ReadPsms for IQuantifiableResultFile

CMD/CMD.csproj

@@ -15,7 +15,7 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.7.82" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.553" />
+    <PackageReference Include="mzLib" Version="2.0.7" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />

GUI/GUI.csproj

@@ -16,7 +16,7 @@
   </PropertyGroup>
   <ItemGroup>
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.553" />
+    <PackageReference Include="mzLib" Version="2.0.7" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.28.0" />

Test/SampleFiles/FraggerPsm_FragPipev21.1_psm.tsv

@@ -0,0 +1,6 @@
+Spectrum	Spectrum File	Peptide	Modified Peptide	Extended Peptide	Prev AA	Next AA	Peptide Length	Charge	Retention	Observed Mass	Calibrated Observed Mass	Observed M/Z	Calibrated Observed M/Z	Calculated Peptide Mass	Calculated M/Z	Delta Mass	Expectation	Hyperscore	Nextscore	PeptideProphet Probability	Number of Enzymatic Termini	Number of Missed Cleavages	Protein Start	Protein End	Intensity	Assigned Modifications	Observed Modifications	Purity	Is Unique	Protein	Protein ID	Entry Name	Gene	Protein Description	Mapped Genes	Mapped Proteins
+20100611_Velos1_TaGe_SA_Hela_1.00003.00003.2	D:\Projects\Chimeras\Mann_11cell_analysis\Hela\MsFragger\Hela_1_1\interact-20100611_Velos1_TaGe_SA_Hela_1.pep.xml	KPVGAAK		KAGGTKPK.KPVGAAK.KPKKAAGG	K	K	7	2	1.9398	669.4164	669.4123	335.7155	335.7135	669.4173	335.7159	-0.0049	0.01675	20.604	12.521	0.9176	2	1	130	136	0			0	TRUE	sp|P16403|H12_HUMAN	P16403	H12_HUMAN	H1-2	Histone H1.2		
+20100611_Velos1_TaGe_SA_Hela_1.00004.00004.2	D:\Projects\Chimeras\Mann_11cell_analysis\Hela\MsFragger\Hela_1_1\interact-20100611_Velos1_TaGe_SA_Hela_1.pep.xml	KPAAAAGAK		KKTPKKAK.KPAAAAGAK.KAKSPKKA	K	K	9	2	2.9446	783.4582	783.4521	392.7364	392.7334	783.4603	392.7374	-0.0081	0.0001384	24.869	16.973	1	2	1	160	168	0			0	TRUE	sp|P10412|H14_HUMAN	P10412	H14_HUMAN	H1-4	Histone H1.4		
+20100611_Velos1_TaGe_SA_Hela_1.00005.00005.2	D:\Projects\Chimeras\Mann_11cell_analysis\Hela\MsFragger\Hela_1_1\interact-20100611_Velos1_TaGe_SA_Hela_1.pep.xml	LGHASDR		AYGQAIAK.LGHASDR.IIAIDGDT	K	I	7	2	4.1263	754.3708	754.3652	378.1927	378.1899	754.3722	378.1934	-0.007	0.1565	14.722	10.374	0.7358	2	0	328	334	0			0	FALSE	sp|P29401|TKT_HUMAN	P29401	TKT_HUMAN	TKT	Transketolase		tr|A0A0B4J1R6|A0A0B4J1R6_HUMAN
+20100611_Velos1_TaGe_SA_Hela_1.00009.00009.2	D:\Projects\Chimeras\Mann_11cell_analysis\Hela\MsFragger\Hela_1_1\interact-20100611_Velos1_TaGe_SA_Hela_1.pep.xml	KAAGGATPK		VGAAKKPK.KAAGGATPK.KSAKKTPK	K	K	9	2	8.8589	799.4532	799.4476	400.7339	400.7311	799.4551	400.7348	-0.0075	0.003204	22.564	14.018	0.9705	2	1	140	148	0			0	TRUE	sp|P16403|H12_HUMAN	P16403	H12_HUMAN	H1-2	Histone H1.2		
+20100611_Velos1_TaGe_SA_Hela_1.00018.00018.2	D:\Projects\Chimeras\Mann_11cell_analysis\Hela\MsFragger\Hela_1_1\interact-20100611_Velos1_TaGe_SA_Hela_1.pep.xml	VVTHGGR		GTAIKNGK.VVTHGGR.VIAVTAIR	K	V	7	2	19.114	724.3984	724.3949	363.2065	363.2047	724.398	363.2063	-0.0031	0.7595	11.978	0	0.8144	2	0	379	385	0			0	TRUE	sp|P22102|PUR2_HUMAN	P22102	PUR2_HUMAN	GART	Trifunctional purine biosynthetic protein adenosine-3		

Test/Test.cs

@@ -223,11 +223,11 @@ public void TestPercolatorReadPsmsGetsRTsFromFileHeader()
             Assert.AreEqual(6, ids.Count);
 
             //strings separated by commas should be taken literally as protein names
-            Assert.AreEqual(11,ids[0].ProteinGroups.Count);
-            List<string> expectedProteinNameStrings = new() { "sp|Q13885|TBB2A_HUMAN", "tr|M0R1I1|M0R1I1_HUMAN", "tr|Q5JP53|Q5JP53_HUMAN", 
-                "tr|M0QZL7|M0QZL7_HUMAN", "sp|P04350|TBB4A_HUMAN", "sp|P07437|TBB5_HUMAN", "sp|Q9BVA1|TBB2B_HUMAN", "tr|M0R278|M0R278_HUMAN", 
+            Assert.AreEqual(11, ids[0].ProteinGroups.Count);
+            List<string> expectedProteinNameStrings = new() { "sp|Q13885|TBB2A_HUMAN", "tr|M0R1I1|M0R1I1_HUMAN", "tr|Q5JP53|Q5JP53_HUMAN",
+                "tr|M0QZL7|M0QZL7_HUMAN", "sp|P04350|TBB4A_HUMAN", "sp|P07437|TBB5_HUMAN", "sp|Q9BVA1|TBB2B_HUMAN", "tr|M0R278|M0R278_HUMAN",
                 "tr|Q5ST81|Q5ST81_HUMAN", "sp|P68371|TBB4B_HUMAN", "tr|M0QY85|M0QY85_HUMAN" };
-            CollectionAssert.AreEquivalent(ids[0].ProteinGroups.Select(n=>n.ProteinGroupName).ToList(), expectedProteinNameStrings);  
+            CollectionAssert.AreEquivalent(ids[0].ProteinGroups.Select(n => n.ProteinGroupName).ToList(), expectedProteinNameStrings);
 
             List<double> actualRetentionTimes = ids.Select(t => Math.Round(t.Ms2RetentionTimeInMinutes, 2)).ToList();
 
@@ -456,7 +456,7 @@ public static void TestParallelProcessingMetaMorpheusOutputWithExtensions()
             File.Delete(proteinsPath);
         }
 
-        [Test]    
+        [Test]
         public static void TestParallelProcessingMetaMorpheusOutputWithExtensionsAndWindowsPath()
         {
             string search = "Parallel";
@@ -652,5 +652,36 @@ public static void TestSettingsPassing()
                 Assert.That(settingsValue, Is.EqualTo(engineValue));
             }
         }
+
+        [Test]
+        [TestCase(@"SampleFiles\FraggerPsm_FragPipev21.1_psm.tsv")]
+        public static void TestReadPsmsValidMsFraggerPsmFile(string path)
+        {
+            // Arrange  
+            var filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, path);
+            Assert.That(File.Exists(filePath));
+            // this is a local file path only used for testing, do not try to access
+            string mzmlPath = @"D:\Projects\Chimeras\Mann_11cell_analysis\Hela\MsFragger\Hela_1_1\20100611_Velos1_TaGe_SA_Hela_1.mzML";
+            SpectraFileInfo sfi = new SpectraFileInfo(mzmlPath, "A", 1, 1, 1);
+            PsmReader psmReader = new();
+
+            // Act  
+            List<Identification> ids = psmReader.ReadPsms(filePath, false, new List<SpectraFileInfo> { sfi });
+
+            // Assert  
+            Assert.IsNotEmpty(ids);
+            Assert.That(ids.Count, Is.GreaterThan(0));
+        }
+
+        [Test]
+        public static void TestReadPsmsThrowsException()
+        {
+            // Arrange  
+            string invalidFilePath = "NonExistentFile.psmtsv";
+            PsmReader psmReader = new();
+
+            // Act & Assert  
+            Assert.DoesNotThrow(() => psmReader.ReadPsms(invalidFilePath, false, new List<SpectraFileInfo>()));
+        }
     }
 }

Test/Test.csproj

@@ -10,9 +10,17 @@
     <GenerateAssemblyFileVersionAttribute>false</GenerateAssemblyFileVersionAttribute>
     <Platforms>AnyCPU</Platforms>
   </PropertyGroup>
+  <ItemGroup>
+    <None Remove="SampleFiles\FraggerPsm_FragPipev21.1_psm.tsv" />
+  </ItemGroup>
+  <ItemGroup>
+    <Content Include="SampleFiles\FraggerPsm_FragPipev21.1_psm.tsv">
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </Content>
+  </ItemGroup>
   <ItemGroup>
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.553" />
+    <PackageReference Include="mzLib" Version="2.0.7" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="nunit" Version="4.2.2" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.6.0" />

Util/PsmReader.cs

@@ -1,10 +1,13 @@
 using FlashLFQ;
 using MzLibUtil;
+using Readers;
 using System;
 using System.Collections.Generic;
 using System.Globalization;
 using System.IO;
 using System.Linq;
+using System.Reflection.Metadata.Ecma335;
+using ThermoFisher.CommonCore.Data.Business;
 using UsefulProteomicsDatabases;
 
 namespace Util
@@ -58,8 +61,41 @@ public PsmReader()
             { PsmFileType.PeptideShaker, new string[] { ", " } },
         };
 
+        // TODO: 
+        // try to cast filetype as IQuantifiableResultFile
+        // var readResult as IQuantifiableResultFile
+        // 1. use Parsefiletype extension  to get supported filetype enum
+        // 2. get ResultFile by passing in filePath and enum
+        // try cast resultFile to IQuantResultFile
+        private static List<Identification> TryReadQuantifiableResultFile(string filepath, bool silent, List<SpectraFileInfo> rawfiles)
+        {
+            try
+            {
+                IQuantifiableResultFile quantifiable = FileReader.ReadQuantifiableResultFile(filepath);
+                List<Identification> identifications = quantifiable.MakeIdentifications(rawfiles);
+                if (!silent)
+                {
+                    Console.WriteLine("Done reading PSMs; found " + identifications.Count);
+                }
+                return identifications;
+            }
+            catch (Exception e)
+            {
+                // not every file read in will be a QuantifiableResultFile, support for this is still in development
+            }
+            return null;
+        }
+
+
         public List<Identification> ReadPsms(string filepath, bool silent, List<SpectraFileInfo> rawfiles, double qValueThreshold = 0.01, bool usePepQValue = false)
         {
+            // check if file path can be read in using readers as QuantifiableResultFile
+            List<Identification> quantifiableIdentifications = TryReadQuantifiableResultFile(filepath, silent, rawfiles);
+            if (quantifiableIdentifications != null)
+            {
+                return quantifiableIdentifications;
+            }
+
             if (_modSequenceToMonoMass == null)
             {
                 _modSequenceToMonoMass = new Dictionary<string, double>();

Util/Util.csproj

@@ -13,7 +13,7 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.7.82" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="mzLib" Version="1.0.553" />
+    <PackageReference Include="mzLib" Version="2.0.7" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>