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added serialized msp to ascii msp #498

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added serialized msp to ascii msp #498

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71 changes: 70 additions & 1 deletion src/Common/CommonStandard/Parser/MspFileParcer.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
using System.Collections.Generic;
using System.IO;
using System.Linq;
using System.Reflection;
using System.Text;

namespace CompMs.Common.Parser
Expand Down Expand Up @@ -183,6 +184,29 @@ public static List<MoleculeMsReference> ReadSerializedLbmLibrary(string file, Li
return usedMspDB;
}

public static void SeializedMspObjToAsciiMsp(string input, string output) {
var mspDB = ReadSerializedMspObject(input);
WriteAsMsp(output, mspDB);
}

public static void SeializedLbmObjToAsciiMspAsPublicUse(string input, string output) {
var mspDB = ReadSerializedMspObject(input);
var queries = LbmQueryParcer.GetLbmQueries(false);
foreach (var query in queries) { query.IsSelected = true; }
var tQueries = getTrueQueryStrings(queries);

var usedMspDB = new List<MoleculeMsReference>();
var counter = 0;
foreach (var mspRecord in mspDB) {
if (tQueries.Contains(mspRecord.CompoundClass + "_" + mspRecord.AdductType.ToString())) {
mspRecord.ScanID = counter;
usedMspDB.Add(mspRecord);
counter++;
}
}
WriteAsLbmMsp(output, usedMspDB);
}

public static void AsciiMspToSerializedMspObj(string input, string output) {
var queries = MspFileReader(input);
MoleculeMsRefMethods.SaveMspToFile(queries, output);
Expand Down Expand Up @@ -505,14 +529,28 @@ public static void WriteAsMsp(string filePath, IEnumerable<MoleculeMsReference>
}
}

public static void WriteAsLbmMsp(string filePath, IEnumerable<MoleculeMsReference> mspRecords) {
using (var stream = File.Open(filePath, FileMode.Create, FileAccess.Write)) {
WriteAsLbmMsp(stream, mspRecords);
}
}

public static void WriteAsMsp(Stream stream, IEnumerable<MoleculeMsReference> mspRecords) {
using (var sw = new StreamWriter(stream, Encoding.ASCII, 512, leaveOpen: true)) {
foreach (var record in mspRecords) {
WriteMspFields(record, sw);
}
}
}


public static void WriteAsLbmMsp(Stream stream, IEnumerable<MoleculeMsReference> mspRecords) {
using (var sw = new StreamWriter(stream, Encoding.ASCII, 512, leaveOpen: true)) {
foreach (var record in mspRecords) {
WriteLbmMspFields(record, sw);
}
}
}

public static void ConvertMspToSeparatedMSPs(string filepath, string folderpath) {
var mspRecords = MspFileReader(filepath);
WriteAsSeparatedMSPs(folderpath, mspRecords);
Expand Down Expand Up @@ -562,6 +600,37 @@ public static void WriteSpectrumAsMsp(MoleculeMsReference record, StreamWriter s
sw.WriteLine();
}

public static void WriteLbmMspFields(MoleculeMsReference record, StreamWriter sw) {
sw.WriteLine("NAME: " + record.Name);
sw.WriteLine("PRECURSORMZ: " + record.PrecursorMz);
sw.WriteLine("PRECURSORTYPE: " + record.AdductType.AdductIonName);
sw.WriteLine("RETENTIONTIME: " + record.ChromXs.RT.Value);
sw.WriteLine("CCS: " + record.CollisionCrossSection);
sw.WriteLine("FORMULA: " + record.Formula);
sw.WriteLine("ONTOLOGY: " + record.CompoundClass);
sw.WriteLine("SMILES: " + record.SMILES);
sw.WriteLine("INCHIKEY: " + record.InChIKey);
sw.WriteLine("IONMODE: " + record.IonMode);
sw.WriteLine("Comment: Computationally generated spectral record in MS-DIAL project");
sw.WriteLine("Num Peaks: " + record.Spectrum.Count);

foreach (var peak in record.Spectrum) {
if (string.IsNullOrEmpty(peak.Comment)) {
sw.WriteLine(peak.Mass + "\t" + peak.Intensity);
}
else {
// tantative version; if user want to split exported msp file by MS-FINDER
if (peak.Comment.Contains(";")) {
sw.WriteLine(peak.Mass + "\t" + peak.Intensity + "\t" + "\"" + peak.Comment.Split(';')[0] + "\"");
}
else {
sw.WriteLine(peak.Mass + "\t" + peak.Intensity);
}
}
}
sw.WriteLine();
}

public static void WriteMspFields(MoleculeMsReference record, StreamWriter sw) {

var adducttype = string.Empty;
Expand Down
13 changes: 10 additions & 3 deletions src/MSDIAL4/MsdialPrivateConsoleApp/Program.cs
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
using Msdial.Lcms.Dataprocess.Algorithm.Clustering;
using CompMs.Common.Parser;
using Msdial.Lcms.Dataprocess.Algorithm.Clustering;
using Rfx.Riken.OsakaUniv;
using System;
using System.Collections.Generic;
using System.Linq;
Expand Down Expand Up @@ -50,13 +52,18 @@ static void Main(string[] args) {
// @"E:\6_Projects\PROJECT_MsMachineLearning\msn\mtbks\neg\mtbks_neg.edge");
//MspManager.MergeMspFiles(@"\\165.93.102.222\Public\MetaboBankPeakPick\ogawa_20240123\input_msn_neg",
// @"E:\6_Projects\PROJECT_MsMachineLearning\msn\mtbks\neg\mtbks_neg.msp");
MspManager.Msp2TextAsMsdialAlignmentResultFormat(@"E:\6_Projects\PROJECT_MsMachineLearning\msn\mtbks\neg\mtbks_neg.msp",
@"E:\6_Projects\PROJECT_MsMachineLearning\msn\mtbks\neg\mtbks_neg.txt");
//MspManager.Msp2TextAsMsdialAlignmentResultFormat(@"E:\6_Projects\PROJECT_MsMachineLearning\msn\mtbks\neg\mtbks_neg.msp",
// @"E:\6_Projects\PROJECT_MsMachineLearning\msn\mtbks\neg\mtbks_neg.txt");

//MspManager.Msp2TextAsMsdialAlignmentResultFormat(
// @"E:\6_Projects\PROJECT_MsMachineLearning\msn\msp\neg\casmi2022_neg.msp",
// @"E:\6_Projects\PROJECT_MsMachineLearning\msn\msp\neg\casmi2022_neg.txt",
// "casmi_neg");

MspFileParser.SeializedLbmObjToAsciiMspAsPublicUse(
@"E:\0_SourceCode\lbm_versions\Msp20250124141632_NCDK_converted_dev\Msp20250124141632_NCDK-TUAT-LC25_converted_dev.lbm2",
@"E:\0_SourceCode\lbm_versions\Msp20250124141632_NCDK_converted_dev\Msp20250124141632_NCDK-TUAT-LC25_converted_dev.msp");

//mspfile = @"D:\9_Spectral library curations\Distributed MSPs\MSMS-RIKEN-Neg-VS15.msp";
//new_mspfile = @"D:\9_Spectral library curations\Distributed MSPs\MSMS-RIKEN-Neg-VS15-For-Statistics.msp";

Expand Down
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