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Bugs: - Moved the interactive question of Thermo's license agreement from parallel processes to upstream. Updates: - Provided the C# source codes that wraps Thermo's MSFileReader.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,213 @@ | ||
| using System; | ||
| using System.Collections.Generic; | ||
| using System.IO; | ||
| using System.Linq; | ||
| using ThermoFisher.CommonCore.Data.Business; | ||
| using ThermoFisher.CommonCore.Data.Interfaces; | ||
| using ThermoFisher.CommonCore.RawFileReader; | ||
|
|
||
| namespace MYSPACE | ||
| { | ||
| public static class StringArrayExtensions | ||
| { | ||
| public static int NthIndexOf(this string[] array, string value, int n) | ||
| { | ||
| int count = 0; | ||
| for (int i = 0; i < array.Length; i++) | ||
| { | ||
| if (array[i] == value) | ||
| { | ||
| count++; | ||
| if (count == n) | ||
| { | ||
| return i; | ||
| } | ||
| } | ||
| } | ||
| return -1; | ||
| } | ||
| } | ||
|
|
||
| public static class IRawDataPlusExtension | ||
| { | ||
| public static void WriteSpectrum(this IRawDataPlus rawFile, string filename, List<int> L) | ||
| { | ||
| using (System.IO.StreamWriter file = new System.IO.StreamWriter(filename)) | ||
| { | ||
| int IndexMonoMZ = 8, IndexIsoWidth = 12; | ||
| double isoMass = 0.0, isoWidth = 0.0; | ||
| string msOrder = "0"; | ||
| bool isCentroidMS2 = true; | ||
|
|
||
| file.WriteLine("RAW\n{0}\n", Path.GetFileName(rawFile.FileName)); | ||
|
|
||
| foreach (int scanNumber in L) | ||
| { | ||
| var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber); | ||
| var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber); | ||
|
|
||
| file.WriteLine("SCAN\n{0}", scanNumber); | ||
| file.WriteLine("TIME\n{0}", Math.Round(Convert.ToDouble(scanStatistics.StartTime), 6)); | ||
|
|
||
| // MS order | ||
| msOrder = scanEvent.MSOrder.ToString().ToLower(); | ||
|
|
||
| if (msOrder == "ms2") | ||
| { | ||
| msOrder = "2"; | ||
| } | ||
| else if (msOrder == "ms") | ||
| { | ||
| msOrder = "1"; | ||
| } | ||
| else | ||
| { | ||
| msOrder = "0"; | ||
| } | ||
|
|
||
| file.WriteLine("MSORDER\n{0}", msOrder); | ||
|
|
||
| // Centroid MS2 | ||
| isCentroidMS2 = scanStatistics.IsCentroidScan && msOrder == "2"; | ||
|
|
||
| if (isCentroidMS2) | ||
| { | ||
| var reaction0 = scanEvent.GetReaction(0); // only available with centroid scans | ||
| isoMass = Math.Round(Convert.ToDouble(reaction0.PrecursorMass), 4); | ||
| isoWidth = Math.Round(Convert.ToDouble(reaction0.IsolationWidth), 4); | ||
| } | ||
|
|
||
| var centroidStream = rawFile.GetCentroidStream(scanNumber, false); | ||
| var NcentroidPeaks = centroidStream.Length; | ||
|
|
||
| if (NcentroidPeaks > 0) | ||
| { | ||
| var scanTrailer = rawFile.GetTrailerExtraInformation(scanNumber); | ||
| IndexMonoMZ = scanTrailer.Labels.NthIndexOf("Monoisotopic M/Z:", 1); | ||
| IndexIsoWidth = scanTrailer.Labels.NthIndexOf("MS2 Isolation Width:", 1); | ||
|
|
||
| double[] masses = new double[NcentroidPeaks]; | ||
| double[] intensities = new double[NcentroidPeaks]; | ||
|
|
||
| for (int i = 0; i < NcentroidPeaks; i++) | ||
| { | ||
| masses[i] = Math.Round(Convert.ToDouble(centroidStream.Masses[i]), 4); | ||
| intensities[i] = Math.Round(Convert.ToDouble(centroidStream.Intensities[i]), 1); | ||
| } | ||
|
|
||
| if (isCentroidMS2) | ||
| { | ||
| file.WriteLine("ISOMASS\n{0}", isoMass); | ||
| file.WriteLine("ISOWIDTH\n{0}", isoWidth); | ||
| } | ||
| else | ||
| { | ||
| if (IndexMonoMZ >= 0) | ||
| { | ||
| file.WriteLine("ISOMASS\n{0}", scanTrailer.Values[IndexMonoMZ]); // "-1.00" for DIA | ||
| } | ||
| else | ||
| { | ||
| file.WriteLine("ISOMASS\n0"); | ||
| } | ||
|
|
||
| if (IndexIsoWidth >= 0) | ||
| { | ||
| file.WriteLine("ISOWIDTH\n{0}", scanTrailer.Values[IndexIsoWidth]); // "-1.00" for DIA | ||
| } | ||
| else | ||
| { | ||
| file.WriteLine("ISOWIDTH\n0"); | ||
| } | ||
| } | ||
|
|
||
| file.WriteLine("NPEAKS\n{0}", NcentroidPeaks); | ||
| file.WriteLine("X\n{0}", string.Join(",", masses)); | ||
| file.WriteLine("Y\n{0}", string.Join(",", intensities)); | ||
| // file.WriteLine("LOWMASS\n{0}", masses[0]); | ||
| // file.WriteLine("HIGHMASS\n{0}", masses[masses.Length - 1]); | ||
| file.WriteLine("TITLE\nFile: {0}; scans: {1}\n", rawFile.FileName, scanNumber); | ||
| } | ||
| else | ||
| { | ||
| file.WriteLine("ISOMASS\n0"); | ||
| file.WriteLine("ISOWIDTH\n0"); | ||
| file.WriteLine("NPEAKS\n0"); | ||
| file.WriteLine("X\n0"); | ||
| file.WriteLine("Y\n0"); | ||
| // file.WriteLine("LOWMASS\n0"); | ||
| // file.WriteLine("HIGHMASS\n0"); | ||
| file.WriteLine("TITLE\nFile: {0}; scans: {1}\n", rawFile.FileName, scanNumber); | ||
| } | ||
|
|
||
| } | ||
| } | ||
|
|
||
| return; | ||
| } | ||
|
|
||
| } | ||
| } | ||
|
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||
|
|
||
| namespace MyApp | ||
| { | ||
| using MYSPACE; | ||
|
|
||
| internal static class Program | ||
| { | ||
| private static void Main(string[] args) | ||
| { | ||
|
|
||
| string filename = string.Empty; | ||
|
|
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| filename = args[0]; | ||
|
|
||
| if (string.IsNullOrEmpty(filename)) | ||
| { | ||
| Console.WriteLine("No RAW file specified!"); | ||
| return; | ||
| } | ||
|
|
||
| try | ||
| { | ||
| var rawFile = RawFileReaderAdapter.FileFactory(filename); | ||
|
|
||
| if (!rawFile.IsOpen || rawFile.IsError) | ||
| { | ||
| Console.WriteLine("Unable to access the RAW file using the RawFileReader class!"); | ||
| return; | ||
| } | ||
|
|
||
| if (rawFile.IsError) | ||
| { | ||
| return; | ||
| } | ||
|
|
||
| if (rawFile.InAcquisition) | ||
| { | ||
| return; | ||
| } | ||
|
|
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| rawFile.SelectInstrument(Device.MS, 1); | ||
|
|
||
| int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum; | ||
| int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum; | ||
| List<int> scans = Enumerable.Range(firstScanNumber, lastScanNumber).ToList(); | ||
|
|
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| if (scans.Count > 0) | ||
| { | ||
| rawFile.WriteSpectrum(args[1], scans); | ||
| } | ||
|
|
||
| return; | ||
| } | ||
| catch (Exception ex) | ||
| { | ||
| Console.WriteLine("Error accessing RAWFileReader library! - " + ex.Message); | ||
| } | ||
| } | ||
|
|
||
| } | ||
| } | ||
|
|
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