Fix string split in glyco protein parsimony

MetaMorpheus/TaskLayer/GlycoSearchTask/GlycoProteinParsimony.cs

@@ -41,10 +41,10 @@ public GlycoProteinParsimony(string proteinAccess, int proteinPos, char aminoAci
 
         public double MaxProbability { get; set; }
 
-        public static Dictionary<string, GlycoProteinParsimony> ProteinLevelGlycoParsimony(List<GlycoSpectralMatch> allPsmsGly)
+        public static Dictionary<(string proteinAccession, string proteinPosition, int glycanId), GlycoProteinParsimony> ProteinLevelGlycoParsimony(List<GlycoSpectralMatch> allPsmsGly)
         {
             //key: proPosId
-            Dictionary<string, GlycoProteinParsimony> localizedGlycan = new Dictionary<string, GlycoProteinParsimony>();
+            Dictionary<(string proteinAccession, string proteinPosition, int glycanId), GlycoProteinParsimony> localizedGlycan = new Dictionary<(string proteinAccession, string proteinPosition, int glycanId), GlycoProteinParsimony>();
 
             foreach (var gsm in allPsmsGly)
             {
@@ -59,7 +59,7 @@ public static Dictionary<string, GlycoProteinParsimony> ProteinLevelGlycoParsimo
                     {
                         int proteinPos = local.Item1 + gsm.OneBasedStartResidueInProtein.Value - 2;
 
-                        string proPosId = gsm.ProteinAccession + "-" + proteinPos.ToString() + "-" + local.Item2;
+                        (string,string,int) proPosId = new (gsm.ProteinAccession, proteinPos.ToString(), local.Item2);
 
                         double prob = -1;
                         if (gsm.SiteSpeciLocalProb != null && gsm.SiteSpeciLocalProb.ContainsKey(local.Item1))

MetaMorpheus/TaskLayer/XLSearchTask/WriteFile.cs

@@ -9,6 +9,7 @@
 using System.IO;
 using System.Linq;
 using System.Xml.Serialization;
+using Easy.Common.Extensions;
 
 namespace TaskLayer
 {
@@ -452,50 +453,51 @@
         }
 
         //The function is to summarize localized glycan by protein site.
-        public static void WriteSeenProteinGlycoLocalization(Dictionary<string, GlycoProteinParsimony> glycoProteinParsimony, string outputPath)
+        public static void WriteSeenProteinGlycoLocalization(Dictionary<(string proteinAccession, string proteinPosition, int glycanId), GlycoProteinParsimony> glycoProteinParsimony, string outputPath)
         {
-            if (glycoProteinParsimony.Count == 0)
+            if (glycoProteinParsimony.Keys.Count == 0)
             { return; }
             var writtenFile = Path.Combine(outputPath);
             using (StreamWriter output = new StreamWriter(writtenFile))
             {
                 output.WriteLine("Protein Accession\tModification Site\tAminoAcid\tLocalized Glycans\tLocalized\tLowest Qvalue\tBest Localization Level\tMax Site Specific Probability");
-                foreach (var item in glycoProteinParsimony.OrderBy(p=>p.Key))
+                foreach (var item in glycoProteinParsimony.OrderBy(i=>i.Key.proteinAccession))
                 {
-                    var x = item.Key.Split('-');
-                    output.WriteLine(
-                        x[0] + "\t" +
-                        x[1] + "\t" +
-                        item.Value.AminoAcid + "\t" +
-                        GlycanBox.GlobalOGlycans[int.Parse(x[2])].Composition + "\t" +
-                        item.Value.IsLocalized + "\t" +
-                        item.Value.MinQValue.ToString("0.000") + "\t" +
-                        item.Value.BestLocalizeLevel + "\t" +
-                        item.Value.MaxProbability.ToString("0.000")
-                        );
+                    if (item.Value != null)
+                    {
+                        output.WriteLine(
+                                item.Key.proteinAccession + "\t" +
+                                item.Key.proteinPosition + "\t" +
+                                item.Value.AminoAcid + "\t" +
+                                GlycanBox.GlobalOGlycans[item.Key.glycanId].Composition + "\t" +
+                                item.Value.IsLocalized + "\t" +
+                                item.Value.MinQValue.ToString("0.000") + "\t" +
+                                item.Value.BestLocalizeLevel + "\t" +
+                                item.Value.MaxProbability.ToString("0.000"));
+
+                    }
                 }
             }
         }
 
         //The function is to summarize localized glycosylation of each protein site. 
-        public static void WriteProteinGlycoLocalization(Dictionary<string, GlycoProteinParsimony> glycoProteinParsimony, string outputPath)
+        public static void WriteProteinGlycoLocalization(Dictionary<(string proteinAccession, string proteinPosition, int glycanId), GlycoProteinParsimony> glycoProteinParsimony, string outputPath)
         {
             if (glycoProteinParsimony.Count == 0)
             { return; }
 
             Dictionary<string, HashSet<string>> localizedglycans = new Dictionary<string, HashSet<string>>();
             foreach (var item in glycoProteinParsimony.Where(p=>p.Value.IsLocalized && p.Value.MinQValue <= 0.01))
             {
-                var x = item.Key.Split('-');
-                var key = x[0] + "-" + x[1];
+                var key = item.Key.proteinAccession + "#" + item.Key.proteinPosition;
                 if ( localizedglycans.ContainsKey(key))
                 {
-                    localizedglycans[key].Add(x[2]);
+                    localizedglycans[key].Add(item.Key.glycanId.ToString());
                 }
                 else
                 {
                     localizedglycans[key] = new HashSet<string>();
-                    localizedglycans[key].Add(x[2]);
+                    localizedglycans[key].Add(item.Key.glycanId.ToString());
                 }
 
             }
@@ -506,7 +508,7 @@
                 output.WriteLine("Protein Accession\tModification Site\tLocalized Glycan Number\tLocalized Glycans");
                 foreach (var local in localizedglycans.OrderBy(p => p.Key))
                 {
-                    var x = local.Key.Split('-');
+                    var x = local.Key.Split('#');
                     output.WriteLine(
                         x[0] + "\t" +
                         x[1] + "\t" +

MetaMorpheus/Test/GlycoTestData/P16150withHyphenInName.fasta

@@ -0,0 +1,8 @@
+>sp|P16150|LEUK_HUMAN Leuko-sialin OS=Homo sapiens OX=9606 GN=SPN PE=1 SV=1
+MATLLLLLGVLVVSPDALGSTTAVQTPTSGEPLVSTSEPLSSKMYTTSITSDPKADSTGD
+QTSALPPSTSINEGSPLWTSIGASTGSPLPEPTTYQEVSIKMSSVPQETPHATSHPAVPI
+TANSLGSHTVTGGTITTNSPETSSRTSGAPVTTAASSLETSRGTSGPPLTMATVSLETSK
+GTSGPPVTMATDSLETSTGTTGPPVTMTTGSLEPSSGASGPQVSSVKLSTMMSPTTSTNA
+STVPFRNPDENSRGMLPVAVLVALLAVIVLVALLLLWRRRQKRRTGALVLSRGGKRNGVV
+DAWAGPAQVPEEGAVTVTVGGSGGDKGSGFPDGEGSSRRPTLTTFFGRRKSRQGSLAMEE
+LKSGSGPSLKGEEEPLVASEDGAVDAPAPDEPEGGDGAAP

MetaMorpheus/Test/Test.csproj

@@ -132,6 +132,9 @@
     <None Update="GlycoTestData\P02649.fasta">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
+    <None Update="GlycoTestData\P16150withHyphenInName.fasta">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
     <None Update="GlycoTestData\P16150.fasta">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>

MetaMorpheus/Test/XLTestNGlyco.cs

@@ -63,18 +63,6 @@ public static void GlyTest_GlyGetTheoreticalFragments()
             var sites = GlycoSpectralMatch.GetPossibleModSites(aPeptideWithSetModifications.Last(), motifs);
             Glycan glycan = Glycan.Struct2Glycan("(N(F)(N(H(H(N))(H(N)))))", 0);
 
-
-            //using (StreamWriter output = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "GlycanFragmentions.txt")))
-            //{
-            //    foreach (var product in fragmentIons)
-            //    {
-            //        foreach (var ion in product.Item2)
-            //        {
-            //            output.WriteLine(ion.Annotation + "\t" + ion.NeutralLoss.ToString() + "\t" + ion.NeutralMass.ToString());
-            //        }
-            //    }
-            //}
-
             CommonParameters commonParameters = new CommonParameters(deconvolutionMassTolerance: new PpmTolerance(20), trimMsMsPeaks: false);
             string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData/Glyco_3383.mgf"); //"25170.mgf"
             MyFileManager myFileManager = new MyFileManager(true);

MetaMorpheus/Test/XLTestOGlyco.cs

@@ -1,7 +1,4 @@
-using Chemistry;
-using EngineLayer;
-using EngineLayer.CrosslinkSearch;
-using EngineLayer.Indexing;
+using EngineLayer;
 using MassSpectrometry;
 using NUnit.Framework;
 using Proteomics;
@@ -13,7 +10,6 @@
 using System.Linq;
 using TaskLayer;
 using UsefulProteomicsDatabases;
-using MzLibUtil;
 using Nett;
 using EngineLayer.GlycoSearch;
 
@@ -443,6 +439,26 @@ public static void OGlycoTest_Run3()
             Directory.Delete(Path.Combine(Environment.CurrentDirectory, @"TESTGlycoData"), true);
         }
 
+        //make sure that hyphens in protein names don't produce a crash during protein inference from glycopeptides
+        [Test]
+        public static void OGlycoTest_Run4()
+        {
+            string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TESTGlycoData");
+            Directory.CreateDirectory(outputFolder);
+
+            var glycoSearchTask = Toml.ReadFile<GlycoSearchTask>(Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\GlycoSearchTaskconfigOGlycoTest_Run.toml"), MetaMorpheusTask.tomlConfig);
+
+            DbForTask db = new(Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\P16150withHyphenInName.fasta"), false);
+            string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\2019_09_16_StcEmix_35trig_EThcD25_rep1_9906.mgf");
+            new EverythingRunnerEngine(new List<(string, MetaMorpheusTask)> { ("Task", glycoSearchTask) }, new List<string> { spectraFile }, new List<DbForTask> { db }, outputFolder).Run();
+
+            var folders = Directory.GetDirectories(outputFolder).Select(b => Path.GetFileName(b)).ToList();
+            var folderContents = Directory.GetFiles(Path.Combine(outputFolder, folders[0])).ToList();
+            Assert.That(folderContents[6].Contains("_AllProteinGroups.tsv"));
+
+            Directory.Delete(outputFolder, true);
+        }
+
         [Test]
         public static void OGlycoTest_GetLeft()
         {