Merge pull request #181 from compomics/1.4.4

Release of 1.4.4
compomics · May 9, 2024 · 29d4e59 · 29d4e59
2 parents 42131e5 + fb5d7bb
commit 29d4e59
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Showing 9 changed files with 207 additions and 179 deletions.
diff --git a/MainClass.cs b/MainClass.cs
@@ -20,7 +20,7 @@ public static class MainClass
         private static readonly ILog Log =
             LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
 
-        public const string Version = "1.4.3";
+        public const string Version = "1.4.4";
         public static void Main(string[] args)
         {
             // Set Invariant culture as default for all further processing
@@ -83,15 +83,15 @@ private static void XicParametersParsing(string[] args)
                     v => parameters.printJsonExample = v != null
                 },
                 {
-                    "o=|output=",
-                    "The output directory. Specify this or an output file. Specifying neither writes to the input directory.",
-                    v => outputDirectory = v
-                },
-                {
-                    "b=|output_file",
+                    "b=|output=",
                     "The output file. Specify this or an output directory. Specifying neither writes to the input directory.",
                     v => outputFile = v
                 },
+                {
+                    "o=|output_directory=",
+                    "The output directory. Specify this or an output file. Specifying neither writes to the input directory.",
+                    v => outputDirectory = v
+                },
                 {
                     "6|base64",
                     "Encodes the content of the xic vectors as base 64 encoded string.",
@@ -103,7 +103,7 @@ private static void XicParametersParsing(string[] args)
                     v => parameters.stdout = v != null
                 },
                 {
-                  "w|warningsAreErrors", "Return non-zero exit code for warnings; default only for errors",
+                    "w|warningsAreErrors", "Return non-zero exit code for warnings; default only for errors",
                     v => parameters.Vigilant = v != null
                 },
                 {
@@ -338,7 +338,7 @@ private static void SpectrumQueryParametersParsing(string[] args)
                     v => parameters.scans = v
                 },
                 {
-                    "b=|output_file",
+                    "b=|output=",
                     "The output file. Specifying none writes the output file to the input file parent directory.",
                     v => parameters.outputFile = v
                 },
@@ -510,15 +510,15 @@ private static void RegularParametersParsing(string[] args)
                     v => parseInput.RawDirectoryPath = v
                 },
                 {
-                    "o=|output=",
-                    "The output directory. Specify this or an output file -b. Specifying neither writes to the input directory.",
-                    v => parseInput.OutputDirectory = v
-                },
-                {
-                    "b=|output_file",
+                    "b=|output=",
                     "The output file. Specify this or an output directory -o. Specifying neither writes to the input directory.",
                     v => parseInput.OutputFile = v
                 },
+                {
+                    "o=|output_directory=",
+                    "The output directory. Specify this or an output file -b. Specifying neither writes to the input directory.",
+                    v => parseInput.OutputDirectory = v
+                },
                 {
                     "s|stdout",
                     "Write to standard output. Cannot be combined with file or directory output. Implies silent logging, i.e. logging level 0",
@@ -766,6 +766,8 @@ private static void RegularParametersParsing(string[] args)
                     if (parseInput.OutputFormat == OutputFormat.IndexMzML) parseInput.OutputFormat = OutputFormat.MzML;
                 }
 
+                parseInput.MaxLevel = parseInput.MsLevel.Max();
+
                 if (parseInput.S3Url != null && parseInput.S3AccessKeyId != null &&
                     parseInput.S3SecretAccessKey != null && parseInput.BucketName != null)
                     if (Uri.IsWellFormedUriString(parseInput.S3Url, UriKind.Absolute))

diff --git a/ParseInput.cs b/ParseInput.cs
@@ -96,6 +96,8 @@ public int Warnings
 
         public HashSet<int> MsLevel { get; set; }
 
+        public int MaxLevel { get; set; }
+
         public bool MgfPrecursor { get; set; }
 
         public bool NoiseData { get; set; }
@@ -136,6 +138,7 @@ public ParseInput()
             Vigilant = false;
             _errors = 0;
             _warnings = 0;
+            MaxLevel = 10;
         }
 
         public ParseInput(string rawFilePath, string rawDirectoryPath, string outputDirectory, OutputFormat outputFormat

diff --git a/README.md b/README.md
@@ -59,12 +59,13 @@ optional subcommands are xic|query (use [subcommand] -h for more info]):
   -d, --input_directory=VALUE
                              The directory containing the raw files (Required).
                                Specify this or an input raw file -i.
-  -o, --output=VALUE         The output directory. Specify this or an output
-                               file -b. Specifying neither writes to the input
-                               directory.
-  -b, --output_file=VALUE    The output file. Specify this or an output
+  -b, --output=VALUE    	 The output file. Specify this or an output
                                directory -o. Specifying neither writes to the
                                input directory.
+  -o, --output_directory=VALUE
+							 The output directory. Specify this or an output
+                               file -b. Specifying neither writes to the input
+                               directory.
   -s, --stdout               Write to standard output. Cannot be combined with
                                file or directory output. Implies silent logging,
                                 i.e. logging level 0
@@ -137,7 +138,7 @@ usage is:
   -h, --help                 Prints out the options.
   -i, --input=VALUE          The raw file input (Required).
   -n, --scans=VALUE          The scan numbers. e.g. "1-5, 20, 25-30"
-  -b, --output_file=VALUE    The output file. Specifying none writes the output
+  -b, --output=VALUE    	 The output file. Specifying none writes the output
                                file to the input file parent directory.
   -p, --noPeakPicking        Don't use the peak picking provided by the native
                                Thermo library. By default peak picking is
@@ -169,12 +170,13 @@ ThermoRawFileParser.exe xic --help
                                Specify this or an input file -i.
   -j, --json=VALUE           The json input file (Required).
   -p, --print_example        Show a json input file example.
-  -o, --output=VALUE         The output directory. Specify this or an output
-                               file. Specifying neither writes to the input
-                               directory.
-  -b, --output_file=VALUE    The output file. Specify this or an output
+  -b, --output=VALUE    	 The output file. Specify this or an output
                                directory. Specifying neither writes to the
                                input directory.
+  -o, --output_directory=VALUE         
+							 The output directory. Specify this or an output
+                               file. Specifying neither writes to the input
+                               directory.
   -6, --base64               Encodes the content of the xic vectors as base 64
                                encoded string.
   -s, --stdout               Pipes the output into standard output. Logging is

diff --git a/Util/CVHelpers.cs b/Util/CVHelpers.cs
@@ -1,4 +1,5 @@
-using ThermoRawFileParser.Writer.MzML;
+using System.Collections.Generic;
+using ThermoRawFileParser.Writer.MzML;
 
 namespace ThermoRawFileParser.Util
 {
@@ -18,4 +19,17 @@ public static CVParamType Copy (this CVParamType old)
             };
         }
     }
+
+    public class CVComparer : IEqualityComparer<CVParamType>
+    {
+        public bool Equals(CVParamType cv1, CVParamType cv2)
+        {
+            return cv1.accession == cv2.accession;
+        }
+
+        public int GetHashCode(CVParamType cv)
+        {
+            return cv.accession.GetHashCode();
+        }
+    }
 }
diff --git a/Writer/MetadataWriter.cs b/Writer/MetadataWriter.cs
@@ -4,7 +4,6 @@
 using System.IO;
 using System.Linq;
 using System.Reflection;
-using System.Web.WebSockets;
 using log4net;
 using Newtonsoft.Json;
 using ThermoFisher.CommonCore.Data;
@@ -122,16 +121,14 @@ public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastSca
             switch (_parseInput.MetadataFormat)
             {
                 case MetadataFormat.JSON:
-                    _metadataFileName = _parseInput.MetadataOutputFile != null
-                        ? _parseInput.MetadataOutputFile
-                        : Path.Combine(_parseInput.OutputDirectory, _parseInput.RawFileNameWithoutExtension) +
+                    _metadataFileName = _parseInput.MetadataOutputFile ?? 
+                        Path.Combine(_parseInput.OutputDirectory, _parseInput.RawFileNameWithoutExtension) +
                           "-metadata.json";
                     WriteJsonMetada(rawFile, firstScanNumber, lastScanNumber);
                     break;
                 case MetadataFormat.TXT:
-                    _metadataFileName = _parseInput.MetadataOutputFile != null
-                        ? _parseInput.MetadataOutputFile
-                        : Path.Combine(_parseInput.OutputDirectory, _parseInput.RawFileNameWithoutExtension) +
+                    _metadataFileName = _parseInput.MetadataOutputFile ??
+                        Path.Combine(_parseInput.OutputDirectory, _parseInput.RawFileNameWithoutExtension) +
                           "-metadata.txt";
                     WriteTextMetadata(rawFile, firstScanNumber, lastScanNumber);
                     break;
@@ -176,43 +173,40 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
                     metadata.addInstrumentProperty(new CVTerm("AFR:0001259", "AFO", "firmware version",
                         rawFile.GetInstrumentData().HardwareVersion));
                 }
-            }
-
 
-            // MS Data
-            foreach (KeyValuePair<string, int> entry in msTypes)
-            {
-                if (entry.Key.Equals(MSOrderType.Ms.ToString()))
-                    metadata.addMSData(new CVTerm("PRIDE:0000481", "PRIDE", "Number of MS1 spectra",
-                        entry.Value.ToString()));
-                if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
-                    metadata.addMSData(new CVTerm("PRIDE:0000482", "PRIDE", "Number of MS2 spectra",
-                        entry.Value.ToString()));
-                if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
-                    metadata.addMSData(new CVTerm("PRIDE:0000483", "PRIDE", "Number of MS3 spectra",
-                        entry.Value.ToString()));
-            }
-
-            metadata.addMSData(new CVTerm("PRIDE:0000472", "PRIDE", "MS min charge",
-                minCharge.ToString(CultureInfo.InvariantCulture)));
-            metadata.addMSData(new CVTerm("PRIDE:0000473", "PRIDE", "MS max charge",
-                maxCharge.ToString(CultureInfo.InvariantCulture)));
-
-            metadata.addMSData(new CVTerm("PRIDE:0000474", "PRIDE", "MS min RT",
-                minTime.ToString(CultureInfo.InvariantCulture)));
-            metadata.addMSData(new CVTerm("PRIDE:0000475", "PRIDE", "MS max RT",
-                maxTime.ToString(CultureInfo.InvariantCulture)));
-
-            metadata.addMSData(new CVTerm("PRIDE:0000476", "PRIDE", "MS min MZ",
-                minMz.ToString(CultureInfo.InvariantCulture)));
-            metadata.addMSData(new CVTerm("PRIDE:0000477", "PRIDE", "MS max MZ",
-                maxMz.ToString(CultureInfo.InvariantCulture)));
-
-            // Scan Settings
-            // Get the start and end time from the RAW file
-
-            if (rawFile.SelectMsData())
-            {
+
+
+                // MS Data
+                foreach (KeyValuePair<string, int> entry in msTypes)
+                {
+                    if (entry.Key.Equals(MSOrderType.Ms.ToString()))
+                        metadata.addMSData(new CVTerm("PRIDE:0000481", "PRIDE", "Number of MS1 spectra",
+                            entry.Value.ToString()));
+                    if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
+                        metadata.addMSData(new CVTerm("PRIDE:0000482", "PRIDE", "Number of MS2 spectra",
+                            entry.Value.ToString()));
+                    if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
+                        metadata.addMSData(new CVTerm("PRIDE:0000483", "PRIDE", "Number of MS3 spectra",
+                            entry.Value.ToString()));
+                }
+
+                metadata.addMSData(new CVTerm("PRIDE:0000472", "PRIDE", "MS min charge",
+                    minCharge.ToString(CultureInfo.InvariantCulture)));
+                metadata.addMSData(new CVTerm("PRIDE:0000473", "PRIDE", "MS max charge",
+                    maxCharge.ToString(CultureInfo.InvariantCulture)));
+
+                metadata.addMSData(new CVTerm("PRIDE:0000474", "PRIDE", "MS min RT",
+                    minTime.ToString(CultureInfo.InvariantCulture)));
+                metadata.addMSData(new CVTerm("PRIDE:0000475", "PRIDE", "MS max RT",
+                    maxTime.ToString(CultureInfo.InvariantCulture)));
+
+                metadata.addMSData(new CVTerm("PRIDE:0000476", "PRIDE", "MS min MZ",
+                    minMz.ToString(CultureInfo.InvariantCulture)));
+                metadata.addMSData(new CVTerm("PRIDE:0000477", "PRIDE", "MS max MZ",
+                    maxMz.ToString(CultureInfo.InvariantCulture)));
+
+                // Scan Settings
+                // Get the start and end time from the RAW file
                 var runHeaderEx = rawFile.RunHeaderEx;
                 var startTime = runHeaderEx.StartTime;
                 var endTime = runHeaderEx.EndTime;
@@ -373,21 +367,20 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
                 {
                     output.Add("Firmware version=" + rawFile.GetInstrumentData().HardwareVersion);
                 }
-            }
-
-            // MS Data
-            output.Add("#MsData");
-            foreach (KeyValuePair<string, int> entry in msTypes)
-            {
-                if (entry.Key.Equals(MSOrderType.Ms.ToString()))
-                    output.Add("Number of MS1 spectra=" + entry.Value);
-                if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
-                    output.Add("Number of MS2 spectra=" + entry.Value);
-                if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
-                    output.Add("Number of MS3 spectra=" + entry.Value);
-            }
 
-            output.AddRange(new List<string>
+                // MS Data
+                output.Add("#MsData");
+                foreach (KeyValuePair<string, int> entry in msTypes)
+                {
+                    if (entry.Key.Equals(MSOrderType.Ms.ToString()))
+                        output.Add("Number of MS1 spectra=" + entry.Value);
+                    if (entry.Key.Equals(MSOrderType.Ms2.ToString()))
+                        output.Add("Number of MS2 spectra=" + entry.Value);
+                    if (entry.Key.Equals(MSOrderType.Ms3.ToString()))
+                        output.Add("Number of MS3 spectra=" + entry.Value);
+                }
+
+                output.AddRange(new List<string>
                 {
                     $"MS min charge={minCharge.ToString(CultureInfo.InvariantCulture)}",
                     $"MS max charge={maxCharge.ToString(CultureInfo.InvariantCulture)}",
@@ -396,11 +389,9 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
                     $"MS min MZ={minMz.ToString(CultureInfo.InvariantCulture)}",
                     $"MS max MZ={maxMz.ToString(CultureInfo.InvariantCulture)}"
                 }
-            );
+                );
 
-            // Scan Settings
-            if (rawFile.SelectMsData())
-            {
+                // Scan Settings
                 // Get the start and end time from the RAW file
                 var startTime = rawFile.RunHeaderEx.StartTime;
                 var endTime = rawFile.RunHeaderEx.EndTime;
@@ -410,7 +401,7 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
                         $"Scan start time={startTime.ToString(CultureInfo.InvariantCulture)}",
                         $"Expected runtime={rawFile.RunHeaderEx.ExpectedRunTime.ToString(CultureInfo.InvariantCulture)}",
                         $"Mass resolution=[MS, MS:1000011, mass resolution, {rawFile.RunHeaderEx.MassResolution.ToString(CultureInfo.InvariantCulture)}]",
-                        "Units=" + rawFile.GetInstrumentData().Units,
+                        $"Units={rawFile.GetInstrumentData().Units}",
                         $"Number of scans={rawFile.RunHeaderEx.SpectraCount}",
                         $"Scan range={firstScanNumber};{lastScanNumber}",
                         $"Time range={startTime.ToString(CultureInfo.InvariantCulture)};{endTime.ToString(CultureInfo.InvariantCulture)}",
@@ -419,6 +410,7 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
                     }
                 );
             }
+
             // Sample Data
             output.Add("#SampleData");
 

diff --git a/Writer/MgfSpectrumWriter.cs b/Writer/MgfSpectrumWriter.cs
@@ -5,11 +5,9 @@
 using System.Reflection;
 using System.Text.RegularExpressions;
 using log4net;
-using ThermoFisher.CommonCore.Data;
 using ThermoFisher.CommonCore.Data.Business;
 using ThermoFisher.CommonCore.Data.FilterEnums;
 using ThermoFisher.CommonCore.Data.Interfaces;
-using ThermoRawFileParser.Util;
 
 namespace ThermoRawFileParser.Writer
 {