nonspecific search engine bug fix and unit test

MetaMorpheus/EngineLayer/NonSpecificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs

@@ -377,7 +377,7 @@ private Tuple<int, PeptideWithSetModifications> Accepts(List<Product> fragments,
                                 updatedMods.Add(key, mod.Value);
                             }
                         }
-                        if (terminalMod != null)
+                        if (terminalMod != null && !updatedMods.Keys.Contains(startResidue - 1))
                         {
                             updatedMods.Add(startResidue - 1, terminalMod);
                         }

MetaMorpheus/Test/SearchEngineTests.cs

@@ -979,6 +979,29 @@ public static void TestNonSpecificEnzymeSearchEngineSingleN()
             Assert.That(allPsmsArray[0].BaseSequence, Is.EqualTo("QQQGGGG"));
         }
 
+        [Test]
+        public static void TestNonSpecificEnzymeSearchEngine()
+        {
+            var myTomlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\NonSpecificSearchToml.toml");
+            var searchTaskLoaded = Toml.ReadFile<SearchTask>(myTomlPath, MetaMorpheusTask.tomlConfig);
+            string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\NonSpecificSearchTest");
+            Directory.CreateDirectory(outputFolder);
+            string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\TaGe_SA_A549_3_snip.mzML");
+            string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\bosTaurusEnamPruned.xml");
+
+            var engineToml = new EverythingRunnerEngine(new List<(string, MetaMorpheusTask)> { ("SearchTOML", searchTaskLoaded) }, new List<string> { myFile }, new List<DbForTask> { new DbForTask(myDatabase, false) }, outputFolder);
+            engineToml.Run();
+
+            string psmFile = Path.Combine(outputFolder, @"SearchTOML\AllPSMs.psmtsv");
+
+            List<PsmFromTsv> parsedPsms = PsmTsvReader.ReadTsv(psmFile, out var warnings);
+
+            Assert.That(parsedPsms.Count, Is.EqualTo(38)); //total psm count
+
+            Directory.Delete(outputFolder, true);
+
+        }
+
 
         [Test]
         public static void TestNonSpecificEnzymeSearchEngineSingleNLowCID()

MetaMorpheus/Test/Test.csproj

@@ -217,6 +217,9 @@
     <None Update="SlicedSearchTaskConfig.toml">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
+    <None Update="TestData\bosTaurusEnamPruned.xml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
     <None Update="TestData\customBCZ.toml">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
@@ -325,6 +328,9 @@
     <None Update="TestData\myPrositLib.msp">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
+    <None Update="TestData\NonSpecificSearchToml.toml">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
     <None Update="TestData\noSAreaderTest.psmtsv">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>

MetaMorpheus/Test/TestData/NonSpecificSearchToml.toml

@@ -0,0 +1,100 @@
+TaskType = "Search"
+
+[SearchParameters]
+DisposeOfFileWhenDone = true
+DoParsimony = true
+ModPeptidesAreDifferent = false
+NoOneHitWonders = false
+MatchBetweenRuns = false
+Normalize = false
+QuantifyPpmTol = 5.0
+DoHistogramAnalysis = false
+SearchTarget = true
+DecoyType = "Reverse"
+MassDiffAcceptorType = "OneMM"
+WritePrunedDatabase = true
+KeepAllUniprotMods = true
+DoLocalizationAnalysis = false
+DoLabelFreeQuantification = false
+UseSharedPeptidesForLFQ = false
+DoMultiplexQuantification = false
+MultiplexModId = "TMT10"
+DoSpectralRecovery = false
+SearchType = "NonSpecific"
+LocalFdrCategories = ["FullySpecific", "SemiSpecific", "NonSpecific"]
+MaxFragmentSize = 10800.0
+MinAllowedInternalFragmentLength = 0
+HistogramBinTolInDaltons = 0.003
+MaximumMassThatFragmentIonScoreIsDoubled = 0.0
+WriteMzId = true
+WritePepXml = false
+WriteHighQValuePsms = true
+WriteDecoys = true
+WriteContaminants = true
+WriteIndividualFiles = true
+WriteSpectralLibrary = false
+UpdateSpectralLibrary = false
+CompressIndividualFiles = false
+TCAmbiguity = "RemoveContaminant"
+IncludeModMotifInMzid = false
+
+[SearchParameters.ModsToWriteSelection]
+'N-linked glycosylation' = 3
+'O-linked glycosylation' = 3
+'Other glycosylation' = 3
+'Common Biological' = 3
+'Less Common' = 3
+Metal = 3
+'2+ nucleotide substitution' = 3
+'1 nucleotide substitution' = 3
+UniProt = 2
+
+[CommonParameters]
+TaskDescriptor = "SearchTask"
+MaxThreadsToUsePerFile = 63
+ListOfModsFixed = ""
+ListOfModsVariable = "Common Variable\tOxidation on M"
+DoPrecursorDeconvolution = true
+UseProvidedPrecursorInfo = true
+DeconvolutionMaxAssumedChargeState = 12
+TotalPartitions = 1
+ProductMassTolerance = "±20.0000 PPM"
+PrecursorMassTolerance = "±15.0000 PPM"
+AddCompIons = true
+QValueThreshold = 0.01
+PepQValueThreshold = 1.0
+ScoreCutoff = 5.0
+QValueCutoffForPepCalculation = 0.005
+ReportAllAmbiguity = true
+NumberOfPeaksToKeepPerWindow = 200
+MinimumAllowedIntensityRatioToBasePeak = 0.01
+NormalizePeaksAccrossAllWindows = false
+TrimMs1Peaks = false
+TrimMsMsPeaks = true
+CustomIons = []
+AssumeOrphanPeaksAreZ1Fragments = true
+MaxHeterozygousVariants = 4
+MinVariantDepth = 1
+AddTruncations = false
+DissociationType = "HCD"
+SeparationType = "HPLC"
+MS2ChildScanDissociationType = "Unknown"
+MS3ChildScanDissociationType = "Unknown"
+UseMostAbundantPrecursorIntensity = true
+
+[CommonParameters.DigestionParams]
+InitiatorMethionineBehavior = "Variable"
+MaxMissedCleavages = 35
+MaxModificationIsoforms = 1024
+SearchModeType = "None"
+FragmentationTerminus = "C"
+SpecificProtease = "singleC"
+GeneratehUnlabeledProteinsForSilac = true
+KeepNGlycopeptide = false
+KeepOGlycopeptide = false
+Protease = "singleC"
+MinPeptideLength = 7
+MaxPeptideLength = 36
+MaxModsForPeptide = 2
+
+[[FileSpecificParameters]]