Optional Digestion Count Output

MetaMorpheus/EngineLayer/ClassicSearch/ClassicSearchEngine.cs

@@ -7,7 +7,6 @@
 using System.Collections.Generic;
 using System.Linq;
 using System.Threading.Tasks;
-using System.Threading;
 using Omics.Modifications;
 using System.Collections.Concurrent;
 
@@ -26,12 +25,14 @@ public class ClassicSearchEngine : MetaMorpheusEngine
         private readonly Ms2ScanWithSpecificMass[] ArrayOfSortedMS2Scans;
         private readonly double[] MyScanPrecursorMasses;
         private readonly bool WriteSpectralLibrary;
+        private readonly bool WriteDigestionCounts;
         private readonly object[] Locks;
+        public readonly ConcurrentDictionary<(string Accession, string BaseSequence), int> DigestionCountDictionary; // Used to track the amount of digestion products from each protein when the option is enabled.
 
         public ClassicSearchEngine(SpectralMatch[] globalPsms, Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans,
             List<Modification> variableModifications, List<Modification> fixedModifications, List<SilacLabel> silacLabels, SilacLabel startLabel, SilacLabel endLabel,
             List<Protein> proteinList, MassDiffAcceptor searchMode, CommonParameters commonParameters, List<(string FileName, CommonParameters Parameters)> fileSpecificParameters,
-            SpectralLibrary spectralLibrary, List<string> nestedIds, bool writeSpectralLibrary)
+            SpectralLibrary spectralLibrary, List<string> nestedIds, bool writeSpectralLibrary, bool writeDigestionCounts = false)
             : base(commonParameters, fileSpecificParameters, nestedIds)
         {
             PeptideSpectralMatches = globalPsms;
@@ -48,6 +49,8 @@ public ClassicSearchEngine(SpectralMatch[] globalPsms, Ms2ScanWithSpecificMass[]
             SearchMode = searchMode;
             SpectralLibrary = spectralLibrary;
             WriteSpectralLibrary = writeSpectralLibrary;
+            WriteDigestionCounts = writeDigestionCounts;
+            DigestionCountDictionary = new();
 
             // Create one lock for each PSM to ensure thread safety
             Locks = new object[PeptideSpectralMatches.Length];
@@ -108,6 +111,9 @@ protected override MetaMorpheusEngineResults RunSpecific()
                         // digest each protein into peptides and search for each peptide in all spectra within precursor mass tolerance
                         foreach (PeptideWithSetModifications peptide in Proteins[i].Digest(CommonParameters.DigestionParams, FixedModifications, VariableModifications, SilacLabels, TurnoverLabels))
                         {
+                            if (WriteDigestionCounts)
+                                DigestionCountDictionary.Increment((peptide.Parent.Accession, peptide.BaseSequence));
+
                             PeptideWithSetModifications reversedOnTheFlyDecoy = null;
 
                             if (SpectralLibrary != null)

MetaMorpheus/EngineLayer/Util/DictionaryExtensions.cs

@@ -0,0 +1,121 @@
+using Nett;
+using System.Collections.Concurrent;
+using System.Collections.Generic;
+using System.Numerics;
+
+namespace EngineLayer;
+
+public static class DictionaryExtensions
+{
+    /// <summary>
+    /// Adds a value to the list associated with the specified key in the dictionary.
+    /// If the key does not exist, a new list is created with the value and added to the dictionary.
+    /// </summary>
+    /// <typeparam name="TKey">The type of the keys in the dictionary.</typeparam>
+    /// <typeparam name="TValues">The type of the values in the lists.</typeparam>
+    /// <param name="dictionary">The dictionary to operate on.</param>
+    /// <param name="key">The key whose value list to add to or create.</param>
+    /// <param name="value">The value to add to the list associated with the specified key.</param>
+    /// <remarks>
+    /// This is not thread-safe!
+    /// </remarks>
+    public static void AddOrCreate<TKey, TValues>(this IDictionary<TKey, IList<TValues>> dictionary, TKey key, TValues value)
+    {
+        if (dictionary.TryGetValue(key, out IList<TValues> values))
+        {
+            values.Add(value);
+        }
+        else
+        {
+            dictionary.Add(key, new List<TValues> { value });
+        }
+    }
+
+    /// <summary>
+    /// Adds a value to the list associated with the specified key in the dictionary.
+    /// If the key does not exist, a new list is created with the value and added to the dictionary.
+    /// </summary>
+    /// <typeparam name="TKey">The type of the keys in the dictionary.</typeparam>
+    /// <typeparam name="TValues">The type of the values in the lists.</typeparam>
+    /// <param name="dictionary">The dictionary to operate on.</param>
+    /// <param name="key">The key whose value list to add to or create.</param>
+    /// <param name="value">The value to add to the list associated with the specified key.</param>
+    /// <param name="lockObject">Object used to lock this specific dictionary</param>
+    /// <remarks>
+    /// This is thread safe for all dictionary types. 
+    /// </remarks>
+    public static void AddOrCreateThreadSafe<TKey, TValues>(this IDictionary<TKey, IList<TValues>> dictionary, TKey key, TValues value, object lockObject)
+    {
+        if (dictionary is ConcurrentDictionary<TKey, IList<TValues>> concurrentDictionary)
+        {
+            concurrentDictionary.AddOrUpdate(key, new List<TValues> { value }, (k, v) =>
+            {
+                // must lock inside the add or update as the List.Add method is not thread safe. 
+                lock (lockObject)
+                {
+                    v.Add(value);
+                    return v;
+                }
+            });
+        }
+        else
+        {
+            lock (lockObject)
+            {
+                if (dictionary.TryGetValue(key, out IList<TValues> values))
+                {
+                    values.Add(value);
+                }
+                else
+                {
+                    dictionary.Add(key, new List<TValues> { value });
+                }
+            }
+        }
+    }
+
+    /// <summary>
+    /// Increments the value associated with the specified key in the dictionary by a defined number with a default of one.
+    /// If the key does not exist, a new entry is created with the value set to one.
+    /// </summary>
+    /// <typeparam name="TKey">The type of the keys in the dictionary.</typeparam>
+    /// <typeparam name="TValue">The type of the values in the dictionary, which must implement <see cref="INumber{TValue}"/>.</typeparam>
+    /// <param name="dictionary">The dictionary to operate on.</param>
+    /// <param name="key">The key whose value to increment or create.</param>
+    /// <param name="incrementBy">The amount to increment by with a default of one</param>
+    public static void Increment<TKey, TValue>(this IDictionary<TKey, TValue> dictionary, TKey key, TValue incrementBy = default)
+    where TValue : INumber<TValue>
+    {
+        TValue incrementValue = incrementBy.Equals(default) ? TValue.One : incrementBy;
+
+        if (dictionary is ConcurrentDictionary<TKey, TValue> concurrentDictionary)
+        {
+            concurrentDictionary.AddOrUpdate(key, incrementValue, (k, v) => v + incrementValue);
+        }
+        else
+        {
+            if (dictionary.TryGetValue(key, out TValue value))
+            {
+                dictionary[key] = value + incrementValue;
+            }
+            else
+            {
+                dictionary.Add(key, incrementValue);
+            }
+        }
+    }
+
+    /// <summary>
+    /// Determines whether the dictionary is null or has no elements.
+    /// </summary>
+    /// <typeparam name="TKey">The type of the keys in the dictionary.</typeparam>
+    /// <typeparam name="TValue">The type of the values in the dictionary.</typeparam>
+    /// <param name="dictionary">The dictionary to check.</param>
+    /// <returns>
+    /// <c>true</c> if the dictionary is null or has no elements; otherwise, <c>false</c>.
+    /// </returns>
+    public static bool IsNullOrEmpty<TKey, TValue>(this IDictionary<TKey, TValue> dictionary)
+    {
+        return dictionary == null || dictionary.Count == 0;
+    }
+}

MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml

@@ -1171,6 +1171,18 @@
                                             </TextBlock>
                                         </ToolTipService.ToolTip>
                                     </CheckBox>
+                                    <CheckBox x:Name="WriteDigestCountCheckBox" Margin="20 0 0 0" 
+                                              Content="Write digestion product count histogram" IsEnabled="{Binding IsChecked, ElementName=ClassicSearchRadioButton}">
+                                        <ToolTipService.ToolTip>
+                                            <TextBlock>
+                                                Checking this box will create an additional output file with a histogram of the number of digestion products per protein.
+                                                <LineBreak/>
+                                                The number of digestion products is limited by the MaxModsPerPeptide parameter and limited to the MaxModifiedIsoforms parameter for each primary sequence generated by each database entry
+                                                <LineBreak/>
+                                                Multiple base sequences can be generated per protein due to variable methionine and splice variants if annotated in a database
+                                            </TextBlock>
+                                        </ToolTipService.ToolTip>
+                                    </CheckBox>
                                 </StackPanel>
                             </Expander>
                         </GroupBox>

MetaMorpheus/GUI/TaskWindows/SearchTaskWindow.xaml.cs

@@ -333,6 +333,7 @@ private void UpdateFieldsFromTask(SearchTask task)
 
             OutputFileNameTextBox.Text = task.CommonParameters.TaskDescriptor;
             CkbMzId.IsChecked = task.SearchParameters.WriteMzId;
+            WriteDigestCountCheckBox.IsChecked = task.SearchParameters.WriteDigestionProductCountFile;
             WriteHighQPsmsCheckBox.IsChecked = task.SearchParameters.WriteHighQValuePsms;
             WriteDecoyCheckBox.IsChecked = task.SearchParameters.WriteDecoys;
             WriteContaminantCheckBox.IsChecked = task.SearchParameters.WriteContaminants;
@@ -651,6 +652,7 @@ private void SaveButton_Click(object sender, RoutedEventArgs e)
             TheTask.SearchParameters.UpdateSpectralLibrary = UpdateSpectralLibraryCheckBox.IsChecked.Value;
             TheTask.SearchParameters.CompressIndividualFiles = CompressIndividualResultsCheckBox.IsChecked.Value;
             TheTask.SearchParameters.IncludeModMotifInMzid = IncludeMotifInModNamesCheckBox.IsChecked.Value;
+            TheTask.SearchParameters.WriteDigestionProductCountFile = WriteDigestCountCheckBox.IsChecked.Value;
 
             if (RemoveContaminantRadioBox.IsChecked.Value)
             {

MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs

@@ -35,7 +35,10 @@ public class PostSearchAnalysisTask : MetaMorpheusTask
         /// Used for storage of results for writing to Results.tsv. It is explained in the method ConstructResultsDictionary()
         /// </summary>
         private Dictionary<(string,string),string> ResultsDictionary { get; set; }
-
+        /// <summary>
+        /// Used for storage of results for writing digestion product counts to a .tsv. 
+        /// </summary>
+        internal IDictionary<(string Accession, string BaseSeqeunce), int> DigestionCountDictionary { get; set; }
         public PostSearchAnalysisTask()
             : base(MyTask.Search)
         {
@@ -110,6 +113,12 @@ public MyTaskResults Run()
                 UpdateSpectralLibrary();
             }
 
+            if (Parameters.SearchParameters.WriteDigestionProductCountFile)
+            {
+                WriteDigestionCountByProtein();
+                WriteDigestionCountHistogram();
+            }
+
             WriteFlashLFQResults();
 
             if (Parameters.ProteinList.Any((p => p.AppliedSequenceVariations.Count > 0)))
@@ -1939,5 +1948,62 @@ private void WritePeakQuantificationResultsToTsv(FlashLfqResults flashLFQResults
 
             FinishedWritingFile(peaksPath, nestedIds);
         }
+
+        /// <summary>
+        /// Writes the digestion product counts for each protein to a .tsv file.
+        /// </summary>
+        private void WriteDigestionCountByProtein()
+        {
+            if (DigestionCountDictionary.IsNullOrEmpty())
+                return;
+
+            var nestedIds = new List<string> { Parameters.SearchTaskId };
+            var countByProteinPath = Path.Combine(Parameters.OutputFolder, $"DigestionCountsBy{GlobalVariables.AnalyteType.GetBioPolymerLabel()}s.tsv");
+
+            // write all values to file
+            using (var writer = new StreamWriter(countByProteinPath))
+            {
+                writer.WriteLine("Protein Accession\tPrimary Sequence\tDigestion Products");
+                foreach (var proteinEntry in DigestionCountDictionary!)
+                {
+                    if (!Parameters.SearchParameters.WriteDecoys && proteinEntry.Key.Accession.StartsWith("DECOY"))
+                        continue;
+                    writer.WriteLine($"{proteinEntry.Key.Accession}\t{proteinEntry.Key.BaseSeqeunce}\t{proteinEntry.Value}");
+                }
+            }
+            FinishedWritingFile(countByProteinPath, nestedIds);
+        }
+
+        /// <summary>
+        /// Writes a histogram of digestion product counts to a .tsv file.
+        /// </summary>
+        private void WriteDigestionCountHistogram()
+        {
+            if (DigestionCountDictionary.IsNullOrEmpty())
+                return;
+
+            var nestedIds = new List<string> { Parameters.SearchTaskId };
+            var countHistogramPath = Path.Combine(Parameters.OutputFolder, $"DigestionCountHistogram.tsv");
+
+            // Create Histogram
+            var countDictionary = new Dictionary<int, int>(CommonParameters.DigestionParams.MaxModificationIsoforms);
+            foreach (var proteinEntry in DigestionCountDictionary!)
+            {
+                if (!Parameters.SearchParameters.WriteDecoys && proteinEntry.Key.Accession.StartsWith("DECOY"))
+                    continue;
+                countDictionary.Increment(proteinEntry.Value);
+            }
+
+            // Write Histogram
+            using (StreamWriter writer = new(countHistogramPath))
+            {
+                writer.WriteLine($"Digestion Products\tCount of {GlobalVariables.AnalyteType.GetBioPolymerLabel()}s");
+                foreach (var count in countDictionary.OrderBy(p => p.Key))
+                {
+                    writer.WriteLine($"{count.Key}\t{count.Value}");
+                }
+            }
+            FinishedWritingFile(countHistogramPath, nestedIds);
+        }
     }
 }

MetaMorpheus/TaskLayer/SearchTask/SearchParameters.cs

@@ -2,7 +2,6 @@
 using UsefulProteomicsDatabases;
 using EngineLayer;
 using Omics.Modifications;
-using Proteomics;
 
 namespace TaskLayer
 {
@@ -32,6 +31,7 @@ public SearchParameters()
             WriteMzId = true;
             WritePepXml = false;
             IncludeModMotifInMzid = false;
+            WriteDigestionProductCountFile = false;
 
             ModsToWriteSelection = new Dictionary<string, int>
             {
@@ -103,5 +103,6 @@ public SearchParameters()
         public SilacLabel EndTurnoverLabel { get; set; } //used for SILAC turnover experiments
         public TargetContaminantAmbiguity TCAmbiguity { get; set; }
         public bool IncludeModMotifInMzid { get; set; }
+        public bool WriteDigestionProductCountFile { get; set; }
     }
 }

MetaMorpheus/TaskLayer/SearchTask/SearchTask.cs

@@ -203,6 +203,8 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
             Status("Searching files...", new List<string> { taskId, "Individual Spectra Files" });
 
             Dictionary<string, int[]> numMs2SpectraPerFile = new Dictionary<string, int[]>();
+            bool collectedDigestionInformation = false;
+            IDictionary<(string Accession, string BaseSequence), int> digestionCountDictionary = null;
             for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++)
             {
                 if (GlobalVariables.StopLoops) { break; }
@@ -374,8 +376,15 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
                 {
                     Status("Starting search...", thisId);
                     var newClassicSearchEngine = new ClassicSearchEngine(fileSpecificPsms, arrayOfMs2ScansSortedByMass, variableModifications, fixedModifications, SearchParameters.SilacLabels,
-                       SearchParameters.StartTurnoverLabel, SearchParameters.EndTurnoverLabel, proteinList, massDiffAcceptor, combinedParams, this.FileSpecificParameters, spectralLibrary, thisId,SearchParameters.WriteSpectralLibrary);
-                    newClassicSearchEngine.Run();
+                       SearchParameters.StartTurnoverLabel, SearchParameters.EndTurnoverLabel, proteinList, massDiffAcceptor, combinedParams, this.FileSpecificParameters, spectralLibrary, thisId,SearchParameters.WriteSpectralLibrary, SearchParameters.WriteDigestionProductCountFile);
+                    var result = newClassicSearchEngine.Run();
+
+                    // The same proteins (all of them) get digested with each classic search engine, therefor we only need to calculate this for the first file that runs
+                    if (!collectedDigestionInformation) 
+                    {
+                        collectedDigestionInformation = true;
+                        digestionCountDictionary = (result.MyEngine as ClassicSearchEngine).DigestionCountDictionary;
+                    }
 
                     ReportProgress(new ProgressEventArgs(100, "Done with search!", thisId));
                 }
@@ -447,7 +456,8 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
             {
                 Parameters = parameters,
                 FileSpecificParameters = this.FileSpecificParameters,
-                CommonParameters = CommonParameters
+                CommonParameters = CommonParameters,
+                DigestionCountDictionary = digestionCountDictionary
             };
             return postProcessing.Run();
         }