not supposed to be hard

smith-chem-wisc · Oct 16, 2024 · 60c2d69 · 60c2d69
1 parent 10b2333
commit 60c2d69
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Showing 7 changed files with 14 additions and 11 deletions.
diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs
@@ -21,7 +21,6 @@ public class FdrAnalysisEngine : MetaMorpheusEngine
  /// </summary>
  public static bool QvalueThresholdOverride // property
  {
- get { return qvalueThresholdOverride; } // get method
  set { qvalueThresholdOverride = value; } // set method
  }
  public FdrAnalysisEngine(List<SpectralMatch> psms, int massDiffAcceptorNumNotches, CommonParameters commonParameters,
@@ -209,6 +208,7 @@ public void CalculateQValue(List<SpectralMatch> psms, bool peptideLevelCalculati
  }
  else
  {
+ //we don't want to apply the QValueThreshod
  if(psms.Count < PsmCountThresholdForInvertedQvalue)
  {
 

diff --git a/MetaMorpheus/Test/MatchIonsOfAllCharges.cs b/MetaMorpheus/Test/MatchIonsOfAllCharges.cs
@@ -20,6 +20,7 @@
 using Omics.Modifications;
 using Omics.SpectrumMatch;
 using static System.Net.WebRequestMethods;
+using EngineLayer.FdrAnalysis;
 
 namespace Test
 {
@@ -425,7 +426,7 @@ public static void TestLibraryUpdate()
 
  string rawCopy = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\UpdateLibrary\rawCopy.mzML");
  System.IO.File.Copy(raw1, rawCopy);
-
+ FdrAnalysisEngine.QvalueThresholdOverride = true;
  EverythingRunnerEngine UpdateLibrary = new(new List<(string, MetaMorpheusTask)> { ("UpdateSpectraFileOutput", task) }, new List<string> { raw1, raw2 }, new List<DbForTask> { new DbForTask(lib, false), new DbForTask( db1,false), new DbForTask(db2, false) }, thisTaskOutputFolder);
 
  UpdateLibrary.Run();
@@ -452,6 +453,7 @@ public static void TestLibraryUpdate()
 
  updatedLib.CloseConnections();
  Directory.Delete(thisTaskOutputFolder, true);
+ FdrAnalysisEngine.QvalueThresholdOverride = false;
  }
 
  [Test]

diff --git a/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs b/MetaMorpheus/Test/PostSearchAnalysisTaskTests.cs
@@ -71,6 +71,7 @@ public static void AllResultsAndResultsTxtContainsCorrectValues_QValue_BottomUp(
  Assert.AreEqual("All target PSMs with q-value <= 0.01: " + TaGe_SA_A549_3_snip_2ExpectedPsms, singleFileResults[5]);
  Assert.AreEqual("All target peptides with q-value <= 0.01: " + TaGe_SA_A549_3_snip_2ExpectedPeptides, singleFileResults[6]);
  Assert.AreEqual("All target protein groups with q-value <= 0.01 (1% FDR): 166", singleFileResults[7]);
+ FdrAnalysisEngine.QvalueThresholdOverride = false;
  }
 
  [Test]
@@ -103,6 +104,7 @@ public static void AllResultsAndResultsTxtContainsCorrectValues_PepQValue_Bottom
  Assert.AreEqual("TaGe_SA_A549_3_snip_2 - Target PSMs with pep q-value <= 0.01: 192", results[13]);
  Assert.AreEqual("TaGe_SA_A549_3_snip_2 - Target peptides with pep q-value <= 0.01: 155", results[14]);
  Assert.AreEqual("TaGe_SA_A549_3_snip_2 - Target protein groups within 1 % FDR: 141", results[15]);
+ FdrAnalysisEngine.QvalueThresholdOverride = false;
  }
 
  /// <summary>
@@ -112,7 +114,6 @@ public static void AllResultsAndResultsTxtContainsCorrectValues_PepQValue_Bottom
  [TestCaseSource(nameof(GetTestCases))]
  public static void AllResultTxtContainsCorrectNumberOfResultLines(EverythingRunnerEngineTestCases testCaseIdentifier)
  {
- FdrAnalysisEngine.QvalueThresholdOverride = true;
  var testCase = EverythingRunnerEngineTestCase.GetTestCase(testCaseIdentifier);
 
  int expectedIndividualFileLines = testCase.DataFileList.Count == 1 || !testCase.WriteIndividualResults 
@@ -158,7 +159,6 @@ public static void AllResultTxtContainsCorrectNumberOfResultLines(EverythingRunn
  [TestCaseSource(nameof(GetTestCases))]
  public static void CorrectFilesAreWrittenWithCorrectName(EverythingRunnerEngineTestCases testCaseIdentifier)
  {
- FdrAnalysisEngine.QvalueThresholdOverride = true;
  var testCase = EverythingRunnerEngineTestCase.GetTestCase(testCaseIdentifier);
  var psmFiles = Directory.GetFiles(testCase.OutputDirectory, "*PSMs.psmtsv", SearchOption.AllDirectories);
  var pepXmlFiles = Directory.GetFiles(testCase.OutputDirectory, "*.pep.xml", SearchOption.AllDirectories);

diff --git a/MetaMorpheus/Test/ProteinGroupTest.cs b/MetaMorpheus/Test/ProteinGroupTest.cs
@@ -14,6 +14,7 @@
 using Omics.Digestion;
 using Omics.Modifications;
 using UsefulProteomicsDatabases;
+using EngineLayer.FdrAnalysis;
 
 namespace Test
 {
@@ -206,6 +207,8 @@ public static void TestModificationInfoListInProteinGroupsOutput()
  string mzmlName = @"TestData\PrunedDbSpectra.mzml";
  string fastaName = @"TestData\DbForPrunedDb.fasta";
  string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestPrunedGeneration");
+
+ FdrAnalysisEngine.QvalueThresholdOverride = false;
  var engine = new EverythingRunnerEngine(taskList, new List<string> { mzmlName }, new List<DbForTask> { new DbForTask(fastaName, false) }, outputFolder);
  engine.Run();
  string final = Path.Combine(MySetUpClass.outputFolder, "task2", "DbForPrunedDbGPTMDproteinPruned.xml");

diff --git a/MetaMorpheus/Test/QuantificationTest.cs b/MetaMorpheus/Test/QuantificationTest.cs
@@ -15,6 +15,7 @@
 using System.Text;
 using Omics.Modifications;
 using TaskLayer;
+using EngineLayer.FdrAnalysis;
 
 namespace Test
 {
@@ -224,6 +225,7 @@ public static void TestProteinQuantFileHeaders(bool hasDefinedExperimentalDesign
  }
 
  // run the search/quantification
+ FdrAnalysisEngine.QvalueThresholdOverride = false;
  SearchTask task = new SearchTask();
  task.RunTask(unitTestFolder, new List<DbForTask> { new DbForTask(dbName, false) }, fileInfos.Select(p => p.FullFilePathWithExtension).ToList(), "");
 

diff --git a/MetaMorpheus/Test/SearchEngineTests.cs b/MetaMorpheus/Test/SearchEngineTests.cs
@@ -111,8 +111,8 @@ public static void TestSearchEngineResultsPsmFromTsv()
  Assert.AreEqual("K", psm.PreviousAminoAcid);
  Assert.AreEqual("P46013", psm.ProteinAccession);
  Assert.AreEqual("Proliferation marker protein Ki-67", psm.ProteinName);
- Assert.That(0.0, Is.EqualTo(psm.QValue).Within(1E-04));
- Assert.That(0.0, Is.EqualTo(psm.QValueNotch).Within(1E-04));
+ Assert.That(0, Is.EqualTo(psm.QValue).Within(1E-04));
+ Assert.That(0, Is.EqualTo(psm.QValueNotch).Within(1E-04));
  Assert.AreEqual(45.59512, psm.RetentionTime);
  Assert.AreEqual(662.486, psm.Score);
  Assert.AreEqual("[2742 to 2761]", psm.StartAndEndResiduesInProtein);

diff --git a/MetaMorpheus/Test/TestToml.cs b/MetaMorpheus/Test/TestToml.cs
@@ -1,11 +1,8 @@
-using Chemistry;
-using EngineLayer;
-using EngineLayer.ClassicSearch;
+using EngineLayer;
 using MassSpectrometry;
 using MzLibUtil;
 using Nett;
 using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert;
-using Proteomics;
 using Proteomics.ProteolyticDigestion;
 using System.Collections.Generic;
 using System.IO;
@@ -14,7 +11,6 @@
 using Omics.Fragmentation;
 using SpectralAveraging;
 using TaskLayer;
-using UsefulProteomicsDatabases;
 using EngineLayer.FdrAnalysis;
 
 namespace Test