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 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"); }
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(); }