Add option to export mProphet features through the command line (#2746)

* Add new arguments for exporting mProphet features

* Add command line option to exclude scores from the exported file

* Update escape sequences

pwiz_tools/Skyline/CommandArgUsage.resx

@@ -681,8 +681,8 @@ first occurrence of any peptide.</value>
 will be removed from the document:
 
 Green = 1.0
-Orange &amp;gt;= 0.5
-Red &amp;lt; 0.5</value>
+Orange &gt;= 0.5
+Red &lt; 0.5</value>
   </data>
   <data name="_refine_max_peptide_peak_rank" xml:space="preserve">
     <value>All transitions with an average area peak ranking
@@ -709,8 +709,8 @@ removed from the document.</value>
 will be removed from the document:
 
 Green = 1.0
-Orange &amp;gt;= 0.5
-Red &amp;lt; 0.5</value>
+Orange &gt;= 0.5
+Red &lt; 0.5</value>
   </data>
   <data name="_refine_min_time_correlation" xml:space="preserve">
     <value>Precursors will be removed from the document
@@ -934,4 +934,16 @@ greater peak area.</value>
   <data name="_exp_speclib_file" xml:space="preserve">
     <value>Export experimental data in the current document to a spectral library file. Peak areas are used as spectrum intensities, peak apex times are used as retention times, and if the document has iRT values they will also be stored in the library.</value>
   </data>
+  <data name="_exp_mprophet_exclude_feature" xml:space="preserve">
+    <value>Use to exclude a particular feature score by name from the exported file. Names can be found in the user interface. This argument may be used multiple times to exclude multiple features. Requires the --exp-mprophet-file argument.</value>
+  </data>
+  <data name="_exp_mprophet_file" xml:space="preserve">
+    <value>Export all the individual feature scores for each peptide, as well as the composite score, the p value, and the q value into the mProphet format.</value>
+  </data>
+  <data name="_exp_mprophet_best_peaks_only" xml:space="preserve">
+    <value>Include feature scores only for the best scoring peaks. Requires the --exp-mprophet-file argument.</value>
+  </data>
+  <data name="_exp_mprophet_targets_only" xml:space="preserve">
+    <value>Include feature scores only for targets. Requires the --exp-mprophet-file argument.</value>
+  </data>
 </root>

pwiz_tools/Skyline/CommandArgs.cs

@@ -692,7 +692,7 @@ public bool SettingLibraryPath
         private static readonly Argument ARG_REINTEGRATE_LOG_TRAINING = new DocArgument(@"reintegrate-log-training",
             (c, p) => c.IsLogTraining = true) {InternalUse = true};
         private static readonly Argument ARG_REINTEGRATE_EXCLUDE_FEATURE = new DocArgument(@"reintegrate-exclude-feature", FEATURE_NAME_VALUE,
-                (c, p) => c.ParseReintegrateExcludeFeature(p))
+                (c, p) => c.ParseExcludeFeature(p, c.ExcludeFeatures))
             { WrapValue = true };
 
         private static readonly ArgumentGroup GROUP_REINTEGRATE = new ArgumentGroup(() => CommandArgUsage.CommandArgs_GROUP_REINTEGRATE_Reintegrate_with_advanced_peak_picking_models, false,
@@ -789,9 +789,9 @@ private List<double> ParseNumberList(NameValuePair pair)
             }
         }
 
-        private bool ParseReintegrateExcludeFeature(NameValuePair pair)
+        private bool ParseExcludeFeature(NameValuePair pair, ICollection<IPeakFeatureCalculator> featureList)
         {
-            string featureName = pair.Value;
+            var featureName = pair.Value;
             var calc = PeakFeatureCalculator.Calculators.FirstOrDefault(c =>
                 Equals(featureName, c.HeaderName) || Equals(featureName, c.Name));
             if (calc == null)
@@ -811,8 +811,8 @@ private bool ParseReintegrateExcludeFeature(NameValuePair pair)
 
                 return false;
             }
-
-            ExcludeFeatures.Add(calc);
+            
+            featureList.Add(calc);
             return true;
         }
 
@@ -1038,15 +1038,35 @@ private bool ValidateChromatogramArgs()
         // For exporting other file types
         public static readonly Argument ARG_SPECTRAL_LIBRARY_FILE = new DocArgument(@"exp-speclib-file", PATH_TO_BLIB,
             (c, p) => c.SpecLibFile= p.ValueFullPath);
+        public static readonly Argument ARG_MPROPHET_FEATURES_FILE = new DocArgument(@"exp-mprophet-file", PATH_TO_CSV,
+            (c, p) => c.MProphetFeaturesFile = p.ValueFullPath);
+        public static readonly Argument ARG_MPROPHET_FEATURES_BEST_SCORING_PEAKS =
+            new DocArgument(@"exp-mprophet-best-peaks-only", (c, p) => c.MProphetUseBestScoringPeaks = true);
+        public static readonly Argument ARG_MPROPHET_FEATURES_TARGETS_ONLY =
+            new DocArgument(@"exp-mprophet-targets-only", (c, p) => c.MProphetTargetsOnly = true);
+        public static readonly Argument ARG_MPROPHET_FEATURES_MPROPHET_EXCLUDE_SCORES = 
+            new DocArgument(@"exp-mprophet-exclude-feature", FEATURE_NAME_VALUE, 
+                (c, p) => c.ParseExcludeFeature(p, c.MProphetExcludeScores)){WrapValue = true};
 
         private static readonly ArgumentGroup GROUP_OTHER_FILE_TYPES = new ArgumentGroup(() => CommandArgUsage.CommandArgs_GROUP_OTHER_FILE_TYPES, false, 
-            ARG_SPECTRAL_LIBRARY_FILE
+            ARG_SPECTRAL_LIBRARY_FILE, ARG_MPROPHET_FEATURES_FILE, ARG_MPROPHET_FEATURES_BEST_SCORING_PEAKS, ARG_MPROPHET_FEATURES_TARGETS_ONLY, 
+            ARG_MPROPHET_FEATURES_MPROPHET_EXCLUDE_SCORES
         );
 
         public string SpecLibFile { get; private set; }
 
         public bool ExportingSpecLib { get { return !string.IsNullOrEmpty(SpecLibFile); } }
 
+        public string MProphetFeaturesFile { get; private set; }
+
+        public bool ExportingMProphetFeatures { get { return !string.IsNullOrEmpty(MProphetFeaturesFile); } }
+
+        public bool MProphetUseBestScoringPeaks { get; private set; }
+
+        public bool MProphetTargetsOnly { get; private set; }
+
+        public List<IPeakFeatureCalculator> MProphetExcludeScores { get; private set; }
+
         // For publishing the document to Panorama
         public static readonly Argument ARG_PANORAMA_SERVER = new DocArgument(@"panorama-server", SERVER_URL_VALUE,
             (c, p) => c.PanoramaServerUri = p.Value);
@@ -2157,6 +2177,8 @@ public CommandArgs(CommandStatusWriter output, bool isDocumentLoaded)
             ExcludeFeatures = new List<IPeakFeatureCalculator>();
             SharedFileType = ShareType.DEFAULT;
 
+            MProphetExcludeScores = new List<IPeakFeatureCalculator>();
+
             ImportBeforeDate = null;
             ImportOnOrAfterDate = null;
         }

pwiz_tools/Skyline/CommandLine.cs

@@ -808,11 +808,24 @@ private bool PerformExportOperations(CommandArgs commandArgs)
             }
 
 
-            if (commandArgs.ExportingSpecLib && !ExportSpecLib(commandArgs.SpecLibFile))
-            { 
-                return false;
+            if (commandArgs.ExportingSpecLib)
+            {
+                if (!ExportSpecLib(commandArgs.SpecLibFile))
+                {
+                    return false;
+                }
             }
 
+            if (commandArgs.ExportingMProphetFeatures)
+            {
+                if (!ExportMProphetFeatures(commandArgs.MProphetFeaturesFile, commandArgs.MProphetTargetsOnly,
+                        commandArgs.MProphetUseBestScoringPeaks, 
+                        new FeatureCalculators(commandArgs.MProphetExcludeScores)))
+                {
+                    return false;
+                }
+            } 
+
             var exportTypes =
                 (string.IsNullOrEmpty(commandArgs.IsolationListInstrumentType) ? 0 : 1) +
                 (string.IsNullOrEmpty(commandArgs.TransListInstrumentType) ? 0 : 1) +
@@ -3149,6 +3162,57 @@ public bool ExportSpecLib(string specLibFile)
             return true;
         }
 
+        /// <summary>
+        /// Export mProphet features as a .csv file
+        /// </summary>
+        /// <param name="mProphetFile">File path to export the mProphet file to</param>
+        /// <param name="targetPeptidesOnly">Do not include decoys, only targets</param>
+        /// <param name="bestOnly">Export best scoring peaks only</param>
+        /// <param name="excludeScores">A list of features to exclude from the exported file</param>
+        /// <returns>True upon successful import, false upon error</returns>
+        public bool ExportMProphetFeatures(string mProphetFile, bool targetPeptidesOnly, bool bestOnly, FeatureCalculators excludeScores)
+        {
+            if (Document.MoleculeCount == 0) // The document must contain targets
+            {
+                _out.WriteLine(Resources.CommandLine_ExportMProphetFeatures_Error__The_document_must_contain_targets_for_which_to_export_mProphet_features_);
+                return false;
+            }
+
+            if (!Document.Settings.HasResults) // The document must contain results
+            {
+                _out.WriteLine(Resources.CommandLine_ExportMProphetFeatures_Error__The_document_must_contain_results_to_export_mProphet_features_);
+                return false;
+            }
+
+            try
+            {
+                var scoringModel = Document.Settings.PeptideSettings.Integration.PeakScoringModel;
+                var mProphetScoringModel = scoringModel as MProphetPeakScoringModel;
+                var handler = new MProphetResultsHandler(Document, mProphetScoringModel);
+                var status = new ProgressStatus(string.Empty);
+                var cultureInfo = LocalizationHelper.CurrentCulture;
+                IProgressMonitor progressMonitor = new CommandProgressMonitor(_out, status);
+                using (var fs = new FileSaver(mProphetFile))
+                using (var writer = new StreamWriter(fs.SafeName))
+                {
+                    handler.ScoreFeatures(progressMonitor);
+                    // Excluding any scores requested by the caller
+                    var calcs = new FeatureCalculators(PeakFeatureCalculator.Calculators.Where(c => excludeScores.IndexOf(c) < 0));
+                    handler.WriteScores(writer, cultureInfo, calcs, bestOnly, !targetPeptidesOnly, progressMonitor);
+                    writer.Close();
+                    fs.Commit();
+                }
+                _out.WriteLine(Resources.CommandLine_ExportMProphetFeatures_mProphet_features_file__0__exported_successfully_, mProphetFile);
+            }
+            catch (Exception x)
+            {
+                _out.WriteLine(Resources.CommandLine_ExportMProphetFeatures_Error__Failure_attempting_to_save_mProphet_features_file__0__, mProphetFile);
+                _out.WriteLine(x.Message);
+                return false;
+            }
+            return true;
+        }
+
         public enum ResolveZipToolConflicts
         {
             terminate,

pwiz_tools/Skyline/FileUI/MProphetFeaturesDlg.resx

@@ -231,6 +231,9 @@
   <data name="&gt;&gt;label2.ZOrder" xml:space="preserve">
     <value>2</value>
   </data>
+  <data name="checkBoxBestOnly.Anchor" type="System.Windows.Forms.AnchorStyles, System.Windows.Forms">
+    <value>Bottom, Left</value>
+  </data>
   <data name="checkBoxBestOnly.AutoSize" type="System.Boolean, mscorlib">
     <value>True</value>
   </data>
@@ -261,6 +264,9 @@
   <data name="&gt;&gt;checkBoxBestOnly.ZOrder" xml:space="preserve">
     <value>1</value>
   </data>
+  <data name="checkBoxTargetsOnly.Anchor" type="System.Windows.Forms.AnchorStyles, System.Windows.Forms">
+    <value>Bottom, Left</value>
+  </data>
   <data name="checkBoxTargetsOnly.AutoSize" type="System.Boolean, mscorlib">
     <value>True</value>
   </data>

pwiz_tools/Skyline/Properties/Resources.resx

@@ -13899,4 +13899,16 @@ If you choose Disable, you can enable Auto-select later with the "Refine > Ad
   <data name="CommandLine_ExportSpecLib_Error__Failure_attempting_to_save_spectral_library_file__0__" xml:space="preserve">
     <value>Error: Failure attempting to save spectral library file {0}.</value>
   </data>
+  <data name="CommandLine_ExportMProphetFeatures_mProphet_features_file__0__exported_successfully_" xml:space="preserve">
+    <value>mProphet features file {0} exported successfully.</value>
+  </data>
+  <data name="CommandLine_ExportMProphetFeatures_Error__The_document_must_contain_targets_for_which_to_export_mProphet_features_" xml:space="preserve">
+    <value>Error: The document must contain targets for which to export mProphet features.</value>
+  </data>
+  <data name="CommandLine_ExportMProphetFeatures_Error__The_document_must_contain_results_to_export_mProphet_features_" xml:space="preserve">
+    <value>Error: The document must contain results to export mProphet features.</value>
+  </data>
+  <data name="CommandLine_ExportMProphetFeatures_Error__Failure_attempting_to_save_mProphet_features_file__0__" xml:space="preserve">
+    <value>Error: Failure attempting to save mProphet features file {0}.</value>
+  </data>
 </root>