public RunInformedWorkflow ( |
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target | /// The Target. /// | |
Résultat |
public void TestSinglePeptideDidNotFind() { string uimfFileLocation = Cheetah; //string netAlignmentFileLocation = @"..\..\..\testFiles\Sarc_MS2_90_6Apr11_Cheetah_11-02-19_NetAlign.csv"; //IInterpolation interpolation = AlignmentImporter.ReadFile(netAlignmentFileLocation); LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters { ChargeStateMax = 5, NetTolerance = 0.2, IsotopicFitScoreThreshold = 0.15, MassToleranceInPpm = 30, NumPointForSmoothing = 9 }; string peptide = "TILDDLRAEDHFSVIDFNQNIR"; double net = 0.48228999972343445; List<Modification> modificationList = new List<Modification>(); //modificationList.Add(Modification.Oxidation); //modificationList.Add(Modification.Carbamidomethylation); //modificationList.Add(Modification.Carbamidomethylation); PeptideTarget target = new PeptideTarget(1, peptide, net, modificationList); LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileLocation, parameters, null); var correlationResult = lcImsPeptideSearchWorkfow.RunInformedWorkflow(target); Console.WriteLine(correlationResult.ReferenceLcImsTargetResult.NormalizedElutionTime); }
public void TestVerySaturatedPeptide() { string uimfFileLocation = Cheetah; LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters { ChargeStateMax = 2, NetTolerance = 0.03, IsotopicFitScoreThreshold = 0.15, MassToleranceInPpm = 30, NumPointForSmoothing = 9 }; string peptide = "NFPSPVDAAFR"; double net = 0.45; PeptideTarget target = new PeptideTarget(1, peptide, net); LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileLocation, parameters); lcImsPeptideSearchWorkfow.RunInformedWorkflow(target); }
public void TestSinglePeptide() { string uimfFileLocation = Cheetah; LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters { ChargeStateMax = 5, NetTolerance = 0.1, IsotopicFitScoreThreshold = 0.15, MassToleranceInPpm = 30, ScanWindowWidth = 4, NumPointForSmoothing = 9 }; string peptide = "DGWHSWPIAHQWPQGPSAVDAAFSWEEK"; double net = 0.4832; PeptideTarget target = new PeptideTarget(1, peptide, net); LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileLocation, parameters); lcImsPeptideSearchWorkfow.RunInformedWorkflow(target); }
public void TestSinglePeptide2() { string uimfFileLocation = Cheetah; LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters { ChargeStateMax = 5, NetTolerance = 0.2, IsotopicFitScoreThreshold = 0.15, MassToleranceInPpm = 30, NumPointForSmoothing = 9 }; string peptide = "ATVLNYLPK"; double net = 0.3612; PeptideTarget target = new PeptideTarget(1, peptide, net); DriftTimeTarget driftTimeTarget = new DriftTimeTarget("Test Target", 19.62, target, 2); target.DriftTimeTargetList.Add(driftTimeTarget); LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileLocation, parameters); ChargeStateCorrelationResult correlationResult = lcImsPeptideSearchWorkfow.RunInformedWorkflow(target); using (ImsTargetResultExporter resultsExporter = new ImsTargetResultExporter("outputSingle.csv")) { if (correlationResult != null) resultsExporter.AppendCorrelationResultToCsv(correlationResult); } }
public void TestCalibration() { string uimfFileLocation = Cheetah; LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters { ChargeStateMax = 5, NetTolerance = 0.5, IsotopicFitScoreThreshold = 0.15, MassToleranceInPpm = 30, NumPointForSmoothing = 9 }; List<PeptideTarget> targetList = MassTagImporter.ImportMassTags("elmer", "MT_Human_Sarcopenia_P789", 1e-10, true); Console.WriteLine("Using " + targetList.Count + " targets for calibration."); List<Tuple<double, double>> netAlignmentInput = new List<Tuple<double, double>>(); List<Tuple<double, double>> massAlignmentInput = new List<Tuple<double, double>>(); LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileLocation, parameters); foreach (var imsTarget in targetList.OrderBy(x => x.NormalizedElutionTime)) { ChargeStateCorrelationResult correlationResult = lcImsPeptideSearchWorkfow.RunInformedWorkflow(imsTarget); if (correlationResult == null || !correlationResult.CorrelatedResults.Any()) continue; LcImsTargetResult result = correlationResult.CorrelatedResults.OrderByDescending(x => x.Intensity).First(); //LcImsTargetResult result = correlationResult.CorrelatedResults.OrderByDescending(X => X.Intensity * (1 - Math.Abs(X.NormalizedElutionTime - imsTarget.NormalizedElutionTime))).First(); //LcImsTargetResult result = correlationResult.CorrelatedResults.OrderBy(X => X.NormalizedElutionTime).First(); //if (netAlignmentInput.Count == 0 || Math.Abs(netAlignmentInput.Last().Item1 - imsTarget.NormalizedElutionTime) > 0.0001) //{ // netAlignmentInput.Add(new Tuple<double, double>(imsTarget.NormalizedElutionTime, result.NormalizedElutionTime)); // massAlignmentInput.Add(new Tuple<double, double>(imsTarget.NormalizedElutionTime, result.PpmError)); //} netAlignmentInput.Add(new Tuple<double, double>(result.NormalizedElutionTime, imsTarget.NormalizedElutionTime)); massAlignmentInput.Add(new Tuple<double, double>(result.IsotopicProfile.MonoPeakMZ, result.PpmError)); } var netAlignmentInputGroup = netAlignmentInput.GroupBy(x => x.Item1).OrderBy(x => x.Key); var massAlignmentInputGroup = massAlignmentInput.GroupBy(x => x.Item1).OrderBy(x => x.Key); netAlignmentInput = netAlignmentInput.OrderBy(x => x.Item1).ToList(); massAlignmentInput = massAlignmentInput.OrderBy(x => x.Item1).ToList(); var groupedNetTuple = netAlignmentInputGroup.Select(x => x.OrderBy(y => Math.Abs(y.Item1 - y.Item2)).First()).ToArray(); //var groupedNetTuple = netAlignmentInputGroup.Select(X => X.Average(Y => Y.Item2)).ToArray(); var groupedMassTuple = massAlignmentInputGroup.Select(x => x.First()).ToArray(); var loessInterpolatorForNetAlignment = new LoessInterpolator(0.1, 4); var loessInterpolatorForMassAlignment = new LoessInterpolator(0.2, 1); //double[] newNetValues = loessInterpolatorForNetAlignment.Smooth(netAlignmentInputGroup.Select(X => X.Key).ToArray(), netAlignmentInputGroup.Select(X => X.Average(Y => Y.Item2)).ToArray()); double[] newNetValues = loessInterpolatorForNetAlignment.Smooth(groupedNetTuple.Select(x => x.Item1).ToArray(), groupedNetTuple.Select(x => x.Item2).ToArray()); double[] newMassValues = loessInterpolatorForMassAlignment.Smooth(groupedMassTuple.Select(x => x.Item1).ToArray(), groupedMassTuple.Select(x => x.Item2).ToArray()); using(StreamWriter writer = new StreamWriter("oldNetValues.csv")) { foreach (var netTuple in groupedNetTuple) { writer.WriteLine(netTuple.Item1 + "," + netTuple.Item2); } } using (StreamWriter writer = new StreamWriter("oldMassValues.csv")) { foreach (var massTuple in groupedMassTuple) { writer.WriteLine(massTuple.Item1 + "," + massTuple.Item2); } } using (StreamWriter writer = new StreamWriter("smoothedNetValues.csv")) { for (int i = 0; i < groupedNetTuple.Length; i++) { writer.WriteLine(groupedNetTuple[i].Item1 + "," + newNetValues[i]); } } using (StreamWriter writer = new StreamWriter("smoothedMassValues.csv")) { for (int i = 0; i < groupedMassTuple.Length; i++) { writer.WriteLine(groupedMassTuple[i].Item1 + "," + newMassValues[i]); } } }
public void TestRunAllTargets() { string uimfFileLocation = Cheetah; string netAlignmentFileLocation = @""; IInterpolation interpolation = AlignmentImporter.ReadFile(netAlignmentFileLocation); LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters { ChargeStateMax = 5, NetTolerance = 0.03, IsotopicFitScoreThreshold = 0.2, MassToleranceInPpm = 30, NumPointForSmoothing = 9 }; List<PeptideTarget> targetList = MassTagImporter.ImportMassTags("elmer", "MT_Human_Sarcopenia_P789"); Console.WriteLine(DateTime.Now + ": Using " + targetList.Count + " targets."); using (ImsTargetResultExporter allResultsExporter = new ImsTargetResultExporter("outputTestAll.csv")) { using (ImsTargetResultExporter resultsExporter = new ImsTargetResultExporter("outputTest.csv")) { LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileLocation, parameters, interpolation); foreach (var imsTarget in targetList) { ChargeStateCorrelationResult correlationResult = lcImsPeptideSearchWorkfow.RunInformedWorkflow(imsTarget); allResultsExporter.AppendResultsOfTargetToCsv(imsTarget); if (correlationResult == null) continue; resultsExporter.AppendCorrelationResultToCsv(correlationResult); } } } }
public void TestInterestingPeptideThatHasOverlappingInterferenceTowardsEndOfElution() { string uimfFileLocation = @"..\..\..\testFiles\Sarc_MS2_90_6Apr11_Cheetah_11-02-19.uimf"; string netAlignmentFileLocation = @"..\..\..\testFiles\Sarc_MS2_90_6Apr11_Cheetah_11-02-19_NetAlign.csv"; IInterpolation interpolation = AlignmentImporter.ReadFile(netAlignmentFileLocation); LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters { ChargeStateMax = 5, NetTolerance = 0.03, IsotopicFitScoreThreshold = 0.15, MassToleranceInPpm = 30, NumPointForSmoothing = 9 }; string peptide = "LCHCPVGYTGPFCDVDTK"; double net = 0.3041; List<Modification> modificationList = new List<Modification>(); //modificationList.Add(Modification.Oxidation); modificationList.Add(Modification.Carbamidomethylation); modificationList.Add(Modification.Carbamidomethylation); modificationList.Add(Modification.Carbamidomethylation); PeptideTarget target = new PeptideTarget(1, peptide, net, modificationList); LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileLocation, parameters, interpolation); var correlationResult = lcImsPeptideSearchWorkfow.RunInformedWorkflow(target); Console.WriteLine(correlationResult.ReferenceLcImsTargetResult.NormalizedElutionTime); }
public void TestDataExtractionSpeedManyTargets() { // Setup Informed workflow parameters LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters { ChargeStateMax = 5, NetTolerance = 0.03, IsotopicFitScoreThreshold = 0.2, MassToleranceInPpm = 30, NumPointForSmoothing = 9 }; Console.WriteLine(DateTime.Now + ": Reading ViperCompatibleMass Tags from MTDB"); List<PeptideTarget> targetList = MassTagImporter.ImportMassTags("elmer", "MT_Human_Sarcopenia_P789"); Console.WriteLine(DateTime.Now + ": Using " + targetList.Count + " targets."); // Put all UIMF Files to process here List<string> uimfFileList = new List<string>(); uimfFileList.Add(Cheetah); // Iterate over each UIMF File for (int i = 0; i < uimfFileList.Count; i++) { string uimfFileLocation = uimfFileList[i]; FileInfo uimfFileInfo = new FileInfo(uimfFileLocation); Console.WriteLine(DateTime.Now + ": Processing " + uimfFileInfo.Name); // NET Alignment string netAlignmentFileName = uimfFileInfo.Name.Replace(".uimf", "_NetAlign.csv"); string netAlignmentLocation = Path.Combine(uimfFileInfo.DirectoryName, netAlignmentFileName); FileInfo netAlignmentFileInfo = new FileInfo(netAlignmentLocation); if (!File.Exists(netAlignmentFileInfo.FullName)) { } else { Console.WriteLine(DateTime.Now + ": Using existing alignment file"); } // Grab the net alignment IInterpolation interpolation = AlignmentImporter.ReadFile(netAlignmentFileInfo.FullName); //LcImsPeptideSearchWorkfow warmupInformedWorkflow = new LcImsPeptideSearchWorkfow(uimfFileInfo.FullName, parameters, interpolation); //foreach (var Target in targetList.Take(10)) //{ // warmupInformedWorkflow.RunInformedWorkflow(Target); //} //warmupInformedWorkflow.PrintFeatureFindStatistics(); //Console.WriteLine("**************************************************************"); //Console.WriteLine("**************************************************************"); //Console.WriteLine("**************************************************************"); LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileInfo.FullName, parameters, interpolation); foreach (var target in targetList) { lcImsPeptideSearchWorkfow.RunInformedWorkflow(target); } //LcImsPeptideSearchWorkfow.PrintFeatureFindStatistics(); // Warmup //LcImsPeptideSearchWorkfow.ExtractData(targetList.Take(10)); // Actual //Random random = new Random(); //LcImsPeptideSearchWorkfow.ExtractData(targetList.OrderBy(X => random.Next()).Take(100)); //LcImsPeptideSearchWorkfow.ExtractData(targetList); } }
public void TestRunAllTargetsSqlOutput() { // Setup sqlite output file by deleting any current file and copying a blank schema over string sqliteSchemaLocation = @"..\..\..\testFiles\informedSchema.db3"; string sqliteOutputLocation = "Sarc_Many_Datasets.db3"; if(File.Exists(sqliteOutputLocation)) File.Delete(sqliteOutputLocation); File.Copy(sqliteSchemaLocation, sqliteOutputLocation); //string uimfFileLocation = @"..\..\..\testFiles\Sarc_MS2_90_6Apr11_Cheetah_11-02-19.uimf"; //string uimfFileLocation = @"..\..\..\testFiles\Sarc_P23_C07_2143_23Feb12_Cheetah_11-05-40.uimf"; //IInterpolation interpolation = AlignmentImporter.ReadFile(netAlignmentFileLocation); // Setup calibration workflow and targets LcImsPeptideSearchParameters calibrationParameters = new LcImsPeptideSearchParameters { ChargeStateMax = 5, NetTolerance = 0.5, IsotopicFitScoreThreshold = 0.15, MassToleranceInPpm = 30, NumPointForSmoothing = 9 }; List<PeptideTarget> calibrationTargetList = MassTagImporter.ImportMassTags("elmer", "MT_Human_Sarcopenia_P789", 1e-10, true); Console.WriteLine("Using " + calibrationTargetList.Count + " targets for calibration."); LcImsPeptideSearchParameters parameters = new LcImsPeptideSearchParameters { ChargeStateMax = 5, NetTolerance = 0.03, IsotopicFitScoreThreshold = 0.2, MassToleranceInPpm = 30, NumPointForSmoothing = 9 }; List<PeptideTarget> targetList = MassTagImporter.ImportMassTags("elmer", "MT_Human_Sarcopenia_P789"); Console.WriteLine(DateTime.Now + ": Reading ViperCompatibleMass Tags from MTDB"); Console.WriteLine(DateTime.Now + ": Using " + targetList.Count + " targets."); List<string> uimfFileList = new List<string>(); uimfFileList.Add(@"..\..\..\testFiles\Sarc_MS2_13_1Apr11_Cheetah_11-02-24.uimf"); //uimfFileList.Add(@"..\..\..\testFiles\Sarc_MS2_27_2Apr11_Cheetah_11-01-11.uimf"); //uimfFileList.Add(@"..\..\..\testFiles\Sarc_MS2_54_6Apr11_Cheetah_11-02-18.uimf"); //uimfFileList.Add(@"..\..\..\testFiles\Sarc_MS2_55_3Apr11_Cheetah_11-02-15.uimf"); //uimfFileList.Add(@"..\..\..\testFiles\Sarc_MS2_73_5Apr11_Cheetah_11-02-24.uimf"); //uimfFileList.Add(@"..\..\..\testFiles\Sarc_MS2_90_6Apr11_Cheetah_11-02-19.uimf"); //uimfFileList.Add(@"..\..\..\testFiles\Sarc_MS2_102_7Apr11_Cheetah_11-02-19.uimf"); //uimfFileList.Add(@"..\..\..\testFiles\Sarc_MS2_119_8Apr11_Cheetah_11-02-18.uimf"); //uimfFileList.Add(@"..\..\..\testFiles\Sarc_MS2_125_8Apr11_Cheetah_11-02-15.uimf"); //uimfFileList.Add(@"..\..\..\testFiles\Sarc_MS2_146_9Apr11_Cheetah_11-02-24.uimf"); using (var connection = new SQLiteConnection(@"Data Source=" + sqliteOutputLocation + ";New=False;")) { connection.Open(); using (var command = new SQLiteCommand(connection)) { using (var transaction = connection.BeginTransaction()) { Console.WriteLine(DateTime.Now + ": Writing ViperCompatibleMass Tags to database"); //foreach (var Target in targetList) //{ // string insertMassTagsQuery = Target.CreateSqlMassTagQueries(); // command.CommandText = insertMassTagsQuery; // command.ExecuteNonQuery(); //} //transaction.Commit(); } for (int i = 0; i < uimfFileList.Count; i++) { string uimfFileLocation = uimfFileList[i]; FileInfo uimfFileInfo = new FileInfo(uimfFileLocation); Console.WriteLine(DateTime.Now + ": Processing " + uimfFileInfo.Name); // NET Alignment string netAlignmentFileName = uimfFileInfo.Name.Replace(".uimf", "_NetAlign.csv"); string netAlignmentLocation = Path.Combine(uimfFileInfo.DirectoryName, netAlignmentFileName); FileInfo netAlignmentFileInfo = new FileInfo(netAlignmentLocation); if (!File.Exists(netAlignmentFileInfo.FullName)) { Console.WriteLine(DateTime.Now + ": Creating alignment file using " + calibrationTargetList.Count + " possible targets."); LcImsPeptideSearchWorkfow calibrationWorkflow = new LcImsPeptideSearchWorkfow(uimfFileLocation, calibrationParameters); List<Tuple<double, double>> netAlignmentInput = new List<Tuple<double, double>>(); int index = 0; // Run calibration workflow on each of the calibration targets foreach (var imsTarget in calibrationTargetList.OrderBy(x => x.NormalizedElutionTime)) { //Console.WriteLine(DateTime.Now + ": Processing Target " + index); ChargeStateCorrelationResult correlationResult = calibrationWorkflow.RunInformedWorkflow(imsTarget); if (correlationResult != null && correlationResult.CorrelatedResults.Any()) { var elutionTimeFilteredResults = correlationResult.CorrelatedResults.Where(x => x.NormalizedElutionTime >= 0.1); if (elutionTimeFilteredResults.Any()) { LcImsTargetResult result = correlationResult.CorrelatedResults.Where(x => x.NormalizedElutionTime >= 0.1).OrderByDescending(x => x.Intensity).First(); netAlignmentInput.Add(new Tuple<double, double>(result.NormalizedElutionTime, imsTarget.NormalizedElutionTime)); } } //Console.WriteLine(DateTime.Now + ": Done Processing Target " + index); imsTarget.RemoveResults(); //Console.WriteLine(DateTime.Now + ": Removed results from Target " + index); index++; } // Place data points at beginning and end to finish off the alignment netAlignmentInput.Add(new Tuple<double, double>(0, 0)); netAlignmentInput.Add(new Tuple<double, double>(1, 1)); // Do LOESS to get NET alignment Console.WriteLine(DateTime.Now + ": Found " + netAlignmentInput.Count + " targets to use for alignment."); var netAlignmentInputGroup = netAlignmentInput.GroupBy(x => x.Item1).OrderBy(x => x.Key); var groupedNetTuple = netAlignmentInputGroup.Select(x => x.OrderBy(y => Math.Abs(y.Item1 - y.Item2)).First()).ToArray(); var loessInterpolatorForNetAlignment = new LoessInterpolator(0.1, 4); double[] xArray = groupedNetTuple.Select(x => x.Item1).ToArray(); double[] yArray = groupedNetTuple.Select(x => x.Item2).ToArray(); double[] newNetValues = loessInterpolatorForNetAlignment.Smooth(xArray, yArray); // Creates a file for the NET Alignment to be stored using (StreamWriter writer = new StreamWriter(netAlignmentFileInfo.FullName)) { for (int j = 0; j < groupedNetTuple.Length; j++) { writer.WriteLine(groupedNetTuple[j].Item1 + "," + newNetValues[j]); } } } else { Console.WriteLine(DateTime.Now + ": Using existing alignment file"); } // Grab the net alignment IInterpolation interpolation = AlignmentImporter.ReadFile(netAlignmentFileInfo.FullName); LcImsPeptideSearchWorkfow lcImsPeptideSearchWorkfow = new LcImsPeptideSearchWorkfow(uimfFileInfo.FullName, parameters, interpolation); //using (var transaction = connection.BeginTransaction()) //{ // string insertDatasetQuery = "INSERT INTO T_Dataset (Dataset_Id, File_Name) VALUES(" + i + ",'" + uimfFileInfo.Name + "');"; // command.CommandText = insertDatasetQuery; // command.ExecuteNonQuery(); // transaction.Commit(); //} List<ChargeStateCorrelationResult> resultList = new List<ChargeStateCorrelationResult>(); foreach (var imsTarget in targetList) { using (var transaction = connection.BeginTransaction()) { ChargeStateCorrelationResult correlationResult = lcImsPeptideSearchWorkfow.RunInformedWorkflow(imsTarget); if (correlationResult != null) { resultList.Add(correlationResult); } //string queries = imsTarget.CreateSqlResultQueries(i); //command.CommandText = queries; //command.ExecuteNonQuery(); //if (correlationResult != null && correlationResult.CorrelationMap.Count > 1) //{ // string correlationQueries = correlationResult.CreateSqlUpdateQueries(); // if (correlationQueries != "") // { // command.CommandText = correlationQueries; // command.ExecuteNonQuery(); // } //} //transaction.Commit(); } // Reset the Target so it can be used again by another dataset imsTarget.RemoveResults(); } foreach (var chargeStateCorrelationResult in resultList) { } } } connection.Close(); } }