Skip to content

Commit

Permalink
Export and import massbank record format for MSFINDER. (#236)
Browse files Browse the repository at this point in the history 
* Add exporting massbank record method for msfinder.

Fix MassBank record expoter.

* Add export button for MassBank record.

* Add MassBank record reader.

* Change MSFINDER to read MassBank records.
  • Loading branch information
@YukiMatsuzawa
YukiMatsuzawa authored Oct 13, 2023
1 parent 6e5e80c commit 8d09509
Show file tree
Hide file tree
Showing 6 changed files with 409 additions and 7 deletions.
176 changes: 173 additions & 3 deletions src/MSDIAL4/MolecularFormulaFinderStandard/File manage/RawDataParcer.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,8 @@

namespace Rfx.Riken.OsakaUniv
{
public sealed class RawDataParcer
public static class RawDataParcer
{
private RawDataParcer() { }

/// <summary>
/// This parcer is used to get the storage of RawData.cs.
/// The result, i.e. RawData bean, will be used to calculate molecular formula and compound structures in MS-FINDER program.
Expand Down Expand Up @@ -240,6 +238,178 @@ public static RawData RawDataFileReader(string filePath, AnalysisParamOfMsfinder
return rawData;
}

public static RawData ReadMassBankRecord(string filePath, AnalysisParamOfMsfinder param)
{
RawData rawData = new RawData() {
RawdataFilePath = filePath,
ScanNumber = -1,
};

string wkstr;
var pattern = new Regex(@"^(?<field>.+):\s*(?<content>((?<subtag>.+?)\s+)?(?<subcontent>.+))$");
using (StreamReader sr = new StreamReader(filePath))
{
var peaks = new Dictionary<double, Peak>();
while (!sr.EndOfStream) {
wkstr = sr.ReadLine();
var match = pattern.Match(wkstr);
if (!match.Success) {
continue;
}
var field = match.Groups["field"].Value;
var content = match.Groups["content"].Value;
var subtag = match.Groups["subtag"].Success ? match.Groups["subtag"].Value : null;
var subcontent = match.Groups["subcontent"].Success ? match.Groups["subcontent"].Value : null;
switch (field) {
case "ACCESSION":
break;
case "RECORD_TITLE":
break;
case "DATE":
break;
case "AUTHORS":
rawData.Authors = content;
break;
case "LICENSE":
rawData.License = content;
break;
case "COPYRIGHT":
break;
case "PUBLICATION":
break;
case "PROJECT":
break;
case "COMMENT":
if (string.IsNullOrEmpty(rawData.Comment)) {
rawData.Comment = string.Empty;
}
rawData.Comment += content;
break;
case "CH$NAME":
rawData.MetaboliteName = rawData.Name = content;
break;
case "CH$COMPOUND_CLASS":
rawData.Ontology = content;
break;
case "CH$FORMULA":
rawData.Formula = content;
break;
case "CH$EXACT_MASS":
break;
case "CH$SMILES":
rawData.Smiles = content;
break;
case "CH$IUPAC":
rawData.Inchi = content;
break;
case "CH$CDK_DEPICT":
break;
case "CH$LINK":
switch (subtag) {
case "INCHIKEY":
rawData.InchiKey = subcontent;
break;
}
break;
case "SP$SCIENTIFIC_NAME":
break;
case "SP$LINEAGE":
break;
case "SP$LINK":
break;
case "SP$SAMPLE":
break;
case "AC$INSTRUMENT":
rawData.Instrument = content;
break;
case "AC$INSTRUMENT_TYPE":
rawData.InstrumentType = content;
break;
case "AC$MASS_SPECTROMETRY":
switch (subtag) {
case "COLLISION_ENERGY":
rawData.Assign(d => d.CollisionEnergy, subcontent.Split()[0]);
break;
}
break;
case "AC$CHROMATOGRAPHY":
switch (subtag) {
case "RETENTION_TIME":
rawData.Assign(d => d.RetentionTime, subcontent.Split()[0]);
break;
case "KOVATS_RTI":
rawData.Assign(d => d.RetentionIndex, subcontent.Split()[0]);
break;
case "CCS":
rawData.Assign(d => d.Ccs, subcontent.Split()[0]);
break;
}
break;
case "AC$GENERAL":
break;
case "MS$FOCUSED_ION":
switch (subtag) {
case "PRECURSOR_M/Z":
rawData.Assign(d => d.PrecursorMz, subcontent);
break;
case "PRECURSOR_TYPE":
rawData.PrecursorType = subcontent;
break;
}
break;
case "MS$DATA_PROCESSING":
break;
case "PK$SPLASH":
break;
case "PK$ANNOTATION":
while (sr.Peek() == ' ') {
var row = sr.ReadLine().Trim().Split(new[] { ' ' }, 2);
var mz = double.Parse(row[0]);
var comments = row[1];
if (!peaks.TryGetValue(mz, out var peak)) {
peak = new Peak { Mz = mz, };
peaks.Add(mz, peak);
}
peak.Comment = comments;
}
break;
case "PK$NUM_PEAK":
rawData.Ms2PeakNumber = int.Parse(content);
break;
case "PK$PEAK":
while (sr.Peek() == ' ') {
var row = sr.ReadLine().Trim().Split();
var mz = double.Parse(row[0]);
var intensity = double.Parse(row[1]);
if (!peaks.TryGetValue(mz, out var peak)) {
peak = new Peak { Mz = mz, };
peaks.Add(mz, peak);
}
peak.Intensity = intensity;
}
break;
}
}

rawData.Ms2Spectrum = new Spectrum();
rawData.Ms2Spectrum.PeakList.AddRange(peaks.OrderBy(kvp => kvp.Key).Select(kvp => kvp.Value));
}

setIsotopicIons(rawData, param.Mass1Tolerance, param.MassTolType);

return rawData;
}

private static void Assign(this RawData rawData, System.Linq.Expressions.Expression<Func<RawData, double>> propertySelector, string content) {
if (double.TryParse(content, out var val)) {
if (propertySelector.Body is System.Linq.Expressions.MemberExpression member) {
if (member.Member is System.Reflection.PropertyInfo info) {
info.SetValue(rawData, val);
}
}
}
}

public static RawData RawDataFileRapidReader(string filePath) {
RawData rawData = new RawData() { RawdataFilePath = filePath };

Expand Down
3 changes: 2 additions & 1 deletion src/MSFINDER/MSFINDER/MainWindow.xaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@
<MenuItem Header="_File">
<MenuItem Name="MenuItem_Import" Header="_Import..." Click="menuItem_Import_Click">
<ToolTipService.ToolTip>
<ToolTip Content="Select a folder including MAT or MSP files." />
<ToolTip Content="Select a folder including MAT, MSP or MassBank record files." />
</ToolTipService.ToolTip>
</MenuItem>

Expand Down Expand Up @@ -126,6 +126,7 @@
<MenuItem Name="MenuItem_Export" Header="_Export">
<MenuItem Name="MenuItem_BatchResultExport" Header="Export batch results" Click="menuItem_BatchResultExport_Click" IsEnabled="True" />
<MenuItem Name="MenuItem_PeakAnnotationResultExportAsMsp" Header="Export peak annotation result as MSP format" Click="menuItem_PeakAnnotationResultExportAsMsp_Click" IsEnabled="True" />
<MenuItem Name="MenuItem_PeakAnnotationResultExportAsMassBankRecord" Header="Export peak annotation result as MassBank record format" Click="menuItem_PeakAnnotationResultExportAsMassBankRecord_Click" IsEnabled="True" />
<MenuItem Name="MenuItem_MolecularNetworkExport" Header="Export nodes and edges for molecular spectrum network" Click="menuItem_MolecularNetworkExport_Click" IsEnabled="True" />
<MenuItem Name="MenuItem_CopyScreenshotToClipBoard" Header="Copy screenshot to clipboard" Click="menuItem_CopyScreenshotToClipboard_Click" IsEnabled="True" />
</MenuItem>
Expand Down
22 changes: 22 additions & 0 deletions src/MSFINDER/MSFINDER/MainWindow.xaml.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -386,6 +386,28 @@ private void menuItem_PeakAnnotationResultExportAsMsp_Click(object sender, Route
}
}

private void menuItem_PeakAnnotationResultExportAsMassBankRecord_Click(object sender, RoutedEventArgs e)
{
if (!checkFileImport()) return;

System.Windows.Forms.FolderBrowserDialog fbd = new System.Windows.Forms.FolderBrowserDialog
{
RootFolder = Environment.SpecialFolder.Desktop,
Description = "Select a folder to export the MassBank records to",
SelectedPath = string.IsNullOrEmpty(this.mainWindowVM.DataStorageBean.ImportFolderPath)
? Environment.GetFolderPath(Environment.SpecialFolder.Desktop)
: this.mainWindowVM.DataStorageBean.ImportFolderPath
};

if (fbd.ShowDialog() == System.Windows.Forms.DialogResult.OK) {
Mouse.OverrideCursor = Cursors.Wait;

ExportUtility.PeakAnnotationResultExportAsMassBankRecord(this.mainWindowVM, fbd.SelectedPath);

Mouse.OverrideCursor = null;
}
}

private void menuItem_Test_Click(object sender, RoutedEventArgs e)
{
var sfd = new SaveFileDialog();
Expand Down
Loading

0 comments on commit 8d09509

Please sign in to comment.