P15172");
var localAlignmentImpl = new SmithWatermanImplementation(
sequenceTomatch: item1,
targetSequence: item2,
scoreProvider: new SimpleScoreProvider(),
gapOpenPenality: 1);
AlignmentImplementationResults result
= localAlignmentImpl.FindOptimalAlignment();
Console.WriteLine("--Optimal Alignment--");
Console.WriteLine(result.TargetSequenceAlignment);
Console.WriteLine(result.SearchSequenceAlignment);
Console.WriteLine("--Optimal Score--");
Console.WriteLine(result.AlignmentScore);
Assert.AreEqual(expected: 19,
actual: result.AlignmentScore,
message: "Mismatching alignment scores");
Assert.AreEqual(
expected: "VE-IL-RNA-IRY-I-E-GL-QA-LL-RDQD",
actual: result.TargetSequenceAlignment,
message: "Mismatching target alignment sequence");
Assert.AreEqual(
expected: "-FE-TL-QMA-QKY-I-E-CL-SQ-IL-KQD",
actual: result.SearchSequenceAlignment,
message: "Mismatching target alignment sequence");
}
public async Task ViterbiDiceRollTenRuns()
{
var diceRollParams = new DiceRollParameters();
SequenceMetadata item1 = await
FastALookupCient.LookupByAccessionIdAsync("DiceRoll");
var viterbiDiceRoll = new ViterbiImpl(diceRollParams, input: item1.Sequence);
List <ViterbiResult> results = viterbiDiceRoll.ExecuteViterbiAndTrain(executionCount: 10);
for (int i = 0; i < 9; i++)
{
Console.WriteLine("Iteration {0}", i + 1);
Console.WriteLine("---------------------------------------------------------------------------");
Console.WriteLine(results[i].PrettyPrint(interestedStateIndex: 1, numberOfHits: 5));
Console.WriteLine(results[i].StateTransitionRepresentaton);
}
Console.WriteLine("Iteration {0}", 10);
Console.WriteLine("---------------------------------------------------------------------------");
Console.WriteLine(results[9].PrettyPrintAllHits(interestedStateIndex: 1));
Console.WriteLine(results[9].StateTransitionRepresentaton);
Assert.IsNotNull(results);
}
static void Main(string[] args)
{
string outputLocation = @"c:\temp\output_jeeshn.txt";
var proteinAccessionIds = new string[]
{
"P15172",
"P17542",
"P10085",
"P16075",
"P13904",
"Q90477",
"Q8IU24",
"P22816",
"Q10574",
"O95363"
};
// Input data for a simple sequence
var item1 = new SequenceMetadata
{
AccessionId = "X1",
Sequence = "deadly"
};
var item2 = new SequenceMetadata
{
AccessionId = "X2",
Sequence = "ddgearlyk"
};
using (var fileStream = File.Open(outputLocation, FileMode.Create))
using (var streamWriter = new StreamWriter(fileStream))
{
// Run the local alignment .
var localAlignmentImpl = new SmithWatermanImplementation(
sequenceTomatch: item1,
targetSequence: item2,
scoreProvider: new Blosum62ScoreProvider(),
gapOpenPenality: 4);
AlignmentImplementationResults result
= localAlignmentImpl.FindOptimalAlignment();
// "Capture" output
WriteToConsoleAndFile(
String.Format("{0} vs {1}", item1.AccessionId, item2.AccessionId), streamWriter);
WriteToConsoleAndFile("Alignment Score", streamWriter);
WriteToConsoleAndFile(result.AlignmentScore.ToString(), streamWriter);
WriteToConsoleAndFile("Alignment", streamWriter);
WriteToConsoleAndFile(result.PrettyPrint(), streamWriter);
WriteToConsoleAndFile("Score Matrix", streamWriter);
WriteToConsoleAndFile(result.PrettyPrintScoreMatrix(), streamWriter);
// P-value calculation
var pvalueCalculator = new PValueCalculator <SmithWatermanImplementation>
(
alignmentImpl: localAlignmentImpl,
permutationLimit: 999
);
//Print p values
string pValue = pvalueCalculator.CalculatePValueAsync().Result;
WriteToConsoleAndFile("Empirical p-value", streamWriter);
WriteToConsoleAndFile(pValue, streamWriter);
WriteToConsoleAndFile(String.Empty, streamWriter);
int[,] scoreMatrix = new int[10, 10];
for (int i = 0; i < proteinAccessionIds.Length; i++)
{
for (int j = 0; j < proteinAccessionIds.Length; j++)
{
// no need to compare same sequences
if (i != j)
{
item1 = FastALookupCient.LookupByAccessionIdAsync(proteinAccessionIds[i]).Result;
item2 = FastALookupCient.LookupByAccessionIdAsync(proteinAccessionIds[j]).Result;
localAlignmentImpl = new SmithWatermanImplementation(
sequenceTomatch: item1,
targetSequence: item2,
scoreProvider: new Blosum62ScoreProvider(),
gapOpenPenality: 4);
result = localAlignmentImpl.FindOptimalAlignment();
// "Capture" output
WriteToConsoleAndFile(
String.Format("{0} vs {1}", item1.AccessionId, item2.AccessionId), streamWriter);
WriteToConsoleAndFile("Alignment Score", streamWriter);
WriteToConsoleAndFile(result.AlignmentScore.ToString(), streamWriter);
WriteToConsoleAndFile("Alignment", streamWriter);
WriteToConsoleAndFile(result.PrettyPrint(), streamWriter);
scoreMatrix[i, j] = result.AlignmentScore;
if (item1.AccessionId == "P15172" &&
(item2.AccessionId == "Q10574" || item2.AccessionId == "O95363"))
{
pvalueCalculator = new PValueCalculator <SmithWatermanImplementation>
(
alignmentImpl: localAlignmentImpl,
permutationLimit: 999
);
//Print p values
pValue = pvalueCalculator.CalculatePValueAsync().Result;
WriteToConsoleAndFile("Empirical p-value", streamWriter);
WriteToConsoleAndFile(pValue, streamWriter);
WriteToConsoleAndFile(String.Empty, streamWriter);
}
}
}
}
var stringBuilder = new StringBuilder();
for (int i = 0; i <= scoreMatrix.GetUpperBound(0); i++)
{
for (int j = 0; j <= scoreMatrix.GetUpperBound(1); j++)
{
if (j >= i)
{
stringBuilder.Append(scoreMatrix[i, j].ToString().PadRight(6, ' '));
}
else
{
stringBuilder.Append("0".PadRight(6, ' '));
}
}
stringBuilder.AppendLine();
}
WriteToConsoleAndFile("Protein scoring matrix", streamWriter);
WriteToConsoleAndFile(stringBuilder.ToString(), streamWriter);
streamWriter.Flush();
fileStream.Flush();
}
Console.ReadLine();
}
