commit before breaking things

smith-chem-wisc · Sep 12, 2024 · ae3b811 · ae3b811
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diff --git a/MetaMorpheus/CMD/CMD.csproj b/MetaMorpheus/CMD/CMD.csproj
@@ -20,9 +20,9 @@
 
  <ItemGroup>
  <PackageReference Include="CommandLineParser" Version="2.9.1" />
- <PackageReference Include="Microsoft.ML" Version="3.0.1" />
- <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
- <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
+ <PackageReference Include="Microsoft.ML" Version="2.0.0" />
+ <PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
+ <PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
  <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
  <PackageReference Include="mzLib" Version="1.0.551" />
  <PackageReference Include="Nett" Version="0.15.0" />

diff --git a/MetaMorpheus/EngineLayer/EngineLayer.csproj b/MetaMorpheus/EngineLayer/EngineLayer.csproj
@@ -17,9 +17,9 @@
  </PropertyGroup>
 
  <ItemGroup>
- <PackageReference Include="Microsoft.ML" Version="3.0.1" />
- <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
- <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
+ <PackageReference Include="Microsoft.ML" Version="2.0.0" />
+ <PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
+ <PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
  <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
  <PackageReference Include="mzLib" Version="1.0.551" />
  <PackageReference Include="NETStandard.Library" Version="2.0.3" />

diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs
@@ -256,22 +256,43 @@ private static void QValueInverted(List<SpectralMatch> psms, bool peptideLevelAn
 
  public static void PepQValueInverted(List<SpectralMatch> psms, bool peptideLevelAnalysis)
  {
- psms.Reverse();
- //this calculation is performed from bottom up. So, we begin the loop by computing qValue
- //and qValueNotch for the last/lowest scoring psm in the bunch
- double qValue = (psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoy + 1) / psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeTarget;
 
- //Assign FDR values to PSMs
- for (int i = 0; i < psms.Count; i++)
- {
- // Stop if canceled
- if (GlobalVariables.StopLoops) { break; }
+ double[] allPEPValues = psms.Select(p => p.FdrInfo.PEP).ToArray();
+ double runningSum = 0;
+ double qValue = 1;
 
- qValue = Math.Min(qValue, (psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoy + 1) / psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeTarget);
+ for (int i = 0; i < allPEPValues.Length; i++)
+ {
+ runningSum += allPEPValues[i];
+ qValue = runningSum / (i + 1);
+ psms[i].GetFdrInfo(peptideLevelAnalysis).PEP_QValue = Math.Round(qValue, 6);
+ }
+
 
- psms[i].GetFdrInfo(peptideLevelAnalysis).PEP_QValue = qValue;
+ psms.Reverse();
+ foreach(var psm in psms)
+ {
+ qValue = Math.Min(qValue, psm.GetFdrInfo(peptideLevelAnalysis).PEP_QValue);
+ psm.GetFdrInfo(peptideLevelAnalysis).PEP_QValue = qValue;
  }
- psms.Reverse(); //we inverted the psms for this calculation. now we need to put them back into the original order
+ psms.Reverse();
+
+ //psms.Reverse();
+ ////this calculation is performed from bottom up. So, we begin the loop by computing qValue
+ ////and qValueNotch for the last/lowest scoring psm in the bunch
+ //double qValue = (psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoy + 1) / psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeTarget;
+
+ ////Assign FDR values to PSMs
+ //for (int i = 0; i < psms.Count; i++)
+ //{
+ // // Stop if canceled
+ // if (GlobalVariables.StopLoops) { break; }
+
+ // qValue = Math.Min(qValue, (psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoy + 1) / psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeTarget);
+
+ // psms[i].GetFdrInfo(peptideLevelAnalysis).PEP_QValue = qValue;
+ //}
+ //psms.Reverse(); //we inverted the psms for this calculation. now we need to put them back into the original order
  }
 
  public void Compute_PEPValue(FdrAnalysisResults myAnalysisResults, List<SpectralMatch> psms)

diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs
@@ -104,14 +104,16 @@ public PepAnalysisEngine(List<SpectralMatch> psms, string searchType, List<(stri
 
  public string ComputePEPValuesForAllPSMs()
  {
- List<PeptideMatchGroup> peptideGroups = UsePeptideLevelQValueForTraining
- ? PeptideMatchGroup.GroupByBaseSequence(AllPsms)
- : PeptideMatchGroup.GroupByIndividualPsm(AllPsms);
+ //List<PeptideMatchGroup> peptideGroups = UsePeptideLevelQValueForTraining
+ // ? PeptideMatchGroup.GroupByBaseSequence(AllPsms)
+ // : PeptideMatchGroup.GroupByIndividualPsm(AllPsms);
 
- if(UsePeptideLevelQValueForTraining && (peptideGroups.Count(g => g.BestMatch.IsDecoy) < 4 || peptideGroups.Count(g => !g.BestMatch.IsDecoy) < 4))
- {
- peptideGroups = PeptideMatchGroup.GroupByIndividualPsm(AllPsms);
- }
+ List<PeptideMatchGroup> peptideGroups = PeptideMatchGroup.GroupByIndividualPsm(AllPsms);
+
+ //if(UsePeptideLevelQValueForTraining && (peptideGroups.Count(g => g.BestMatch.IsDecoy) < 4 || peptideGroups.Count(g => !g.BestMatch.IsDecoy) < 4))
+ //{
+ // peptideGroups = PeptideMatchGroup.GroupByIndividualPsm(AllPsms);
+ //}
 
  int numGroups = 4;
  List<int>[] peptideGroupIndices = GetPeptideGroupIndices(peptideGroups, numGroups);

diff --git a/MetaMorpheus/GUI/GUI.csproj b/MetaMorpheus/GUI/GUI.csproj
@@ -51,9 +51,9 @@
  <ItemGroup>
  <PackageReference Include="MarkdownSharp" Version="2.0.5" />
  <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
- <PackageReference Include="Microsoft.ML" Version="3.0.1" />
- <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
- <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
+ <PackageReference Include="Microsoft.ML" Version="2.0.0" />
+ <PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
+ <PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
  <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
  <PackageReference Include="mzLib" Version="1.0.551" />
  <PackageReference Include="Nett" Version="0.15.0" />

diff --git a/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs b/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs
@@ -137,36 +137,38 @@ private void CalculatePsmAndPeptideFdr(List<SpectralMatch> psms, string analysis
  // this could cause weird PSM FDR issues
 
  Status("Estimating PSM FDR...", Parameters.SearchTaskId);
-
- List<int> psmsAboveQ = new List<int>();
- List<int> peptidesAboveQ = new List<int>();
- List<int> psmsAbovePepQ = new List<int>();
- List<int> peptidesAbovePepQ = new List<int>();
-
- for (int i = 0; i < 10; i++)
- {
- var tempPsms = psms
- .Select(p => new PeptideSpectralMatch(p))
- .Cast<SpectralMatch>()
- .ToList(); 
- new FdrAnalysisEngine(tempPsms, Parameters.NumNotches, CommonParameters, this.FileSpecificParameters,
+ new FdrAnalysisEngine(psms, Parameters.NumNotches, CommonParameters, this.FileSpecificParameters,
  new List<string> { Parameters.SearchTaskId }, analysisType: analysisType, doPEP: doPep, outputFolder: Parameters.OutputFolder).Run();
- psmsAboveQ.Add(tempPsms.Count(p => p.FdrInfo.QValue <= 0.01));
- peptidesAboveQ.Add(tempPsms.Count(p => p.PeptideFdrInfo.QValue <= 0.01));
- psmsAbovePepQ.Add(tempPsms.Count(p => p.FdrInfo.PEP_QValue <= 0.01));
- peptidesAbovePepQ.Add(tempPsms.Count(p => p.PeptideFdrInfo.PEP_QValue <= 0.01));
- }
+
+ //List<int> psmsAboveQ = new List<int>();
+ //List<int> peptidesAboveQ = new List<int>();
+ //List<int> psmsAbovePepQ = new List<int>();
+ //List<int> peptidesAbovePepQ = new List<int>();
+
+ //for (int i = 0; i < 10; i++)
+ //{
+ // var tempPsms = psms
+ // .Select(p => new PeptideSpectralMatch(p))
+ // .Cast<SpectralMatch>()
+ // .ToList(); 
+ // new FdrAnalysisEngine(tempPsms, Parameters.NumNotches, CommonParameters, this.FileSpecificParameters,
+ // new List<string> { Parameters.SearchTaskId }, analysisType: analysisType, doPEP: doPep, outputFolder: Parameters.OutputFolder).Run();
+ // psmsAboveQ.Add(tempPsms.Count(p => p.FdrInfo.QValue <= 0.01));
+ // peptidesAboveQ.Add(tempPsms.Count(p => p.PeptideFdrInfo.QValue <= 0.01));
+ // psmsAbovePepQ.Add(tempPsms.Count(p => p.FdrInfo.PEP_QValue <= 0.01));
+ // peptidesAbovePepQ.Add(tempPsms.Count(p => p.PeptideFdrInfo.PEP_QValue <= 0.01));
+ //}
 
- // write summary text
- using(StreamWriter writer = new StreamWriter(@"C:\Users\Alex\PEP_NoRandomOrdering.tsv"))
- {
- writer.WriteLine("PSMs Q\tPeptides Q\tPSMs PEP-Q\tPeptides PEP-Q");
- for(int i = 0; i < 10; i++)
- {
- writer.WriteLine(String.Join('\t', psmsAboveQ[i], peptidesAboveQ[i], psmsAbovePepQ[i], peptidesAbovePepQ[i]));
- }
- }
- throw new Exception("PEP Seed Results written to file");
+ //// write summary text
+ //using(StreamWriter writer = new StreamWriter(@"C:\Users\Alex\PEP_NoRandomOrdering.tsv"))
+ //{
+ // writer.WriteLine("PSMs Q\tPeptides Q\tPSMs PEP-Q\tPeptides PEP-Q");
+ // for(int i = 0; i < 10; i++)
+ // {
+ // writer.WriteLine(String.Join('\t', psmsAboveQ[i], peptidesAboveQ[i], psmsAbovePepQ[i], peptidesAbovePepQ[i]));
+ // }
+ //}
+ //throw new Exception("PEP Seed Results written to file");
  Status("Done estimating PSM FDR!", Parameters.SearchTaskId);
  }
 

diff --git a/MetaMorpheus/TaskLayer/TaskLayer.csproj b/MetaMorpheus/TaskLayer/TaskLayer.csproj
@@ -17,9 +17,9 @@
 
  <ItemGroup>
  <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
- <PackageReference Include="Microsoft.ML" Version="3.0.1" />
- <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
- <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
+ <PackageReference Include="Microsoft.ML" Version="2.0.0" />
+ <PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
+ <PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
  <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
  <PackageReference Include="mzLib" Version="1.0.551" />
  <PackageReference Include="NetSerializer" Version="4.1.2" />