Merge branch 'JohnnyDeconv' of https://github.com/nbollis/mzLib into …

…JohnnyDeconv

mzLib/Proteomics/Protein/Protein.cs

@@ -76,14 +76,14 @@ public Protein(string sequence, string accession, string organism = null, List<T
 
         /// <summary>
         /// Protein construction that clones a protein but assigns a different base sequence
-        /// For use in SILAC experiments
+        /// For use in SILAC experiments and in decoy construction
         /// </summary>
         /// <param name="originalProtein"></param>
-        /// <param name="silacSequence"></param>
+        /// <param name="newBaseSequence"></param>
         /// <param name="silacAccession"></param>
-        public Protein(Protein originalProtein, string silacSequence)
+        public Protein(Protein originalProtein, string newBaseSequence)
         {
-            BaseSequence = silacSequence;
+            BaseSequence = newBaseSequence;
             Accession = originalProtein.Accession;
             NonVariantProtein = originalProtein.NonVariantProtein;
             Name = originalProtein.Name;
@@ -156,7 +156,7 @@ public Protein(string variantBaseSequence, Protein protein, IEnumerable<Sequence
         /// <summary>
         /// Base sequence, which may contain applied sequence variations.
         /// </summary>
-        public string BaseSequence { get; }
+        public string BaseSequence { get; private set; }
 
         public string Organism { get; }
         public bool IsDecoy { get; }
@@ -206,6 +206,7 @@ public string GetUniProtFastaHeader()
         {
             var n = GeneNames.FirstOrDefault();
             string geneName = n == null ? "" : n.Item2;
+
             return string.Format("mz|{0}|{1} {2} OS={3} GN={4}", Accession, Name, FullName, Organism, geneName);
         }
 
@@ -801,6 +802,103 @@ private static string GetName(IEnumerable<SequenceVariation> appliedVariations,
             }
         }
 
+        /// <summary>
+        /// This function takes in a decoy protein and a list of forbidden sequences that the decoy
+        /// protein should not contain. Optionally, a list of the peptides within the base sequence
+        /// of the decoy protein that need to be scrambled can be passed as well. It will scramble the required sequences,
+        /// leaving cleavage sites intact. 
+        /// </summary>
+        /// <param name="originalDecoyProtein"> A Decoy protein to be cloned </param>
+        /// <param name="digestionParams"> Digestion parameters </param>
+        /// <param name="forbiddenSequences"> A HashSet of forbidden sequences that the decoy protein should not contain. Typically, a set of target base sequences </param>
+        /// <param name="sequencesToScramble"> Optional IEnumberable of sequences within the decoy protein that need to be replaced.
+        ///                                     If this is passed, only sequences within the IEnumerable will be replaced!!! </param>
+        /// <returns> A cloned copy of the decoy protein with a scrambled sequence </returns>
+        public static Protein ScrambleDecoyProteinSequence(
+            Protein originalDecoyProtein,
+            DigestionParams digestionParams,
+            HashSet<string> forbiddenSequences,
+            IEnumerable<string> sequencesToScramble = null)
+        {
+            // If no sequencesToScramble are passed in, we check to see if any 
+            // peptides in the decoy are forbidden sequences
+            sequencesToScramble = sequencesToScramble ?? originalDecoyProtein
+                .Digest(digestionParams, new List<Modification>(), new List<Modification>())
+                .Select(pep => pep.FullSequence)
+                .Where(forbiddenSequences.Contains);
+            if(sequencesToScramble.Count() == 0)
+            {
+                return originalDecoyProtein;
+            }
+
+            string scrambledProteinSequence = originalDecoyProtein.BaseSequence;
+            // 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);
+                    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);
+                        scrambleAttempts++;
+                    }
+                    scrambledProteinSequence = scrambledProteinSequence.Replace(peptideSequence, scrambledPeptideSequence);
+                }
+            }
+
+            return new Protein(originalDecoyProtein, scrambledProteinSequence);
+        }
+
+        private static Random rng = new Random(42);
+
+        /// <summary>
+        /// Scrambles a peptide sequence, preserving the position of any cleavage sites.
+        /// </summary>
+        public static string ScrambleSequence(string sequence, List<DigestionMotif> motifs)
+        {
+            // First, find the location of every cleavage motif. These sites shouldn't be scrambled.
+            HashSet<int> zeroBasedCleavageSitesLocations = new();
+            foreach (var motif in motifs)
+            {
+                for (int i = 0; i < sequence.Length; i++)
+                {
+                    (bool fits, bool prevents) = motif.Fits(sequence, i);
+                    if (fits && !prevents)
+                    {
+                        zeroBasedCleavageSitesLocations.Add(i);
+                    }
+                }
+            }
+
+            // Next, scramble the sequence using the Fisher-Yates shuffle algorithm.
+            char[] sequenceArray = sequence.ToCharArray();
+            int n = sequenceArray.Length;
+            while(n > 1)
+            {
+                n--;
+                if(zeroBasedCleavageSitesLocations.Contains(n))
+                {
+                    // Leave the cleavage site in place
+                    continue;
+                }
+                int k = rng.Next(n + 1);
+                // don't swap the position of a cleavage site
+                while(zeroBasedCleavageSitesLocations.Contains(k))
+                {
+                    k = rng.Next(n + 1);
+                }
+                char temp = sequenceArray[k];
+                sequenceArray[k] = sequenceArray[n];
+                sequenceArray[n] = temp;
+            }
+
+            return new string(sequenceArray);
+        }
+
         public int CompareTo(Protein other)
         {
             //permits sorting of proteins

mzLib/Test/TestProteinDigestion.cs

@@ -16,6 +16,7 @@
 using UsefulProteomicsDatabases;
 using static Chemistry.PeriodicTable;
 using Stopwatch = System.Diagnostics.Stopwatch;
+using System.Runtime.CompilerServices;
 
 namespace Test
 {
@@ -359,6 +360,78 @@ public static void Test_ProteinDigest()
             Assert.AreEqual("MED[mt:mod1 on D]EEK", pep2.FullSequence);
         }
 
+        [Test]
+        public static void TestDecoyScramblerReplacesPeptides()
+        {
+            DigestionParams d = new DigestionParams(
+                        maxMissedCleavages: 1,
+                        minPeptideLength: 5,
+                        initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
+
+            Protein target = new Protein("MEDEEKFVGYKYGVFK", "target");
+            Protein decoy = new Protein("EEDEMKYGVFKFVGYK", "decoy");
+
+            var targetPep = target.Digest(d, new List<Modification>(), new List<Modification>());
+            var decoyPep = decoy.Digest(d, new List<Modification>(), new List<Modification>());
+
+            HashSet<string> targetPepSeqs = targetPep.Select(p => p.FullSequence).ToHashSet();
+            var offendingDecoys = decoyPep.Where(p => targetPepSeqs.Contains(p.FullSequence)).Select(d => d.FullSequence).ToList();
+
+            Assert.AreEqual(2, offendingDecoys.Count);
+
+            Protein scrambledDecoy = Protein.ScrambleDecoyProteinSequence(decoy,  d, targetPepSeqs, offendingDecoys);
+            var scrambledPep = scrambledDecoy.Digest(d, new List<Modification>(), new List<Modification>());
+
+            Assert.AreEqual(decoyPep.Count(), scrambledPep.Count());
+            Assert.IsFalse(scrambledPep.Any(p => offendingDecoys.Contains(p.FullSequence)));
+
+            // Check to make sure that decoy generation also works in no offending sequences are passed in
+            scrambledDecoy = Protein.ScrambleDecoyProteinSequence(decoy, d, targetPepSeqs);
+            scrambledPep = scrambledDecoy.Digest(d, new List<Modification>(), new List<Modification>());
+
+            Assert.AreEqual(decoyPep.Count(), scrambledPep.Count());
+            Assert.IsFalse(scrambledPep.Any(p => offendingDecoys.Contains(p.FullSequence)));
+        }
+
+        [Test, Timeout(5000)]
+        public static void TestDecoyScramblerNoInfiniteLoops()
+        {
+            DigestionParams d = new DigestionParams(
+                        maxMissedCleavages: 0,
+                        minPeptideLength: 3,
+                        initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
+
+            Protein target = new Protein("MEK", "target");
+            Protein decoy = new Protein("EMK", "decoy");
+
+            var targetPep = target.Digest(d, new List<Modification>(), new List<Modification>());
+            var decoyPep = decoy.Digest(d, new List<Modification>(), new List<Modification>());
+
+            HashSet<string> targetPepSeqs = targetPep.Select(p => p.FullSequence).ToHashSet();
+
+            // We'll pretend that this is also a target sequence and can't be used as a decoy
+            HashSet<string> offendingDecoys = new HashSet<string> { "EMK" };
+
+            // You can't win in this scenario, there's no way to scramble that results in a different decoy
+            Protein scrambledDecoy = Protein.ScrambleDecoyProteinSequence(decoy, d, targetPepSeqs.Union(offendingDecoys).ToHashSet(), offendingDecoys);
+            var scrambledPep = scrambledDecoy.Digest(d, new List<Modification>(), new List<Modification>());
+
+            Assert.AreEqual(decoyPep.Count(), scrambledPep.Count());
+
+            d = new DigestionParams(
+                        maxMissedCleavages: 1,
+                        minPeptideLength: 3,
+                        initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
+
+            offendingDecoys = new HashSet<string> { "KEK" };
+
+            var impossibleDecoy = new Protein("KEK", "target"); // This guy could crash the shuffling algorithm
+            scrambledDecoy = Protein.ScrambleDecoyProteinSequence(impossibleDecoy, d, offendingDecoys, offendingDecoys);
+
+            Assert.AreEqual("KEK", scrambledDecoy.BaseSequence);
+
+        }
+
         [Test]
         /// <summary>
         /// Tests that a PeptideWithSetModifications object can be parsed correctly from a string, with mod info

mzLib/mzLib.nuspec

@@ -14,7 +14,7 @@
     <dependencies>
       <group targetFramework="net8.0">
         <!--net8.0 target-->
-        <dependency id="Easy.Common" version="4.3.0" />
+        <dependency id="Easy.Common" version="6.7.0" />
         <dependency id="MathNet.Numerics" version="5.0.0" />
         <dependency id="Microsoft.Win32.Registry" version="5.0.0" />
         <dependency id="NetSerializer" version="4.1.1" />
@@ -24,7 +24,7 @@
       </group>
       <group targetFramework="net8.0-windows7.0">
         <!--net8.0 target with OxyPlot-->
-        <dependency id="Easy.Common" version="4.3.0" />
+        <dependency id="Easy.Common" version="6.7.0" />
         <dependency id="MathNet.Numerics" version="5.0.0" />
         <dependency id="Microsoft.Win32.Registry" version="5.0.0" />
         <dependency id="NetSerializer" version="4.1.1" />