MsPathFinderT result reading

mzLib/Chemistry/ChemicalFormula.cs

@@ -19,9 +19,11 @@
 using MzLibUtil;
 using System;
 using System.Collections.Generic;
+using System.ComponentModel.DataAnnotations.Schema;
 using System.Globalization;
 using System.Linq;
 using System.Text;
+using System.Text.Json.Serialization;
 using System.Text.RegularExpressions;
 
 namespace Chemistry
@@ -65,7 +67,7 @@ public ChemicalFormula(IHasChemicalFormula capFormula)
             Elements = new Dictionary<Element, int>(capFormula.ThisChemicalFormula.Elements);
         }
 
-        public ChemicalFormula ThisChemicalFormula => this;
+        [JsonIgnore] public ChemicalFormula ThisChemicalFormula => this;
 
         /// <summary>
         /// Gets the average mass of this chemical formula

mzLib/Readers/ExternalResults/IndividualResultRecords/MsPathFinderTResult.cs

@@ -0,0 +1,101 @@
+using CsvHelper.Configuration.Attributes;
+using CsvHelper.Configuration;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using Chemistry;
+
+namespace Readers
+{
+    public class MsPathFinderTResult
+    {
+        public static CsvConfiguration CsvConfiguration { get; } = new CsvConfiguration(System.Globalization.CultureInfo.InvariantCulture)
+        {
+            Delimiter = "\t",
+            HasHeaderRecord = true,
+            IgnoreBlankLines = true,
+            TrimOptions = CsvHelper.Configuration.TrimOptions.InsideQuotes,
+            BadDataFound = null,
+        };
+
+
+        [Name("Scan")]
+        public int OneBasedScanNumber { get; set; }
+
+        [Name("Pre")]
+        public char PreviousResidue { get; set; }
+
+        [Name("Sequence")]
+        public string BaseSequence { get; set; }
+
+        [Name("Post")]
+        public char NextResidue { get; set; }
+
+        [Name("Modifications")]
+        public string Modifications { get; set; }
+
+        [Name("Composition")]
+        [TypeConverter(typeof(MsPathFinderTCompositionToChemicalFormulaConverter))]
+        public ChemicalFormula ChemicalFormula { get; set; }
+
+        [Name("ProteinName")]
+        public string ProteinName { get; set; }
+
+        [Name("ProteinDesc")]
+        public string ProteinDescription { get; set; }
+
+        [Name("ProteinLength")]
+        public int Length { get; set; }
+
+        [Name("Start")]
+        public int OneBasedStartResidue { get; set; }
+
+        [Name("End")]
+        public int OneBasedEndResidue { get; set; }
+
+        [Name("Charge")]
+        public int Charge { get; set; }
+
+        [Name("MostAbundantIsotopeMz")]
+        public double MostAbundantIsotopeMz { get; set; }
+
+        [Name("Mass")]
+        public double MonoisotopicMass { get; set; }
+
+        [Name("Ms1Features")]
+        public int Ms1Features { get; set; }
+
+        [Name("#MatchedFragments")]
+        public int NumberOfMatchedFragments { get; set; }
+
+        [Name("Probability")]
+        public double Probability { get; set; }
+
+        [Name("SpecEValue")]
+        public double SpecEValue { get; set; }
+
+        [Name("EValue")]
+        public double EValue { get; set; }
+
+        [Name("QValue")]
+        [Optional]
+        public double QValue { get; set; }
+
+        [Name("PepQValue")]
+        [Optional]
+        public double PepQValue { get; set; }
+
+        #region InterpretedFields
+
+        [Ignore] private string _accession = null;
+        [Ignore] public string Accession => _accession ??= ProteinName.Split('|')[1].Trim();
+
+        [Ignore] private bool? _isDecoy = null;
+        [Ignore] public bool IsDecoy => _isDecoy ??= ProteinName.StartsWith("XXX");
+        [Optional] public string FileNameWithoutExtension { get; set; }
+
+        #endregion
+    }
+}

mzLib/Readers/ExternalResults/ResultFiles/MsPathFinderTResultFile.cs

@@ -0,0 +1,50 @@
+using CsvHelper;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using Easy.Common.Extensions;
+
+namespace Readers
+{
+    public class MsPathFinderTResultFile : ResultFile<MsPathFinderTResult>, IResultFile
+    {
+        public override SupportedFileType FileType { get; }
+        public override Software Software { get; set; }
+
+        public MsPathFinderTResultFile(string filePath) : base(filePath, Software.MsPathFinderT)
+        {
+            FileType = filePath.ParseFileType();
+        }
+
+        public MsPathFinderTResultFile() : base()
+        {
+            FileType = FilePath.IsNullOrEmpty() ? SupportedFileType.MsPathFinderTAllResults : FilePath.ParseFileType();
+        }
+
+        public override void LoadResults()
+        {
+            using var csv = new CsvReader(new StreamReader(FilePath), MsPathFinderTResult.CsvConfiguration);
+            Results = csv.GetRecords<MsPathFinderTResult>().ToList();
+            if (Results.Any() && Results.First().FileNameWithoutExtension.IsNullOrEmpty())
+                Results.ForEach(p => p.FileNameWithoutExtension = string.Join("_", Path.GetFileNameWithoutExtension(FilePath).Split('_')[..^1]));
+        }
+
+        public override void WriteResults(string outputPath)
+        {
+            if (!CanRead(outputPath))
+                outputPath += FileType.GetFileExtension();
+
+            using (var csv = new CsvWriter(new StreamWriter(File.Create(outputPath)), MsPathFinderTResult.CsvConfiguration))
+            {
+                csv.WriteHeader<MsPathFinderTResult>();
+                foreach (var result in Results)
+                {
+                    csv.NextRecord();
+                    csv.WriteRecord(result);
+                }
+            }
+        }
+    }
+}

mzLib/Readers/Util/Converters.cs

@@ -2,14 +2,15 @@
 using CsvHelper.Configuration;
 using CsvHelper.TypeConversion;
 using MzLibUtil;
+using System.Text;
 
 namespace Readers
 {
     /// <summary>
     /// Converts a list of doubles delimited by semicolons to a list of doubles
     /// To be used with CsvHelper
     /// </summary>
-    public class SemicolonDelimitedToDoubleListConverter : DefaultTypeConverter
+    internal class SemicolonDelimitedToDoubleListConverter : DefaultTypeConverter
     {
         public override object ConvertFromString(string text, IReaderRow row, MemberMapData memberMapData)
         {
@@ -24,7 +25,7 @@ public override string ConvertToString(object value, IWriterRow row, MemberMapDa
         }
     }
 
-    public class DashToNullOrDoubleConverter : DefaultTypeConverter
+    internal class DashToNullOrDoubleConverter : DefaultTypeConverter
     {
         public override object ConvertFromString(string text, IReaderRow row, MemberMapData memberMapData)
         {
@@ -37,7 +38,7 @@ public override string ConvertToString(object value, IWriterRow row, MemberMapDa
         }
     }
 
-    public class CommaDelimitedToIntegerArrayTypeConverter : DefaultTypeConverter
+    internal class CommaDelimitedToIntegerArrayTypeConverter : DefaultTypeConverter
     {
         public override object ConvertFromString(string text, IReaderRow row, MemberMapData memberMapData)
         {
@@ -53,7 +54,7 @@ public override string ConvertToString(object value, IWriterRow row, MemberMapDa
         }
     }
 
-    public class CommaDelimitedToStringArrayTypeConverter : DefaultTypeConverter
+    internal class CommaDelimitedToStringArrayTypeConverter : DefaultTypeConverter
     {
         public override object ConvertFromString(string text, IReaderRow row, MemberMapData memberMapData)
         {
@@ -69,4 +70,65 @@ public override string ConvertToString(object value, IWriterRow row, MemberMapDa
             return string.Join(',', list);
         }
     }
+
+    /// <summary>
+    /// Converts the chemical formula from MsPathFinderT to MetaMorpheus
+    /// MsPathFinderT: "C(460) H(740) N(136) O(146) S(0)"
+    /// MetaMorpheus: "C460H740N136O146S"
+    /// </summary>
+    internal class MsPathFinderTCompositionToChemicalFormulaConverter : DefaultTypeConverter
+    {
+        public override object ConvertFromString(string text, IReaderRow row, MemberMapData memberMapData)
+        {
+            var composition = text.Split(' ').Where(p => p != "").ToArray();
+            var chemicalFormula = new Chemistry.ChemicalFormula();
+            foreach (var element in composition)
+            {
+                var elementSplit = element.Split('(');
+                var elementName = elementSplit[0];
+                var elementCount = int.Parse(elementSplit[1].Replace(")", ""));
+                chemicalFormula.Add(elementName, elementCount);
+            }
+            return chemicalFormula;
+        }
+
+        public override string ConvertToString(object value, IWriterRow row, MemberMapData memberMapData)
+        {
+            var chemicalFormula = value as Chemistry.ChemicalFormula ?? throw new Exception("Cannot convert input to ChemicalFormula");
+            var sb = new StringBuilder();
+
+            bool onNumber = false;
+            foreach (var character in chemicalFormula.Formula)
+            {
+                if (!char.IsDigit(character)) // if is a letter
+                {
+                    if (onNumber)
+                    {
+                        sb.Append(") " + character);
+                        onNumber = false;
+                    }
+                    else
+                        sb.Append(character);
+                }
+                else
+                {
+                    if (!onNumber)
+                    {
+                        sb.Append("(" + character);
+                        onNumber = true;
+                    }
+                    else
+                        sb.Append(character);
+                }
+            }
+
+            var stringForm = sb.ToString();
+            if (char.IsDigit(stringForm.Last()))
+                stringForm += ")";
+            else
+                stringForm += "(1)";
+
+            return stringForm;
+        }
+    }
 }

mzLib/Readers/Util/Software.cs

@@ -1,5 +1,4 @@
-
-namespace Readers
+namespace Readers
 {
     public enum Software
     {
@@ -11,5 +10,6 @@ public enum Software
         MaxQuant,
         Toppic,
         MsFragger, // files tested were from fragpipe v21.1
+        MsPathFinderT,
     }
 }

mzLib/Readers/Util/SupportedFileTypes.cs

@@ -22,6 +22,9 @@ public enum SupportedFileType
         MsFraggerPsm,
         MsFraggerPeptide,
         MsFraggerProtein,
+        MsPathFinderTTargets,
+        MsPathFinderTDecoys,
+        MsPathFinderTAllResults,
     }
 
     public static class SupportedFileTypeExtensions
@@ -54,10 +57,12 @@ public static string GetFileExtension(this SupportedFileType type)
                 SupportedFileType.MsFraggerPsm => "psm.tsv",
                 SupportedFileType.MsFraggerPeptide => "peptide.tsv",
                 SupportedFileType.MsFraggerProtein => "protein.tsv",
+                SupportedFileType.MsPathFinderTTargets => "_IcTarget.tsv",
+                SupportedFileType.MsPathFinderTDecoys => "_IcDecoy.tsv",
+                SupportedFileType.MsPathFinderTAllResults => "_IcTDA.tsv",
                 _ => throw new MzLibException("File type not supported")
             };
         }
-
         public static SupportedFileType ParseFileType(this string filePath)
         {
             switch (Path.GetExtension(filePath).ToLower())
@@ -99,6 +104,12 @@ public static SupportedFileType ParseFileType(this string filePath)
                         return SupportedFileType.MsFraggerPeptide;
                     if (filePath.EndsWith(SupportedFileType.MsFraggerProtein.GetFileExtension(), StringComparison.InvariantCultureIgnoreCase))
                         return SupportedFileType.MsFraggerProtein;
+                    if (filePath.EndsWith(SupportedFileType.MsPathFinderTTargets.GetFileExtension(), StringComparison.InvariantCultureIgnoreCase))
+                        return SupportedFileType.MsPathFinderTTargets;
+                    if (filePath.EndsWith(SupportedFileType.MsPathFinderTDecoys.GetFileExtension(), StringComparison.InvariantCultureIgnoreCase))
+                        return SupportedFileType.MsPathFinderTDecoys;
+                    if (filePath.EndsWith(SupportedFileType.MsPathFinderTAllResults.GetFileExtension(), StringComparison.InvariantCultureIgnoreCase))
+                        return SupportedFileType.MsPathFinderTAllResults;
 
                     // these tsv cases are just .tsv and need an extra step to determine the type
                     // currently need to distinguish between FlashDeconvTsv and MsFraggerPsm

mzLib/Test/FileReadingTests/ExternalFileTypes/MsPathFinderT_AllResults_IcTda.tsv

@@ -0,0 +1,7 @@
+Scan	Pre	Sequence	Post	Modifications	Composition	ProteinName	ProteinDesc	ProteinLength	Start	End	Charge	MostAbundantIsotopeMz	Mass	Ms1Features	#MatchedFragments	Probability	SpecEValue	EValue	QValue	PepQValue
+1180	M	PKRKVSSAEGAAKEEPKRRSARLSAKPPAKVEAKPKKAAAKDKSSDKKVQTKGKRGAKGKQAEVANQETKEDLPAENGETKTEESPASDEAGEKEAKSD	-		C(442) H(756) N(140) O(156) S(0)	sp|P05114|HMGN1_HUMAN	Non-histone chromosomal protein HMG-14 OS=Homo sapiens OX=9606 GN=HMGN1 PE=1 SV=3	101	2	100	15	702.8454697	10521.55277	0	61	1.0	9.99E-308	9.99E-308	0	0
+1180	-	EKTEDKAQDTVAITQIFINGQYGEDAHKDYERGSDRIKKYKVRSGKKLEGTMDEYNIISAKKNVHKATKNRQKYNKINELIGQSNLYSRGF	T		C(460) H(740) N(136) O(146) S(1)	XXX_sp|Q2G1S6|SSL5_STAA8	"Staphylococcal superantigen-like 5 OS=Staphylococcus aureus (strain NCTC 8325 "	235	1	91	15	703.9044982	10537.4382	670	5	0.0017	2.399925E-07	0.009145	10	10
+1180	T	DKGQATLRLANIALFVKVHFMSPIKWSATFFMALLYGAEGSIHKLLGNLIPKVRAVIIKKDIVGSSVRLN	-		C(358) H(585) N(95) O(89) S(2)	XXX_sp|Q2GGT3|SYR_EHRCR	"Arginine--tRNA ligase OS=Ehrlichia chaffeensis (strain ATCC CRL-10679 "	577	507	576	11	701.6776982	7703.361219	427	12	7.2369E-05	2.143132E-05	0.816662	10	10
+1180	-	MSQDTEVDMKDVELNELEPEKQPMNAADGAAAGEKNGLVKIKVAEDETEAGVKFTGLSKEELLKVAGSPGWVRTRWALLLLFWLGWLGMLAGAVVII	V		C(473) H(758) N(120) O(142) S(4)	sp|P10852|4F2_MOUSE	Amino acid transporter heavy chain SLC3A2 OS=Mus musculus OX=10090 GN=Slc3a2 PE=1 SV=1	527	1	97	15	702.7063795	10519.46642	660	9	3.1386E-04	1.311625E-06	0.049981	10	10
+1180	-	MAPGSVTSDISPSSTSTAGSSRSPESEKPGPSHGGVPPGGPSHSSLPVGRRHPPVLRMVLEALQAGEQRRGTSVAAIKLYILHKYPTVDVLRFKYLLKQA	L		C(463) H(753) N(137) O(139) S(2)	sp|Q8IZA3|H18_HUMAN	Histone H1.8 OS=Homo sapiens OX=9606 GN=H1-8 PE=2 SV=1	347	1	100	15	702.7786627	10520.55066	661	8	8.4705E-05	1.802522E-06	0.068687	10	10
+1181	M	PKRKVSSAEGAAKEEPKRRSARLSAKPPAKVEAKPKKAAAKDKSSDKKVQTKGKRGAKGKQAEVANQETKEDLPAENGETKTEESPASDEAGEKEAKSD	-		C(442) H(756) N(140) O(156) S(0)	sp|P05114|HMGN1_HUMAN	Non-histone chromosomal protein HMG-14 OS=Homo sapiens OX=9606 GN=HMGN1 PE=1 SV=3	101	2	100	14	752.9767692	10521.55277	0	60	1.0	9.99E-308	9.99E-308	0	0

mzLib/Test/FileReadingTests/ExternalFileTypes/MsPathFinderT_DecoyResults_IcDecoy.tsv

@@ -0,0 +1,7 @@
+Scan	Pre	Sequence	Post	Modifications	Composition	ProteinName	ProteinDesc	ProteinLength	Start	End	Charge	MostAbundantIsotopeMz	Mass	Ms1Features	#MatchedFragments	Probability	SpecEValue	EValue
+1180	-	EKTEDKAQDTVAITQIFINGQYGEDAHKDYERGSDRIKKYKVRSGKKLEGTMDEYNIISAKKNVHKATKNRQKYNKINELIGQSNLYSRGF	T		C(460) H(740) N(136) O(146) S(1)	XXX_sp|Q2G1S6|SSL5_STAA8	"Staphylococcal superantigen-like 5 OS=Staphylococcus aureus (strain NCTC 8325 "	235	1	91	15	703.9044982	10537.4382	670	5	0.0017	2.399925E-07	0.009145
+1180	T	DKGQATLRLANIALFVKVHFMSPIKWSATFFMALLYGAEGSIHKLLGNLIPKVRAVIIKKDIVGSSVRLN	-		C(358) H(585) N(95) O(89) S(2)	XXX_sp|Q2GGT3|SYR_EHRCR	"Arginine--tRNA ligase OS=Ehrlichia chaffeensis (strain ATCC CRL-10679 "	577	507	576	11	701.6776982	7703.361219	427	12	7.2369E-05	2.143132E-05	0.816662
+1181	R	RGRLFKAHFTMLLSVLHKAGAALKPRPAGSVQLYCHLLRPPRPATPAAEPFGHPEGADCPFSTFSLETRGIGPYLSLAYIFLNKDGRSRLRTYGCA	P		C(477) H(745) N(137) O(124) S(4)	XXX_sp|Q6UXT8|ALKL1_HUMAN	ALK and LTK ligand 1 OS=Homo sapiens OX=9606 GN=ALKAL1 PE=1 SV=1	130	2	97	14	751.7593204	10504.50849	655	9	0.0152	5.839E-08	0.002225
+1181	-	EKTEDKAQDTVAITQIFINGQYGEDAHKDYERGSDRIKKYKVRSGKKLEGTMDEYNIISAKKNVHKATKNRQKYNKINELIGQSNLYSRGF	T		C(460) H(740) N(136) O(146) S(1)	XXX_sp|Q2G1S6|SSL5_STAA8	"Staphylococcal superantigen-like 5 OS=Staphylococcus aureus (strain NCTC 8325 "	235	1	91	14	754.1114426	10537.4382	670	4	1.6191E-04	9.002121E-07	0.034303
+1181	-	SALTILDEVVDLVAKTIEVIKLTSYDANGKQFNQEEFITNIPSVLSGYVTLADDANAFIDAPSDAKSRFGTGEFKVSKEIGLRVLHNRITNGGIQVQ	K		C(469) H(752) N(124) O(150) S(0)	XXX_sp|P10592|HSP72_YEAST	"Heat shock protein SSA2 OS=Saccharomyces cerevisiae (strain ATCC 204508 "	640	1	97	14	752.9731998	10521.5028	662	8	1.1724E-04	1.072104E-06	0.040854
+1181	N	PAELTKRVQLDMVCRIKEPLRSVKPLPSLAAPSVSSPQLASKSAATKVSMSFSAYMLKMISPVNRAQRCSPQSYRTHVTSPMKRSAVVSEYLSHDP	T		C(459) H(763) N(133) O(136) S(7)	XXX_sp|Q9PTQ7|DMRT1_CHICK	Doublesex- and mab-3-related transcription factor 1 OS=Gallus gallus OX=9031 GN=DMRT1 PE=2 SV=2	366	2	97	14	754.1867306	10538.49223	671	8	1.8379E-04	2.215391E-06	0.08442

mzLib/Test/FileReadingTests/ExternalFileTypes/MsPathFinderT_TargetResults_IcTarget.tsv

@@ -0,0 +1,7 @@
+Scan	Pre	Sequence	Post	Modifications	Composition	ProteinName	ProteinDesc	ProteinLength	Start	End	Charge	MostAbundantIsotopeMz	Mass	Ms1Features	#MatchedFragments	Probability	SpecEValue	EValue
+592	M	PKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGKKGKADAGKEGNNPAENGDAKTDQAQKAEGAGDAK	-		C(395) H(673) N(129) O(127) S(0)	sp|P05204|HMGN2_HUMAN	Non-histone chromosomal protein HMG-17 OS=Homo sapiens OX=9606 GN=HMGN2 PE=1 SV=3	91	2	90	14	662.5096855	9256.016953	531	17	0.9999	1.642469E-36	6.258791E-32
+595	M	PKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGKKGKADAGKEGNNPAENGDAKTDQAQKAEGAGDAK	-		C(395) H(673) N(129) O(127) S(0)	sp|P05204|HMGN2_HUMAN	Non-histone chromosomal protein HMG-17 OS=Homo sapiens OX=9606 GN=HMGN2 PE=1 SV=3	91	2	90	15	618.4095249	9256.016953	531	12	0.2209	2.528896E-17	9.636612E-13
+1089	M	PKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGKKGKADAGKEGNNPAENGDAKTDQAQKAEGAGDAK	-		C(395) H(673) N(129) O(127) S(0)	sp|P05204|HMGN2_HUMAN	Non-histone chromosomal protein HMG-17 OS=Homo sapiens OX=9606 GN=HMGN2 PE=1 SV=3	91	2	90	15	618.4095249	9256.016953	530	6	1.1566E-04	1.241835E-14	4.732136E-10
+1090	M	PKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGKKGKADAGKEGNNPAENGDAKTDQAQKAEGAGDAK	-		C(395) H(673) N(129) O(127) S(0)	sp|P05204|HMGN2_HUMAN	Non-histone chromosomal protein HMG-17 OS=Homo sapiens OX=9606 GN=HMGN2 PE=1 SV=3	91	2	90	14	662.5096855	9256.016953	530	7	0.0039	1.27173E-17	4.846056E-13
+1169	M	PKRKVSSAEGAAKEEPKRRSARLSAKPPAKVEAKPKKAAAKDKSSDKKVQTKGKRGAKGKQAEVANQETKEDLPAENGETKTEESPASDEAGEKEAKSD	-		C(442) H(756) N(140) O(156) S(0)	sp|P05114|HMGN1_HUMAN	Non-histone chromosomal protein HMG-14 OS=Homo sapiens OX=9606 GN=HMGN1 PE=1 SV=3	101	2	100	15	702.8454697	10521.55277	662	13	0.9938	6.040125E-20	2.30165E-15
+1169	M	PKRKSPENTEGKDGSKVTKQEPTRRSARLSAKPAPPKPEPKPRKTSAKKEPGAKISRGAKGKKEEKQEAGKEGTAPSENGETKAEEAQKTESVDNEGE	-		C(442) H(749) N(141) O(156) S(0)	sp|Q15651|HMGN3_HUMAN	High mobility group nucleosome-binding domain-containing protein 3 OS=Homo sapiens OX=9606 GN=HMGN3 PE=1 SV=2	100	2	99	15	703.3086896	10528.50107	666	7	0.161	3.706717E-14	1.412482E-09