private static void ProcessFile(IRawDataPlus rawFile, int firstScanNumber, int lastScanNumber, ParseInput parseInput)
{
if (parseInput.MetadataFormat != MetadataFormat.NONE)
{
MetadataWriter metadataWriter;
if (parseInput.MetadataOutputFile != null)
{
metadataWriter = new MetadataWriter(null, parseInput.MetadataOutputFile);
}
else
{
metadataWriter = new MetadataWriter(parseInput.OutputDirectory,
parseInput.RawFileNameWithoutExtension);
}
switch (parseInput.MetadataFormat)
{
case MetadataFormat.JSON:
metadataWriter.WriteJsonMetada(rawFile, firstScanNumber, lastScanNumber);
break;
case MetadataFormat.TXT:
metadataWriter.WriteMetadata(rawFile, firstScanNumber, lastScanNumber);
break;
}
}
if (parseInput.OutputFormat != OutputFormat.NONE)
{
SpectrumWriter spectrumWriter;
switch (parseInput.OutputFormat)
{
case OutputFormat.MGF:
spectrumWriter = new MgfSpectrumWriter(rawFile, parseInput);
spectrumWriter.Write(firstScanNumber, lastScanNumber);
break;
case OutputFormat.MzML:
case OutputFormat.IndexMzML:
spectrumWriter = new MzMlSpectrumWriter(rawFile, parseInput);
spectrumWriter.Write(firstScanNumber, lastScanNumber);
break;
case OutputFormat.Parquet:
spectrumWriter = new ParquetSpectrumWriter(rawFile, parseInput);
spectrumWriter.Write(firstScanNumber, lastScanNumber);
break;
}
}
//Log.Info("Finished parsing " + parseInput.RawFilePath);
Console.WriteLine("Finished parsing " + parseInput.RawFilePath);
}
/// <summary>
/// Extract the RAW file metadata and spectra in MGF format.
/// </summary>
/// <param name="parseInput">the parse input object</param>
public static void Parse(ParseInput parseInput)
{
// Check to see if the RAW file name was supplied as an argument to the program
if (string.IsNullOrEmpty(parseInput.RawFilePath))
{
throw new Exception("No RAW file specified!");
}
// Check to see if the specified RAW file exists
if (!File.Exists(parseInput.RawFilePath))
{
throw new Exception(@"The file doesn't exist in the specified location - " + parseInput.RawFilePath);
}
Log.Info("Started parsing " + parseInput.RawFilePath);
// Create the IRawDataPlus object for accessing the RAW file
//var rawFile = RawFileReaderAdapter.FileFactory(rawFilePath);
IRawDataPlus rawFile;
using (rawFile = RawFileReaderFactory.ReadFile(parseInput.RawFilePath))
{
if (!rawFile.IsOpen)
{
throw new Exception("Unable to access the RAW file using the RawFileReader class!");
}
// Check for any errors in the RAW file
if (rawFile.IsError)
{
throw new Exception($"Error opening ({rawFile.FileError}) - {parseInput.RawFilePath}");
}
// Check if the RAW file is being acquired
if (rawFile.InAcquisition)
{
throw new Exception("RAW file still being acquired - " + parseInput.RawFilePath);
}
// Get the number of instruments (controllers) present in the RAW file and set the
// selected instrument to the MS instrument, first instance of it
rawFile.SelectInstrument(Device.MS, 1);
// Get the first and last scan from the RAW file
var firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
var lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
if (parseInput.OutputMetadata != MetadataFormat.NON)
{
var metadataWriter = new MetadataWriter(parseInput.OutputDirectory, parseInput.RawFileNameWithoutExtension);
if (parseInput.OutputMetadata == MetadataFormat.JSON)
{
metadataWriter.WriteJsonMetada(rawFile, firstScanNumber, lastScanNumber);
}
if (parseInput.OutputMetadata == MetadataFormat.TXT)
{
metadataWriter.WriteMetada(rawFile, firstScanNumber, lastScanNumber);
}
}
if (parseInput.OutputFormat != OutputFormat.NON)
{
SpectrumWriter spectrumWriter;
switch (parseInput.OutputFormat)
{
case OutputFormat.Mgf:
spectrumWriter = new MgfSpectrumWriter(parseInput);
spectrumWriter.Write(rawFile, firstScanNumber, lastScanNumber);
break;
case OutputFormat.Mzml:
spectrumWriter = new MzMlSpectrumWriter(parseInput);
spectrumWriter.Write(rawFile, firstScanNumber, lastScanNumber);
break;
case OutputFormat.Parquet:
spectrumWriter = new ParquetSpectrumWriter(parseInput);
spectrumWriter.Write(rawFile, firstScanNumber, lastScanNumber);
break;
}
}
Log.Info("Finished parsing " + parseInput.RawFilePath);
}
}
/// <summary>
/// Process and extract the given RAW file.
/// </summary>
/// <param name="parseInput">the parse input object</param>
private static void ProcessFile(ParseInput parseInput)
{
// Create the IRawDataPlus object for accessing the RAW file
IRawDataPlus rawFile;
using (rawFile = RawFileReaderFactory.ReadFile(parseInput.RawFilePath))
{
if (!rawFile.IsOpen)
{
throw new RawFileParserException("Unable to access the RAW file using the native Thermo library.");
}
// Check for any errors in the RAW file
if (rawFile.IsError)
{
throw new RawFileParserException($"Error opening ({rawFile.FileError}) - {parseInput.RawFilePath}");
}
// Check if the RAW file is being acquired
if (rawFile.InAcquisition)
{
throw new RawFileParserException("RAW file still being acquired - " + parseInput.RawFilePath);
}
// Get the number of instruments (controllers) present in the RAW file and set the
// selected instrument to the MS instrument, first instance of it
rawFile.SelectInstrument(Device.MS, 1);
rawFile.IncludeReferenceAndExceptionData = parseInput.ExData;
// Get the first and last scan from the RAW file
var firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
var lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
if (parseInput.MetadataFormat != MetadataFormat.NONE)
{
MetadataWriter metadataWriter;
if (parseInput.MetadataOutputFile != null)
{
metadataWriter = new MetadataWriter(null, parseInput.MetadataOutputFile);
}
else
{
metadataWriter = new MetadataWriter(parseInput.OutputDirectory,
parseInput.RawFileNameWithoutExtension);
}
switch (parseInput.MetadataFormat)
{
case MetadataFormat.JSON:
metadataWriter.WriteJsonMetada(rawFile, firstScanNumber, lastScanNumber);
break;
case MetadataFormat.TXT:
metadataWriter.WriteMetadata(rawFile, firstScanNumber, lastScanNumber);
break;
}
}
if (parseInput.OutputFormat != OutputFormat.NONE)
{
SpectrumWriter spectrumWriter;
switch (parseInput.OutputFormat)
{
case OutputFormat.MGF:
spectrumWriter = new MgfSpectrumWriter(parseInput);
spectrumWriter.Write(rawFile, firstScanNumber, lastScanNumber);
break;
case OutputFormat.MzML:
case OutputFormat.IndexMzML:
spectrumWriter = new MzMlSpectrumWriter(parseInput);
spectrumWriter.Write(rawFile, firstScanNumber, lastScanNumber);
break;
case OutputFormat.Parquet:
spectrumWriter = new ParquetSpectrumWriter(parseInput);
spectrumWriter.Write(rawFile, firstScanNumber, lastScanNumber);
break;
}
}
Log.Info("Finished parsing " + parseInput.RawFilePath);
}
}
