コード例 #1
0
        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);
        }
コード例 #2
0
        /// <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);
            }
        }
コード例 #3
0
        /// <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);
            }
        }