MSFragger Results Folder Reader

mzLib/Readers/ExternalResults/BaseClasses/IQuantifiableResultFile.cs

@@ -24,6 +24,6 @@ public interface IQuantifiableResultFile : IResultFile
         /// </summary>
         /// <param name="fullFilePath"> list of file paths associated with each distinct record </param>
         /// <returns> Dictionary of file names and their associted full paths </returns>
-        public Dictionary<string, string> FileNametoFilePath(List<string> fullFilePath);
+        public Dictionary<string, string> FileNameToFilePath(List<string> fullFilePath);
     }
 }

mzLib/Readers/ExternalResults/IndividualResultRecords/ExperimentAnnotation.cs

@@ -0,0 +1,45 @@
+using CsvHelper.Configuration;
+using CsvHelper.Configuration.Attributes;
+using System;
+using System.Collections.Generic;
+using System.Globalization;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace Readers
+{
+    /// <summary>
+    /// A class representing a single entry in an experiment_annotation.tsv file
+    /// </summary>
+    public class ExperimentAnnotation
+    {
+        public static CsvConfiguration CsvConfiguration = new CsvConfiguration(CultureInfo.InvariantCulture)
+        {
+            Delimiter = "\t",
+            HasHeaderRecord = true,
+            IgnoreBlankLines = true,
+            TrimOptions = TrimOptions.Trim,
+            BadDataFound = null,
+        };
+
+        #region experiment_annotation Fields
+
+        [Name("file")]
+        public string File { get; set; }
+
+        [Name("sample")]
+        public string Sample { get; set; }
+
+        [Name("sample_name")]
+        public string SampleName { get; set; }
+
+        [Name("condition")]
+        public string Condition { get; set; }
+
+        [Name("replicate")]
+        public string Replicate { get; set; }
+
+        #endregion
+    }
+}

mzLib/Readers/ExternalResults/ResultFiles/ExperimentAnnotationFile.cs

@@ -0,0 +1,54 @@
+using CsvHelper;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace Readers
+{
+    /// <summary>
+    /// Concrete Product for reading and representing a experiment annotation file
+    /// </summary>
+    public class ExperimentAnnotationFile: ResultFile<ExperimentAnnotation>, IResultFile
+    {
+        public override SupportedFileType FileType => SupportedFileType.ExperimentAnnotation;
+
+        public override Software Software { get; set; }
+
+        public ExperimentAnnotationFile(string filePath) : base(filePath, Software.MsFragger) { }
+
+        /// <summary>
+        /// Constructor used to initialize from the factory method
+        /// </summary>
+        public ExperimentAnnotationFile() : base() { }
+
+        /// <summary>
+        /// Load Results to the Results List from the given filepath
+        /// </summary>
+        public override void LoadResults()
+        {
+            using var csv = new CsvReader(new StreamReader(FilePath), ExperimentAnnotation.CsvConfiguration);
+            Results = csv.GetRecords<ExperimentAnnotation>().ToList();
+        }
+
+        /// <summary>
+        /// Writes results to a specific output path
+        /// </summary>
+        /// <param name="outputPath">destination path</param>
+        public override void WriteResults(string outputPath)
+        {
+            if (!CanRead(outputPath))
+                outputPath += FileType.GetFileExtension();
+
+            using var csv = new CsvWriter(new StreamWriter(File.Create(outputPath)), ExperimentAnnotation.CsvConfiguration);
+
+            csv.WriteHeader<ExperimentAnnotation>();
+            foreach (var result in Results)
+            {
+                csv.NextRecord();
+                csv.WriteRecord(result);
+            }
+        }
+    }
+}

mzLib/Readers/ExternalResults/ResultFiles/MsFraggerCombinedResults.cs

@@ -0,0 +1,171 @@
+using CsvHelper;
+using Readers.ExternalResults.BaseClasses;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using System.IO;
+using MathNet.Numerics;
+
+namespace Readers
+{
+    public class MsFraggerCombinedResults : ResultFile<MsFraggerPsm>, IResultFile, IQuantifiableResultFile
+    {
+        #region Properties/Fields
+
+        public string FullFolderPath => FilePath; // The full file path to the folder of MSFragger results
+        private List<string> allPsmFilePaths; // List of the full file paths to the psm files of every sample
+
+        // A list of all the MSFraggerPsmFile objects that correspond to each sample within an experiment
+        public List<MsFraggerPsmFile> AllPsmFiles { get; private set; }
+
+        // Contains descriptive information on every ms data file in the experiment (sample name, full path to the ms data file, etc.)
+        public ExperimentAnnotationFile ExperimentAnnotations { get; private set; }
+
+        #endregion
+
+        #region IResultFile Implementatation
+
+        public override SupportedFileType FileType => SupportedFileType.MsFraggerPsm;
+        public override Software Software { get; set; }
+        public MsFraggerCombinedResults(string filePath) : base(filePath, Software.MsFragger) { }
+
+        /// <summary>
+        /// Loads the results from each psm.tsv file in the results folder, builds one list of MsFraggerPsms,
+        /// and Calls LoadExperimentAnnotation, FindAllFilePaths, LoadPsmResults,
+        /// then selects every results from each MsFraggerPsmFile in AllPsmFiles and writes them to one concatenated list. 
+        /// </summary>
+        public override void LoadResults()
+        {
+            LoadExperimentAnnotationResults();
+            FindAllFilePaths();
+            LoadPsmResults();
+
+            List<MsFraggerPsm> concatList = new List<MsFraggerPsm>();
+            foreach (var file in AllPsmFiles)
+            {
+                concatList.AddRange(file);
+            }
+
+            Results = concatList;
+        }
+
+        public override void WriteResults(string outputPath)
+        {
+            throw new NotImplementedException("Method not yet implemented.");
+        }
+
+        #endregion
+
+        /// <summary>
+        /// Checks for existence of experiment annotation file and loads its it as an ExperimentAnnotationResultFile, 
+        /// then sets the ExperimentAnnotations property
+        /// </summary>
+        /// <exception cref="FileNotFoundException"></exception>
+        public void LoadExperimentAnnotationResults()
+        {
+            string combinedFilePath = Path.Combine(FullFolderPath, "experiment_annotation.tsv");
+            if (!File.Exists(combinedFilePath)) { throw new FileNotFoundException("The experiment_annotation.tsv file was not found"); }
+
+            ExperimentAnnotations = new ExperimentAnnotationFile(combinedFilePath);
+        }
+
+        /// <summary>
+        /// For each path in AllPsmFilePaths, creates and loads an MsFraggerPsmFile. 
+        /// Then constructs the AllPsmFiles list
+        /// </summary>
+        public void LoadPsmResults()
+        {
+            AllPsmFiles = new List<MsFraggerPsmFile>();
+
+            foreach(var path in allPsmFilePaths)
+            {
+                MsFraggerPsmFile file = new MsFraggerPsmFile(path);
+                AllPsmFiles.Add(file);
+            }
+        }
+
+        public IEnumerable<IQuantifiableRecord> GetQuantifiableResults() => Results;
+
+        /// <summary>
+        /// Links the file name associated with the an IQuantifiableRecord 
+        /// to the raw file path of MassSpec data in the fullFilePath list
+        /// </summary>
+        /// <param name="filePaths"> list of file paths associated with each distinct record </param>
+        /// <returns> Dictionary of file names and their associted full paths </returns>
+        public Dictionary<string, string> FileNameToFilePath(List<string> filePaths)
+        {
+            Dictionary<string, string> allFiles = new Dictionary<string, string>();
+
+            allFiles = AllPsmFiles.Select(file => file.FileNameToFilePath(filePaths))
+                                  .SelectMany(dictionary => dictionary)
+                                  .GroupBy(x => x.Key)
+                                  .Select(keyValuePair => keyValuePair.First())
+                                  .ToDictionary(fileName => fileName.Key, filePath => filePath.Value);
+
+            return allFiles;
+        }
+
+        /// <summary>
+        /// Links the file name associated with IQuantifiableRecord to the raw file path pf MassSpec file 
+        /// using the full file paths from the experiment annotation file.
+        /// </summary>
+        /// <returns> Dictionary of file names and their associted full paths </returns>
+        public Dictionary<string, string> FileNameToFilePath()
+        {
+            List<string> filePaths = ExperimentAnnotations.Select(psm => psm.File).Distinct().ToList();
+            List<string> fileNames = Results.Select(psm => psm.FileName).Distinct().ToList();
+            Dictionary<string, string> allFiles = new Dictionary<string, string>();
+
+            foreach (var name in fileNames)
+            {
+                string fileName = Path.GetFileName(name);
+
+                // MSFragger results append the raw file with "interact-" and replace .raw with .pep.xml
+                // In order to correctly match the file names, these changes must be removed
+                fileName = fileName.Replace("interact-", "").Replace(".pep.xml", "");
+
+                foreach (var path in filePaths)
+                {
+                    if (path.Contains(fileName) && !allFiles.ContainsKey(name))
+                    {
+                        allFiles.Add(name, path);
+                        break;
+                    }
+                }
+            }
+
+            return allFiles;
+        }
+
+        /// <summary>
+        /// Uses the ExperimentAnnotations to locate each psm.tsv file in the results folder. 
+        /// Adds the path to each psm.tsv file in the results folder to AllPsmFilePaths
+        /// </summary>
+        /// <exception cref="FileNotFoundException"></exception>
+        private void FindAllFilePaths()
+        {
+            allPsmFilePaths = new List<string>();
+
+            List<string> sampleNames = ExperimentAnnotations.Select(psm => psm.SampleName).Distinct().ToList();
+            string[] directoryEntries = Directory.GetDirectories(FullFolderPath);
+
+            foreach (var directoryEntry in directoryEntries)
+            {
+                string directoryName = Path.GetFileName(directoryEntry.TrimEnd(Path.DirectorySeparatorChar));
+
+                foreach (var sample in sampleNames)
+                {
+                    if (directoryName.Equals(sample))
+                    {
+                        string psmFile = Path.Combine(directoryEntry, "psm.tsv");
+                        if (!File.Exists(psmFile)) { throw new FileNotFoundException("This psm.tsv file was not found"); }
+
+                        allPsmFilePaths.Add(psmFile);
+                    }
+                }
+            }
+        }
+    }
+}

mzLib/Readers/ExternalResults/ResultFiles/MsFraggerPsmFile.cs

@@ -48,7 +48,7 @@ public override void WriteResults(string outputPath)
         /// </summary>
         /// <param name="fullFilePath"> list of all full file paths associted with a given result </param>
         /// <returns> dictionary with key fileName and value fullFilePath </returns>
-        public Dictionary<string, string> FileNametoFilePath (List<string> fullFilePath)
+        public Dictionary<string, string> FileNameToFilePath (List<string> fullFilePath)
         {
             List<string> rawFileNames = Results.Select(psm => psm.FileName).Distinct().ToList();
             fullFilePath = fullFilePath.Distinct().ToList();

mzLib/Readers/Util/SupportedFileTypes.cs

@@ -26,7 +26,8 @@ public enum SupportedFileType
         MsPathFinderTTargets,
         MsPathFinderTDecoys,
         MsPathFinderTAllResults,
-        CruxResult
+        CruxResult,
+        ExperimentAnnotation
     }
 
     public static class SupportedFileTypeExtensions
@@ -64,6 +65,7 @@ public static string GetFileExtension(this SupportedFileType type)
                 SupportedFileType.MsPathFinderTDecoys => "_IcDecoy.tsv",
                 SupportedFileType.MsPathFinderTAllResults => "_IcTDA.tsv",
                 SupportedFileType.CruxResult => ".txt",
+                SupportedFileType.ExperimentAnnotation => "experiment_annotation.tsv",
                 _ => throw new MzLibException("File type not supported")
             };
         }

mzLib/Test/FileReadingTests/ExternalFileTypes/EditedMSFraggerResults/A_1/psm.tsv

@@ -0,0 +1,5 @@
+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	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
+Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_11860_1x02nguL_8.00906.00906.3	E:\MadeleineH\Kelly_TwoProteomeMSFragger\A_1\interact-Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_11860_1x02nguL_8.pep.xml	VKEDPDGEHAR		SISGRPIK.VKEDPDGEHAR.RAMQKVMA	K	R	11	3	2111.248	1251.5845	1251.5914	418.2021	418.2044	1251.5842	418.202	0.0072	0.05469976	15.518	11.386	0.8908	2	1	144	154	208463.97			0	FALSE	sp|P52272|HNRPM_HUMAN	P52272	HNRPM_HUMAN	HNRNPM	Heterogeneous nuclear ribonucleoprotein M		"tr|M0QYQ7|M0QYQ7_HUMAN, tr|M0R019|M0R019_HUMAN, tr|M0R0N3|M0R0N3_HUMAN, tr|M0R2T0|M0R2T0_HUMAN"
+Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_11860_1x02nguL_8.00917.00917.3	E:\MadeleineH\Kelly_TwoProteomeMSFragger\A_1\interact-Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_11860_1x02nguL_8.pep.xml	NEEDEGHSNSSPR		GAKIDASK.NEEDEGHSNSSPR.HSEAATAQ	K	H	13	3	2113.596	1456.5808	1456.5822	486.5342	486.5347	1456.5814	486.5344	0.0007	0.007893147	17.911	0	1	2	0	73	85	349264.44			0	FALSE	sp|Q14103|HNRPD_HUMAN	Q14103	HNRPD_HUMAN	HNRNPD	Heterogeneous nuclear ribonucleoprotein D0		"tr|A0A994J4B1|A0A994J4B1_HUMAN, tr|A0A994J4R1|A0A994J4R1_HUMAN, tr|D6RAF8|D6RAF8_HUMAN, tr|D6RD83|D6RD83_HUMAN"
+Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_11860_1x02nguL_8.00947.00947.3	E:\MadeleineH\Kelly_TwoProteomeMSFragger\A_1\interact-Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_11860_1x02nguL_8.pep.xml	VGQADDSTKPTNK		IGSFSGIR.VGQADDSTKPTNK.ASSTSITS	R	A	13	3	2120.3625	1359.6602	1359.6622	454.2273	454.228	1359.663	454.2283	-0.0007	0.001409289	12.904	0	0.9994	2	1	1339	1351	171548.62			0	FALSE	sp|P35658|NU214_HUMAN	P35658	NU214_HUMAN	NUP214	Nuclear pore complex protein Nup214		"tr|A0A494C1F2|A0A494C1F2_HUMAN, tr|A0A8Q3SHZ4|A0A8Q3SHZ4_HUMAN, tr|B7ZAV2|B7ZAV2_HUMAN, tr|E9PKD2|E9PKD2_HUMAN, tr|H0Y837|H0Y837_HUMAN"
+Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_11860_1x02nguL_8.01021.01021.3	E:\MadeleineH\Kelly_TwoProteomeMSFragger\A_1\interact-Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_11860_1x02nguL_8.pep.xml	AEQEAEEPRK		IAERARIK.AEQEAEEPRK.THSEEFTN	K	T	10	3	2136.586	1185.5615	1185.5641	396.1944	396.1953	1185.5625	396.1948	0.0015	0.151182	10.782	0	0.9548	2	1	106	115	125972.164			0	FALSE	sp|Q9H788|SH24A_HUMAN	Q9H788	SH24A_HUMAN	SH2D4A	SH2 domain-containing protein 4A		tr|H0YAT1|H0YAT1_HUMAN

mzLib/Test/FileReadingTests/ExternalFileTypes/EditedMSFraggerResults/A_2/psm.tsv

@@ -0,0 +1,5 @@
+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	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
+Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_2215_HeYe_1.01005.01005.2	E:\MadeleineH\Kelly_TwoProteomeMSFragger\A_2\interact-Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_2215_HeYe_1.pep.xml	HAVSEGTK		IIPGEIAK.HAVSEGTK.AVTKYTSA	K	A	8	2	1938.0153	827.4154	827.4152	414.715	414.7149	827.4137	414.7141	0.0015	1.57772E-05	21.993	14.41	0.9994	2	0	110	117	8907404			0	FALSE	sp|O60814|H2B1K_HUMAN	O60814	H2B1K_HUMAN	H2BC12	Histone H2B type 1-K	"H2BC1, H2BC11, H2BC12L, H2BC13, H2BC14, H2BC15, H2BC17, H2BC18, H2BC21, H2BC26, H2BC3, H2BC4, H2BC5, H2BC9, H2BK1"	"sp|A0A2R8Y619|H2BK1_HUMAN, sp|P06899|H2B1J_HUMAN, sp|P23527|H2B1O_HUMAN, sp|P33778|H2B1B_HUMAN, sp|P57053|H2BFS_HUMAN, sp|P58876|H2B1D_HUMAN, sp|P62807|H2B1C_HUMAN, sp|Q16778|H2B2E_HUMAN, sp|Q5QNW6|H2B2F_HUMAN, sp|Q8N257|H2B3B_HUMAN, sp|Q93079|H2B1H_HUMAN, sp|Q96A08|H2B1A_HUMAN, sp|Q99877|H2B1N_HUMAN, sp|Q99879|H2B1M_HUMAN, sp|Q99880|H2B1L_HUMAN, tr|U3KQK0|U3KQK0_HUMAN"
+Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_2215_HeYe_1.01551.01551.2	E:\MadeleineH\Kelly_TwoProteomeMSFragger\A_2\interact-Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_2215_HeYe_1.pep.xml	YDSTHGR		DYAAYMFK.YDSTHGR.YAGEVSHD	K	Y	7	2	1976.3535	834.3639	834.3626	418.1892	418.1886	834.362	418.1883	0.0005	0.01685582	15.593	0	0.9997	2	0	47	53	1.96E+07			0	FALSE	sp|P00359|G3P3_YEAST	P00359	G3P3_YEAST	TDH3	Glyceraldehyde-3-phosphate dehydrogenase 3	"GAPDHS, TDH1, TDH2"	"sp|O14556|G3PT_HUMAN, sp|P00358|G3P2_YEAST, sp|P00360|G3P1_YEAST, tr|K7EP73|K7EP73_HUMAN"
+Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_2215_HeYe_1.01565.01565.3	E:\MadeleineH\Kelly_TwoProteomeMSFragger\A_2\interact-Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_2215_HeYe_1.pep.xml	AESSQTCHSEQGDK	AESSQTCHSEQGDK	KSTQNSFR.AESSQTCHSEQGDK.KMEEKNSG	R	K	14	3	1977.164	1562.6292	1562.6265	521.8837	521.8828	1562.6267	521.8828	-0.0002	8.61986E-05	27.758	10.626	1	2	0	600	613	4579535.5	7C(57.0215)		0	TRUE	sp|P46063|RECQ1_HUMAN	P46063	RECQ1_HUMAN	RECQL	ATP-dependent DNA helicase Q1		
+Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_2215_HeYe_1.01607.01607.3	E:\MadeleineH\Kelly_TwoProteomeMSFragger\A_2\interact-Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_2215_HeYe_1.pep.xml	VTSTGRPGHASR		ERSPWWVR.VTSTGRPGHASR.FMEDTAAE	R	F	12	3	1979.2815	1224.6323	1224.6318	409.218	409.2179	1224.6322	409.218	-0.0003	0.9328038	10.648	0	0.9687	2	1	198	209	1587950.4			0	FALSE	sp|Q03154|ACY1_HUMAN	Q03154	ACY1_HUMAN	ACY1	Aminoacylase-1	ABHD14A-ACY1	"tr|A0A1B0GU86|A0A1B0GU86_HUMAN, tr|A0A1B0GV31|A0A1B0GV31_HUMAN, tr|A0A1B0GVA5|A0A1B0GVA5_HUMAN, tr|A0A1B0GW23|A0A1B0GW23_HUMAN, tr|C9JMV9|C9JMV9_HUMAN, tr|C9JYZ0|C9JYZ0_HUMAN"

mzLib/Test/FileReadingTests/ExternalFileTypes/EditedMSFraggerResults/experiment_annotation.tsv

@@ -0,0 +1,3 @@
+file	sample	sample_name	condition	replicate
+E:\MadeleineH\Raw_Files\Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_11860_1x02nguL_8.raw	A_1	A_1	A	1
+E:\MadeleineH\Raw_Files\Ex_AuLC1_30m_2D19_3_20um30cm_SPE50_15118120_OTOT_2215_HeYe_1.raw	A_2	A_2	A	2

mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs

@@ -56,6 +56,7 @@ public static void EnsureAllExtensionsAreUnique()
         [Test]
         public static void TestSupportedFileTypeExtension_Errors()
         {
+
             string badTest = "badFile.taco";
             Exception e = Assert.Throws<MzLibException>(() => badTest.ParseFileType());
             Assert.That(e?.Message, Is.EqualTo($"File type not supported"));