Merge pull request #87 from compomics/uvdata

Version 1.3.0

Author: caetera

.gitignore

@@ -2,6 +2,6 @@
 bin/
 obj/
 *.log
-ThermoRawFileParser.sln.DotSettings.user
+*.sln.DotSettings.user
 .vs/
-
+*.csproj.user

MainClass.cs

@@ -17,7 +17,7 @@ public static class MainClass
         private static readonly ILog Log =
             LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
 
-        public const string Version = "1.2.3";
+        public const string Version = "1.3.0";
 
         public static void Main(string[] args)
         {
@@ -409,6 +409,11 @@ private static void RegularParametersParsing(string[] args)
                     "Don't use zlib compression for the m/z ratios and intensities. By default zlib compression is enabled.",
                     v => parseInput.NoZlibCompression = v != null
                 },
+                {
+                    "a|allDetectors",
+                    "Extract additonal detector data: UV/PDA etc",
+                    v => parseInput.AllDetectors = v != null
+                },
                 {
                     "l=|logging=", "Optional logging level: 0 for silent, 1 for verbose.",
                     v => logFormatString = v
@@ -499,7 +504,7 @@ private static void RegularParametersParsing(string[] args)
                 {
                     if (parseInput.RawFilePath != null)
                     {
-                        parseInput.OutputDirectory = Path.GetDirectoryName(parseInput.RawFilePath);
+                        parseInput.OutputDirectory = Path.GetDirectoryName(Path.GetFullPath(parseInput.RawFilePath));
                     }
                     else if (parseInput.RawDirectoryPath != null)
                     {

ParseInput.cs

@@ -65,6 +65,8 @@ public string RawFilePath
 
         public bool NoZlibCompression { get; set; }
 
+        public bool AllDetectors { get; set; }
+
         public LogFormat LogFormat { get; set; }
 
         public bool IgnoreInstrumentErrors { get; set; }
@@ -98,6 +100,7 @@ public ParseInput()
             NoZlibCompression = false;
             LogFormat = LogFormat.DEFAULT;
             IgnoreInstrumentErrors = false;
+            AllDetectors = false;
         }
 
         public ParseInput(string rawFilePath, string rawDirectoryPath, string outputDirectory, OutputFormat outputFormat

README.md

@@ -71,6 +71,7 @@ optional subcommands are xic|query (use [subcommand] -h for more info]):
   -z, --noZlibCompression    Don't use zlib compression for the m/z ratios and
                                intensities. By default zlib compression is
                                enabled.
+  -a, --allDetectors         Extract additonal detector data: UV/PDA etc
   -l, --logging=VALUE        Optional logging level: 0 for silent, 1 for
                                verbose.
   -e, --ignoreInstrumentErrors

ThermoRawFileParser.csproj.user

@@ -1,7 +1,10 @@
 using System;
 using System.IO;
+using System.Linq;
+using System.Net.PeerToPeer.Collaboration;
 using System.Xml.Serialization;
 using IO.Mgf;
+using MzLibUtil;
 using NUnit.Framework;
 using ThermoRawFileParser;
 using ThermoRawFileParser.Writer.MzML;
@@ -66,6 +69,8 @@ public void TestMzml()
 
             Assert.AreEqual("1", testMzMl.run.chromatogramList.count);
             Assert.AreEqual(1, testMzMl.run.chromatogramList.chromatogram.Length);
+
+            Assert.AreEqual(48, testMzMl.run.chromatogramList.chromatogram[0].defaultArrayLength);
         }
 
         [Test]
@@ -98,5 +103,36 @@ public void TestIndexedMzML()
             Assert.AreEqual("chromatogram", testMzMl.indexList.index[1].name.ToString());
             Assert.AreEqual(1, testMzMl.indexList.index[1].offset.Length);
         }
+
+        [Test]
+        public void TestMzML_MS2()
+        {
+            // Get temp path for writing the test mzML
+            var tempFilePath = Path.GetTempPath();
+
+            var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/small2.RAW");
+            var parseInput = new ParseInput(testRawFile, null, tempFilePath, OutputFormat.MzML);
+
+            RawFileParser.Parse(parseInput);
+
+            // Deserialize the mzML file
+            var xmlSerializer = new XmlSerializer(typeof(mzMLType));
+            var testMzMl = (mzMLType)xmlSerializer.Deserialize(new FileStream(
+                Path.Combine(tempFilePath, "small2.mzML"), FileMode.Open, FileAccess.Read, FileShare.ReadWrite));
+
+            Assert.AreEqual(95, testMzMl.run.spectrumList.spectrum.Length);
+
+            var precursor = testMzMl.run.spectrumList.spectrum[16].precursorList.precursor[0].selectedIonList.selectedIon[0];
+            var selectedMz = Double.Parse(precursor.cvParam.Where(cv => cv.accession == "MS:1000744").First().value);
+            Assert.IsTrue(selectedMz - 604.7592 < 0.001);
+
+            var selectedZ = int.Parse(precursor.cvParam.Where(cv => cv.accession == "MS:1000041").First().value);
+            Assert.AreEqual(selectedZ , 2);
+
+            //var selectedI = Double.Parse(precursor.cvParam.Where(cv => cv.accession == "MS:1000042").First().value);
+            //Assert.IsTrue(selectedI - 10073 < 1);
+
+            Assert.AreEqual(95, testMzMl.run.chromatogramList.chromatogram[0].defaultArrayLength);
+        }
     }
 }

ThermoRawFileParserTest/WriterTests.cs

@@ -65,7 +65,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                         IReaction reaction = GetReaction(scanEvent, scanNumber);
 
                         Writer.WriteLine("BEGIN IONS");
-                        Writer.WriteLine($"TITLE={ConstructSpectrumTitle(scanNumber)}");
+                        Writer.WriteLine($"TITLE={ConstructSpectrumTitle((int)Device.MS, 1, scanNumber)}");
                         Writer.WriteLine($"SCANS={scanNumber}");
                         Writer.WriteLine(
                             $"RTINSECONDS={(time * 60).ToString(CultureInfo.InvariantCulture)}");