public static void Uptimize()
{
string fastaFile = @"C:\_IRIC\Data\NB\peptide.fasta";
DBOptions dbOptions = PositionnalIsomerSolver.CreateOptions(fastaFile, @"C:\_IRIC\Data\NB\Units2\", 8, 0.05, new PeptidAce.Utilities.Interfaces.ConSolCommandLine());
dbOptions.dProduct = 0.0917981081138356;
dbOptions.dPrecursor = 0.345789190542786;
dbOptions.dMatchingProductFraction = 0.427418045898628;
dbOptions.dMatchingProduct = 0;
dbOptions.dIntensityFraction = 0.429418127252449;
dbOptions.dIntensity = 0;
dbOptions.dProtein = 0.692270441303156;
dbOptions.dPeptideScore = 0.636739763262095;
dbOptions.dFragmentScore = 0.0229058195943506;
dbOptions.fullFragment = new FullFragments(true);
string project = @"C:\_IRIC\Data\NB\ProjectTest_AllAce_Spiked_QEPlus_Apr21.csv";
Samples samples = new Samples(project, 0, dbOptions);
Uptimizer.Run(samples, dbOptions);
dbOptions.Save(dbOptions.OutputFolder + "UptimizedOptions.csv");
}
private double GetNbTimesFit(DBOptions dbOptions, int nbProductsToKeep, double precision, out double area)
{
long nbRatios = 0;
double nbTimes = 0;
area = 0.0;
List <CharacterizedPrecursor> Isomers = new List <CharacterizedPrecursor>();
Isomers.Add(this);
ElutionCurve curve = new ElutionCurve();
foreach (Query query in this.Queries)
{
//double overFlow = 0;
double underFlow = 0;
double percentError = 0;
Dictionary <CharacterizedPrecursor, PositionnalIsomerSolver.SolvedResult> finalRatios = PositionnalIsomerSolver.SolveFromSpectrum(Isomers, nbProductsToKeep, precision, query.spectrum.Peaks, dbOptions.productMassTolerance,
query.spectrum.PrecursorIntensityPerMilliSecond * query.spectrum.InjectionTime, out underFlow, out percentError, dbOptions.ConSole);
if (percentError < 0.5)
{
curve.AddPoint(query.spectrum.RetentionTimeInMin * 1000.0 * 60.0, finalRatios[this].Ratio * query.spectrum.PrecursorIntensityPerMilliSecond);
nbTimes += finalRatios[this].NbFitTimes;
nbRatios++;
}
}
if (nbRatios > 2 && curve.GetNbPoints() > this.Queries.Count * 0.5)
{
curve.Compute();
if (curve.Area > 0)
{
area = curve.Area;
}
}
return(nbTimes / (double)nbRatios);
}
public void OnNavigatedTo(NavigationEventArgs e)
{
//if (!isUpToDate)
if (solverPTR != PepIso.solver)
{
solverPTR = PepIso.solver;
// isUpToDate = true;
ModernTabList.Links.Clear();
ModernTabList.SelectedSource = null;
Dictionary <string, string> parameters = GetParams(e.Source.OriginalString);
if (parameters.ContainsKey("Sample"))
{
string sampleName = parameters["Sample"];
foreach (double mzKey in solverPTR.characterizedPeptides.Keys)
{
if (solverPTR.characterizedPeptides[mzKey].Count > 0)
{
//Mixed Deconvoluted curves
foreach (Sample sample in solverPTR.characterizedPeptides[mzKey].Keys)
//foreach (Sample sample in PepIso.solver.characterizedPeptides.Keys)
{
string name = sample.Name;
if (name.CompareTo(sampleName) == 0)
{
//bool found = false;
//foreach (MixedPrecursor mp in PepIso.solver.mixedPrecursors[sample])
// if (mp.MZ == mzKey && mp.PeptideRatios.Count > 0)
// found = true;
//if (found)
{
Uri source = new Uri("/Content/ResultsPeptides.xaml?mzKey=" + mzKey.ToString() + "&Sample=" + name, UriKind.Relative);
ModernTabList.Links.Add(new Link
{
DisplayName = ((float)mzKey).ToString(),
Source = source
});
if (ModernTabList.SelectedSource == null)
{
ModernTabList.SelectedSource = source;
}
}
break;
}
}
//Mixed Results
/*foreach (Sample sample in PepIso.solver.mixedPrecursors.Keys)
* {
* string name = sample.Name;
* ModernTabList.Links.Add(new Link
* {
* DisplayName = name + " Curves",
* Source = new Uri("/Content/ResultsMixed.xaml?mzKey=" + mzKey + "&Sample=" + name, UriKind.Relative)
* });
* }//*/
}
}
}
}
}
/// <summary>
/// Computes a curve [precursor observed intensity ; correction so that precursor computed intensity from fragments matches observed intensity]
/// </summary>
/// <param name="dbOptions"></param>
/// <param name="nbProductsToKeep"></param>
/// <returns></returns>
private ElutionCurve GetNormalizingCurve(DBOptions dbOptions, int nbProductsToKeep)
{
List <CharacterizedPrecursor> Isomers = new List <CharacterizedPrecursor>();
Isomers.Add(this);
ElutionCurve curve = new ElutionCurve();
foreach (Query query in this.Queries)
{
double timeInMilliSeconds = query.spectrum.RetentionTimeInMin * 60.0 * 1000.0;
double underFlow = 0;
double percentError = 0;
double intInTrap = query.spectrum.PrecursorIntensityPerMilliSecond * query.spectrum.InjectionTime;
Dictionary <CharacterizedPrecursor, PositionnalIsomerSolver.SolvedResult> finalRatios = PositionnalIsomerSolver.SolveFromSpectrum(Isomers, nbProductsToKeep, query.spectrum.Peaks, dbOptions.productMassTolerance,
intInTrap, query.spectrum.PrecursorIntensity,
out underFlow, out percentError, dbOptions.ConSole);
if (percentError < 0.5 && finalRatios[this].NbFitTimes > 0)
{
double ratio = intInTrap / finalRatios[this].NbFitTimes;
if (ratio > 0.5 && ratio < 2)
{
curve.AddPoint(intInTrap, intInTrap / finalRatios[this].NbFitTimes);
}
}
}
curve.Compute(CurveType.LINEAR, true);
return(curve);
}
private void Button_Click_1(object sender, RoutedEventArgs e)
{
if (conSol == null)
{
conSol = new ConSolBasic(AddTextOutput);
}
//PeptidAce.Iso.UnitTests.StatsMaker.ProjectMerge(conSol);
//PeptidAce.Iso.UnitTests.PisTest.Uptimize();
if (ButtonRun.IsEnabled && CheckParams())
{
ButtonRun.IsEnabled = false;
TextConsol.Text = "Launching Peptide Isomer solver ... ";
runningTask = new Task(() =>
{
PositionnalIsomerSolver newSolver = new PositionnalIsomerSolver();
try
{
newSolver.precTolPpm = precursorMassTolPPm;
newSolver.prodTolDa = productMassTolPPm;
newSolver.nbMinFragments = nbMinFragments;
newSolver.nbMaxFragments = nbMaxFragments;
newSolver.Solve(peptideFiles, mixedFiles, fastaFile, Utilities.vsCSV.GetFolder(mixedFiles[0]), conSol);
solver = newSolver;
}
catch (Exception ex)
{
AddTextOutput(ex.Message);
AddTextOutput(ex.StackTrace);
}
try
{
ButtonRun.Dispatcher.Invoke(
System.Windows.Threading.DispatcherPriority.Normal,
new Action(
delegate()
{
ButtonRun.IsEnabled = true;
AddTextOutput("\nDone! Your results are available in 'csv' files in these folders :\n" +
"\n" + Utilities.vsCSV.GetFolder(mixedFiles[0]) + "Identifications" +
"\n" + Utilities.vsCSV.GetFolder(mixedFiles[0]) + "Combined" +
"\n" + Utilities.vsCSV.GetFolder(mixedFiles[0]) + "Individual");
ModernUI.Pages.Home.UpdateLinks(newSolver.SpikedSamples, newSolver.mixedPrecursors);
}
));
}
catch (Exception ex)
{
AddTextOutput(ex.Message);
AddTextOutput(ex.StackTrace);
}
});
runningTask.Start();
}
}
public static void ProjectMerge(PeptidAce.Utilities.Interfaces.IConSol console)
{
string strProjectAll = @"C:\_IRIC\Data\NB\ProjectFile_EverythingReplicates_Oct.csv";
string project = @"C:\_IRIC\Data\NB\ProjectTest_AllAce_Spiked_19Oct.csv";
string fastaFile = @"C:\_IRIC\Data\NB\peptide.fasta";
DBOptions options = PositionnalIsomerSolver.CreateOptions(fastaFile, @"C:\_IRIC\Data\NB\Units\", 8, 0.05, console);
Samples samplesMixed = new Samples(strProjectAll, 0, options);
Samples samplesSynth = new Samples(project, 0, options);
PositionnalIsomerSolver newSolver = new PositionnalIsomerSolver();
newSolver.precTolPpm = 15;
newSolver.prodTolDa = 0.05;
newSolver.nbMinFragments = 5;
newSolver.nbMaxFragments = 5;
string[] synths = new string[samplesSynth.Count];
for (int i = 0; i < synths.Length; i++)
{
synths[i] = samplesSynth[i].sSDF;
}
string[] mixed = new string[samplesMixed.Count];
for (int i = 0; i < mixed.Length; i++)
{
mixed[i] = samplesMixed[i].sSDF;
}
newSolver.Solve(synths, mixed, fastaFile, Utilities.vsCSV.GetFolder(mixed[0]), options.ConSole);
//Precompute Spiked peptide identifications
Result SpikedResult = Ace.Start(options, samplesSynth, false, false);
Result mixedResult = Ace.Start(options, samplesMixed, false, false);
//Compute all usable spiked peptides
Dictionary <double, Dictionary <Sample, CharacterizedPrecursor> > characterizedPeptides = CharacterizedPrecursor.GetSpikedPrecursors(samplesSynth, SpikedResult, options, newSolver.nbMinFragments, newSolver.nbMaxFragments);
Dictionary <Sample, List <MixedPrecursor> > mixedPrecursors = new Dictionary <Sample, List <MixedPrecursor> >();
foreach (Sample mixedSample in samplesMixed)
{
mixedPrecursors.Add(mixedSample, MixedPrecursor.GetMixedPrecursors(mixedSample, mixedResult, options, characterizedPeptides));
}
Dictionary <Sample, List <Dictionary <CharacterizedPrecursor, MaxFlowElutionCurve> > > results = new Dictionary <Sample, List <Dictionary <CharacterizedPrecursor, MaxFlowElutionCurve> > >();
//Get the list of precursors to characterize
foreach (Sample mixedSample in samplesMixed)
{
foreach (double keyMz in characterizedPeptides.Keys)
{
//List<Dictionary<CharacterizedPrecursor, MaxFlowElutionCurve>> listOfRatios = new List<Dictionary<CharacterizedPrecursor, MaxFlowElutionCurve>>();
foreach (MixedPrecursor mPrec in mixedPrecursors[mixedSample])
{
if (mPrec.MZ == keyMz)
{
// Compute Max Flow for this precursor
Dictionary <CharacterizedPrecursor, MaxFlowElutionCurve> ratios = PositionnalIsomerSolver.GetRatios(characterizedPeptides, mPrec, options, newSolver.nbMinFragments, newSolver.nbMaxFragments);
if (!results.ContainsKey(mixedSample))
{
results.Add(mixedSample, new List <Dictionary <CharacterizedPrecursor, MaxFlowElutionCurve> >());
}
results[mixedSample].Add(ratios);
}
}
}
}
List <CharacterizedPrecursor> precursors = new List <CharacterizedPrecursor>();
foreach (Dictionary <Sample, CharacterizedPrecursor> dic in characterizedPeptides.Values)
{
foreach (CharacterizedPrecursor cP in dic.Values)
{
precursors.Add(cP);
}
}
//Create average of each characterized peptide plus standard deviance
vsCSVWriter writerArea = new vsCSVWriter(@"C:\_IRIC\Data\NB\Merge\stats_Area.csv");
string lineC = "Count,";
foreach (CharacterizedPrecursor cP in precursors)
{
lineC += cP.Peptide.Sequence + ",";
}
lineC += "Intensity per ms,";
foreach (CharacterizedPrecursor cP in precursors)
{
lineC += cP.Peptide.Sequence + ",";
}
lineC += "Standard Deviation Count,";
foreach (CharacterizedPrecursor cP in precursors)
{
lineC += cP.Peptide.Sequence + ",";
}
lineC += "Standard Deviation per ms,";
foreach (CharacterizedPrecursor cP in precursors)
{
lineC += cP.Peptide.Sequence + ",";
}
writerArea.AddLine(lineC);
foreach (int cond in samplesMixed.GetConditions())
{
Dictionary <CharacterizedPrecursor, Dictionary <int, MaxFlowElutionCurve> > deconvoluted = new Dictionary <CharacterizedPrecursor, Dictionary <int, MaxFlowElutionCurve> >();
string sampleName = "";
foreach (Sample mixedSample in results.Keys)
{
if (mixedSample.PROJECT.CONDITION == cond)
{
sampleName = vsCSV.GetFileName_NoExtension(mixedSample.sSDF);
foreach (Dictionary <CharacterizedPrecursor, MaxFlowElutionCurve> ratio in results[mixedSample])
{
foreach (CharacterizedPrecursor cP in ratio.Keys)
{
if (ratio[cP].eCurveCount.Area > 0)
{
if (!deconvoluted.ContainsKey(cP))
{
deconvoluted.Add(cP, new Dictionary <int, MaxFlowElutionCurve>());
}
if (deconvoluted[cP].ContainsKey(mixedSample.PROJECT.REPLICATE))
{
if (deconvoluted[cP][mixedSample.PROJECT.REPLICATE].eCurveCount.Area < ratio[cP].eCurveCount.Area)
{
deconvoluted[cP][mixedSample.PROJECT.REPLICATE] = ratio[cP];
}
}
else
{
deconvoluted[cP].Add(mixedSample.PROJECT.REPLICATE, ratio[cP]);
}
//deconvoluted[cP].Add(ratio[cP]);
}
}
}
}
}
Dictionary <int, double> totalIntensityCount = new Dictionary <int, double>();
Dictionary <int, double> totalIntensityPerMs = new Dictionary <int, double>();
foreach (CharacterizedPrecursor cP in precursors)
{
if (deconvoluted.ContainsKey(cP))
{
foreach (int keyRep in deconvoluted[cP].Keys)
//foreach (MaxFlowElutionCurve curve in deconvoluted[cP])
{
if (!totalIntensityCount.ContainsKey(keyRep))
{
totalIntensityCount.Add(keyRep, 0.0);
totalIntensityPerMs.Add(keyRep, 0.0);
}
MaxFlowElutionCurve curve = deconvoluted[cP][keyRep];
totalIntensityCount[keyRep] += curve.eCurveCount.Area;
totalIntensityPerMs[keyRep] += curve.eCurvePerMs.Area;
}
}
}
string lineArea = sampleName + ",";
string lineMS = ",";
string stdDevCount = "";
string stdDevMS = "";
//1) Compute an average out of the replicates
foreach (CharacterizedPrecursor cP in precursors)
{
if (deconvoluted.ContainsKey(cP))
{
double averageAreaMS = 0;
double averageAreaCount = 0;
foreach (MaxFlowElutionCurve curve in deconvoluted[cP].Values)
{
averageAreaCount += curve.eCurveCount.Area;
averageAreaMS += curve.eCurvePerMs.Area;
}
if (averageAreaCount > 0)
{
averageAreaCount = (averageAreaCount / ((double)deconvoluted[cP].Count));
averageAreaMS = (averageAreaMS / ((double)deconvoluted[cP].Count));
double deNormAverageCount = 0.0;
double deNormAveragePerMs = 0.0;
List <double> repAreaCount = new List <double>();
List <double> repAreaMS = new List <double>();
foreach (int keyRep in deconvoluted[cP].Keys)
{
MaxFlowElutionCurve curve = deconvoluted[cP][keyRep];
double tmpCount = (curve.eCurveCount.Area / totalIntensityCount[keyRep]) * averageAreaCount;
deNormAverageCount += tmpCount;
repAreaCount.Add(tmpCount);
double tmpPerMs = (curve.eCurvePerMs.Area / totalIntensityPerMs[keyRep]) * averageAreaMS;
deNormAveragePerMs += tmpPerMs;
repAreaMS.Add(tmpPerMs);
}
lineArea += (deNormAverageCount / ((double)repAreaCount.Count)) + ",";
lineMS += (deNormAveragePerMs / ((double)repAreaMS.Count)) + ",";
if (repAreaCount.Count > 1)
{
stdDevCount += MathNet.Numerics.Statistics.ArrayStatistics.StandardDeviation(repAreaCount.ToArray()) + ",";
stdDevMS += MathNet.Numerics.Statistics.ArrayStatistics.StandardDeviation(repAreaMS.ToArray()) + ",";
}
else
{
stdDevCount += ",";
stdDevMS += ",";
}
}
else
{
lineArea += ",";
lineMS += ",";
stdDevCount += ",";
stdDevMS += ",";
}
}
else
{
lineArea += ",";
lineMS += ",";
stdDevCount += ",";
stdDevMS += ",";
}
}
writerArea.AddLine(lineArea + lineMS + "," + stdDevCount + "," + stdDevMS);
//2) Add replicates results (to use for standard deviation)
}
writerArea.WriteToFile();
}
