Modified decoy scrambler to no longer use static Random generator (#798)

* Modified decoy scrambler to no longer use static Random generator

* Added additional tests

* Better tests

mzLib/Proteomics/Protein/Protein.cs

@@ -836,21 +836,22 @@ public static Protein ScrambleDecoyProteinSequence(
             string scrambledProteinSequence = originalDecoyProtein.BaseSequence;
             // Clone the original protein's modifications
             var scrambledModificationDictionary = originalDecoyProtein.OriginalNonVariantModifications.ToDictionary(kvp => kvp.Key, kvp => kvp.Value);
+            Random rng = new Random(42);
 
             // Start small and then go big. If we scramble a zero-missed cleavage peptide, but the missed cleavage peptide contains the previously scrambled peptide
             // Then we can avoid unnecessary operations as the scrambledProteinSequence will no longer contain the longer sequence of the missed cleavage peptide
             foreach(string peptideSequence in sequencesToScramble.OrderBy(seq => seq.Length))
             {
                 if(scrambledProteinSequence.Contains(peptideSequence))
                 {
-                    string scrambledPeptideSequence = ScrambleSequence(peptideSequence, digestionParams.DigestionAgent.DigestionMotifs, 
+                    string scrambledPeptideSequence = ScrambleSequence(peptideSequence, digestionParams.DigestionAgent.DigestionMotifs, rng,
                         out var swappedArray);
                     int scrambleAttempts = 1;
 
                     // Try five times to scramble the peptide sequence without creating a forbidden sequence
                     while(forbiddenSequences.Contains(scrambledPeptideSequence) & scrambleAttempts <= 5)
                     {
-                        scrambledPeptideSequence = ScrambleSequence(peptideSequence, digestionParams.DigestionAgent.DigestionMotifs,
+                        scrambledPeptideSequence = ScrambleSequence(peptideSequence, digestionParams.DigestionAgent.DigestionMotifs, rng,
                             out swappedArray);
                         scrambleAttempts++;
                     }
@@ -896,13 +897,11 @@ public static Protein ScrambleDecoyProteinSequence(
             return newProtein;
         }
 
-        private static Random rng = new Random(42);
-
         /// <summary>
         /// Scrambles a peptide sequence, preserving the position of any cleavage sites.
         /// </summary>
         /// <param name="swappedPositionArray">An array that maps the previous position (index) to the new position (value)</param>
-        public static string ScrambleSequence(string sequence, List<DigestionMotif> motifs, out int[] swappedPositionArray)
+        public static string ScrambleSequence(string sequence, List<DigestionMotif> motifs, Random rng, out int[] swappedPositionArray)
         {
             // First, find the location of every cleavage motif. These sites shouldn't be scrambled.
             HashSet<int> zeroBasedCleavageSitesLocations = new();

mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs

@@ -1,4 +1,4 @@
-// opyright 2016 Stefan Solntsev
+// Copyright 2016 Stefan Solntsev
 //
 // This file (ChemicalFormula.cs) is part of Chemistry Library.
 //
@@ -28,6 +28,7 @@
 using Omics.Modifications;
 using UsefulProteomicsDatabases;
 using Stopwatch = System.Diagnostics.Stopwatch;
+using NUnit.Framework.Legacy;
 
 namespace Test.DatabaseTests
 {
@@ -81,6 +82,39 @@ public static void LoadIsoforms()
             Assert.AreEqual("Q14103-4", proteinXml[9].Accession);
         }
 
+        [Test]
+        [TestCase("cRAP_databaseGPTMD.xml", DecoyType.None)]
+        [TestCase("uniprot_aifm1.fasta", DecoyType.None)]
+        [TestCase("cRAP_databaseGPTMD.xml", DecoyType.Reverse)]
+        [TestCase("uniprot_aifm1.fasta", DecoyType.Reverse)]
+        public void LoadingIsReproducible(string fileName, DecoyType decoyType)
+        {
+            // Load in proteins
+            var dbPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", fileName);
+            List<Protein> proteins1 = null;
+            List<Protein> proteins2 = null;
+            if(fileName.Contains(".xml"))
+            {
+                proteins1 = ProteinDbLoader.LoadProteinXML(dbPath, true, decoyType, null, false, null, out var unknownModifications);
+                proteins2 = ProteinDbLoader.LoadProteinXML(dbPath, true, decoyType, null, false, null, out unknownModifications);
+            }
+            else if (fileName.Contains(".fasta"))
+            {
+                proteins1 = ProteinDbLoader.LoadProteinFasta(dbPath, true, decoyType, false, out var unknownModifications);
+                proteins2 = ProteinDbLoader.LoadProteinFasta(dbPath, true, decoyType, false, out unknownModifications);
+            }
+            else
+            {
+                Assert.Fail("Unknown file type");
+            }
+
+            // check are equivalent lists of proteins
+            Assert.AreEqual(proteins1.Count, proteins2.Count);
+            // Because decoys are written in a parallel environment, there is no guarantee that the orders will be the same
+            CollectionAssert.AreEquivalent(proteins1.Select(p => p.Accession), proteins2.Select(p => p.Accession));
+            CollectionAssert.AreEquivalent(proteins1.Select(p => p.BaseSequence), proteins2.Select(p => p.BaseSequence));
+        }
+
         [Test]
         public static void LoadModWithNl()
         {

mzLib/Test/TestProteinDigestion.cs

@@ -361,6 +361,73 @@ public static void Test_ProteinDigest()
             Assert.AreEqual("MED[mt:mod1 on D]EEK", pep2.FullSequence);
         }
 
+        [Test]
+        [TestCase("cRAP_databaseGPTMD.xml")]
+        [TestCase("uniprot_aifm1.fasta")]
+        public static void TestDecoyScramblingIsReproducible(string fileName)
+        {
+            // Load in proteins
+            var dbPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", fileName);
+            DecoyType decoyType = DecoyType.Reverse;
+            List<Protein> proteins1 = null;
+            List<Protein> proteins2 = null;
+            if (fileName.Contains(".xml"))
+            {
+                proteins1 = ProteinDbLoader.LoadProteinXML(dbPath, true, decoyType, null, false, null, out var unknownModifications);
+                proteins2 = ProteinDbLoader.LoadProteinXML(dbPath, true, decoyType, null, false, null, out unknownModifications);
+            }
+            else if (fileName.Contains(".fasta"))
+            {
+                proteins1 = ProteinDbLoader.LoadProteinFasta(dbPath, true, decoyType, false, out var unknownModifications);
+                proteins2 = ProteinDbLoader.LoadProteinFasta(dbPath, true, decoyType, false, out unknownModifications);
+            }
+            else
+            {
+                Assert.Fail("Unknown file type");
+            }
+
+            DigestionParams d = new DigestionParams(
+                        maxMissedCleavages: 1,
+                        minPeptideLength: 5,
+                        initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
+            // Digest target proteins
+            var pepsToReplace = proteins1.Where(p => !p.IsDecoy)
+                .SelectMany(p => p.Digest(d, new List<Modification>(), new List<Modification>()).ToList())
+                .Select(pep => pep.BaseSequence)
+                .ToHashSet();
+
+            // Ensure at least one decoy peptide from each protein is problematic and must be replaced
+            var singleDecoyPeptides = proteins1
+                .Where(p => p.IsDecoy)
+                .Select(p => p.Digest(d, new List<Modification>(), new List<Modification>()).Skip(2).Take(1))
+                .Select(pwsm => pwsm.First().BaseSequence)
+                .ToHashSet();
+
+            //modify targetpeptides in place
+            pepsToReplace.UnionWith(singleDecoyPeptides);
+
+            // Scramble every decoy from db1
+            List<Protein> decoys1 = new();
+            foreach (var protein in proteins1.Where(p => p.IsDecoy))
+            {
+                decoys1.Add(Protein.ScrambleDecoyProteinSequence(protein, d, pepsToReplace));
+            }
+            // Scramble every decoy from db2
+            List<Protein> decoys2 = new();
+            foreach (var protein in proteins2.Where(p => p.IsDecoy))
+            {
+                decoys2.Add(Protein.ScrambleDecoyProteinSequence(protein, d, pepsToReplace));
+            }
+
+            // check are equivalent lists of proteins
+            Assert.AreEqual(decoys1.Count, decoys2.Count);
+            foreach (var decoyPair in decoys1.Concat(decoys2).GroupBy(p => p.Accession))
+            {
+                Assert.AreEqual(2, decoyPair.Count());
+                Assert.AreEqual(decoyPair.First().BaseSequence, decoyPair.Last().BaseSequence);
+            }
+        }
+
         [Test]
         public static void TestDecoyScramblerReplacesPeptides()
         {