file input parameter added

Author: ypriverol

MainClass.cs

@@ -15,6 +15,7 @@ public static void Main(string[] args)
         {
             string rawFilePath = null;
             string outputDirectory = null;
+            string outputFile = null; 
             string outputFormatString = null;
             var outputFormat = OutputFormat.NONE;
             var gzip = false;
@@ -44,6 +45,10 @@ public static void Main(string[] args)
                     "o=|output=", "The output directory.",
                     v => outputDirectory = v
                 },
+                {
+                    "b=|output_file", "The output file to export spectra", 
+                    v => outputFile = v 
+                }, 
                 {
                     "f=|format=",
                     "The output format for the spectra (0 for MGF, 1 for mzMl, 2 for indexed mzML, 3 for Parquet)",
@@ -196,7 +201,7 @@ public static void Main(string[] args)
                         .RaiseConfigurationChanged(EventArgs.Empty);
                 }
 
-                var parseInput = new ParseInput(rawFilePath, outputDirectory, outputFormat, gzip, outputMetadataFormat,
+                var parseInput = new ParseInput(rawFilePath, outputDirectory, outputFile, outputFormat, gzip, outputMetadataFormat,
                     s3url, s3AccessKeyId, s3SecretAccessKey, bucketName, ignoreInstrumentErrors, noPeakPicking);
                 RawFileParser.Parse(parseInput);
             }

ParseInput.cs

@@ -1,4 +1,5 @@
 using System.IO;
+using System.Resources;
 using ThermoRawFileParser.Writer;
 
 namespace ThermoRawFileParser
@@ -20,6 +21,11 @@ public class ParseInput
         /// </summary>
         public OutputFormat OutputFormat { get; }
 
+        /// <summary>
+        /// The output file 
+        /// </summary>>
+        public string OutputFile { get; }
+
         /// <summary>
         /// Gzip the output file.
         /// </summary>
@@ -54,7 +60,7 @@ public class ParseInput
 
         private string bucketName;
 
-        public ParseInput(string rawFilePath, string outputDirectory, OutputFormat outputFormat, bool gzip,
+        public ParseInput(string rawFilePath, string outputDirectory, string outputFile, OutputFormat outputFormat, bool gzip,
             MetadataFormat outputMetadata, string s3url, string s3AccessKeyId,
             string s3SecretAccessKey, string bucketName,
             bool ignoreInstrumentErrors, bool noPeakPicking
@@ -65,6 +71,7 @@ public ParseInput(string rawFilePath, string outputDirectory, OutputFormat outpu
             RawFileName = splittedPath[splittedPath.Length - 1];
             RawFileNameWithoutExtension = Path.GetFileNameWithoutExtension(RawFileName);
             OutputDirectory = outputDirectory;
+            OutputFile = outputFile; 
             OutputFormat = outputFormat;
             Gzip = gzip;
             OutputMetadata = outputMetadata;
@@ -77,6 +84,10 @@ public ParseInput(string rawFilePath, string outputDirectory, OutputFormat outpu
 
             if (S3url != null && S3AccessKeyId != null && S3SecretAccessKey != null && bucketName != null)
                 InitializeS3Bucket();
+
+            if (OutputDirectory == null && OutputFile != null)
+                OutputDirectory = Path.GetDirectoryName(OutputFile); 
+
         }
 
         private void InitializeS3Bucket()

RawFileParser.cs

@@ -64,8 +64,7 @@ public static void Parse(ParseInput parseInput)
 
                 if (parseInput.OutputMetadata != MetadataFormat.NONE)
                 {
-                    var metadataWriter = new MetadataWriter(parseInput.OutputDirectory,
-                        parseInput.RawFileNameWithoutExtension);
+                    var metadataWriter = new MetadataWriter(parseInput.OutputDirectory, parseInput.RawFileNameWithoutExtension);
                     switch (parseInput.OutputMetadata)
                     {
                         case MetadataFormat.JSON:

ThermoRawFileParserTest/WriterTests.cs

@@ -19,7 +19,7 @@ public void TestMgf()
             var tempFilePath = Path.GetTempPath();
 
             var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"small.RAW");
-            var parseInput = new ParseInput(testRawFile, tempFilePath, OutputFormat.MGF, false, MetadataFormat.NONE,
+            var parseInput = new ParseInput(testRawFile, tempFilePath, null, OutputFormat.MGF, false, MetadataFormat.NONE,
                 null, null, null, null, false, false);
 
             RawFileParser.Parse(parseInput);
@@ -40,7 +40,7 @@ public void TestMzml()
             var tempFilePath = Path.GetTempPath();
 
             var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"small.RAW");
-            var parseInput = new ParseInput(testRawFile, tempFilePath, OutputFormat.MzML, false, MetadataFormat.NONE,
+            var parseInput = new ParseInput(testRawFile, tempFilePath, null, OutputFormat.MzML, false, MetadataFormat.NONE,
                 null, null, null, null, false, false);
 
             RawFileParser.Parse(parseInput);
@@ -66,7 +66,7 @@ public void TestIndexedMzML()
             Console.WriteLine(tempFilePath);
 
             var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"small.RAW");
-            var parseInput = new ParseInput(testRawFile, tempFilePath, OutputFormat.IndexMzML, false,
+            var parseInput = new ParseInput(testRawFile, tempFilePath, null, OutputFormat.IndexMzML, false,
                 MetadataFormat.NONE,
                 null, null, null, null, false, false);
 

Writer/SpectrumWriter.cs

@@ -39,18 +39,34 @@ protected SpectrumWriter(ParseInput parseInput)
         /// <param name="extension">The extension of the output file</param>
         protected void ConfigureWriter(string extension)
         {
-            var fullExtension = ParseInput.Gzip ? extension + ".gzip" : extension;
-            if (!ParseInput.Gzip || ParseInput.OutputFormat == OutputFormat.IndexMzML)
+            if (ParseInput.OutputFile == null)
             {
-                Writer = File.CreateText(ParseInput.OutputDirectory + "//" + ParseInput.RawFileNameWithoutExtension +
-                                         extension);
+                var fullExtension = ParseInput.Gzip ? extension + ".gzip" : extension;
+                if (!ParseInput.Gzip || ParseInput.OutputFormat == OutputFormat.IndexMzML)
+                {
+                    Writer = File.CreateText(ParseInput.OutputDirectory + "//" + ParseInput.RawFileNameWithoutExtension +
+                                             extension);
+                }
+                else
+                {
+                    var fileStream = File.Create(ParseInput.OutputDirectory + "//" + ParseInput.RawFileNameWithoutExtension + fullExtension);
+                    var compress = new GZipStream(fileStream, CompressionMode.Compress);
+                    Writer = new StreamWriter(compress);
+                } 
             }
             else
             {
-                var fileStream = File.Create(ParseInput.OutputDirectory + "//" +
-                                             ParseInput.RawFileNameWithoutExtension + fullExtension);
-                var compress = new GZipStream(fileStream, CompressionMode.Compress);
-                Writer = new StreamWriter(compress);
+                if (!ParseInput.Gzip || ParseInput.OutputFormat == OutputFormat.IndexMzML)
+                {
+                    Writer = File.CreateText(ParseInput.OutputFile); 
+                }
+                else
+                {
+                    var fileName = ParseInput.Gzip ? ParseInput.OutputFile + ".gzip" : ParseInput.OutputFile;
+                    var fileStream = File.Create(fileName);
+                    var compress = new GZipStream(fileStream, CompressionMode.Compress);
+                    Writer = new StreamWriter(compress);
+                }
             }
         }