|
public RunInformedWorkflow ( |
||
| target | /// The Target. /// | |
| return | ||
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();
}
}