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nielshulstaertnielshulstaert
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Merge branch 'ypriverol-master'
2 parents ec571a3 + dbe7017 commit 87c79ea

38 files changed

Lines changed: 369 additions & 18 deletions

‎.travis.yml‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
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language: csharp
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solution: ThermoRawFileParser.sln
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‎App.config‎

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@@ -0,0 +1,6 @@
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<?xml version="1.0" encoding="utf-8" ?>
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<configuration>
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<runtime>
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<loadFromRemoteSources enabled="true" />
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</runtime>
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</configuration>

‎MainClass.cs‎

Lines changed: 6 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,7 @@ public static void Main(string[] args)
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{
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string rawFilePath = null;
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string outputDirectory = null;
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string outputFile = null;
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string outputFormatString = null;
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var outputFormat = OutputFormat.NONE;
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var gzip = false;
@@ -44,6 +45,10 @@ public static void Main(string[] args)
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"o=|output=", "The output directory.",
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v => outputDirectory = v
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},
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{
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"b=|output_file", "The output file to export spectra",
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v => outputFile = v
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},
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{
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"f=|format=",
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"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)
196201
.RaiseConfigurationChanged(EventArgs.Empty);
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}
198203

199-
var parseInput = new ParseInput(rawFilePath, outputDirectory, outputFormat, gzip, outputMetadataFormat,
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var parseInput = new ParseInput(rawFilePath, outputDirectory, outputFile, outputFormat, gzip, outputMetadataFormat,
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s3url, s3AccessKeyId, s3SecretAccessKey, bucketName, ignoreInstrumentErrors, noPeakPicking);
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RawFileParser.Parse(parseInput);
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}

‎ParseInput.cs‎

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@@ -1,4 +1,5 @@
11
using System.IO;
2+
using System.Resources;
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using ThermoRawFileParser.Writer;
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namespace ThermoRawFileParser
@@ -20,6 +21,11 @@ public class ParseInput
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/// </summary>
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public OutputFormat OutputFormat { get; }
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/// <summary>
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/// The output file
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/// </summary>>
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public string OutputFile { get; }
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/// <summary>
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/// Gzip the output file.
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/// </summary>
@@ -54,7 +60,7 @@ public class ParseInput
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private string bucketName;
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57-
public ParseInput(string rawFilePath, string outputDirectory, OutputFormat outputFormat, bool gzip,
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public ParseInput(string rawFilePath, string outputDirectory, string outputFile, OutputFormat outputFormat, bool gzip,
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MetadataFormat outputMetadata, string s3url, string s3AccessKeyId,
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string s3SecretAccessKey, string bucketName,
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bool ignoreInstrumentErrors, bool noPeakPicking
@@ -65,6 +71,7 @@ public ParseInput(string rawFilePath, string outputDirectory, OutputFormat outpu
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RawFileName = splittedPath[splittedPath.Length - 1];
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RawFileNameWithoutExtension = Path.GetFileNameWithoutExtension(RawFileName);
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OutputDirectory = outputDirectory;
74+
OutputFile = outputFile;
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OutputFormat = outputFormat;
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Gzip = gzip;
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OutputMetadata = outputMetadata;
@@ -77,6 +84,10 @@ public ParseInput(string rawFilePath, string outputDirectory, OutputFormat outpu
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7885
if (S3url != null && S3AccessKeyId != null && S3SecretAccessKey != null && bucketName != null)
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InitializeS3Bucket();
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88+
if (OutputDirectory == null && OutputFile != null)
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OutputDirectory = Path.GetDirectoryName(OutputFile);
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}
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8293
private void InitializeS3Bucket()

‎RawFileParser.cs‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -64,8 +64,7 @@ public static void Parse(ParseInput parseInput)
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6565
if (parseInput.OutputMetadata != MetadataFormat.NONE)
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{
67-
var metadataWriter = new MetadataWriter(parseInput.OutputDirectory,
68-
parseInput.RawFileNameWithoutExtension);
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var metadataWriter = new MetadataWriter(parseInput.OutputDirectory, parseInput.RawFileNameWithoutExtension);
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switch (parseInput.OutputMetadata)
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{
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case MetadataFormat.JSON:

‎ThermoRawFileParser.csproj‎

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@@ -141,6 +141,7 @@
141141
<Compile Include="Writer\SpectrumWriter.cs" />
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</ItemGroup>
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<ItemGroup>
144+
<None Include="App.config" />
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<None Include="packages.config" />
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</ItemGroup>
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<ItemGroup>

‎ThermoRawFileParserTest/WriterTests.cs‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -19,8 +19,8 @@ public void TestMgf()
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var tempFilePath = Path.GetTempPath();
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var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"small.RAW");
22-
var parseInput = new ParseInput(testRawFile, tempFilePath, OutputFormat.MGF, false, MetadataFormat.NONE,
23-
null, null, null, null, false);
22+
var parseInput = new ParseInput(testRawFile, tempFilePath, null, OutputFormat.MGF, false, MetadataFormat.NONE,
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null, null, null, null, false, false);
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2525
RawFileParser.Parse(parseInput);
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@@ -40,8 +40,8 @@ public void TestMzml()
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var tempFilePath = Path.GetTempPath();
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4242
var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"small.RAW");
43-
var parseInput = new ParseInput(testRawFile, tempFilePath, OutputFormat.MzML, false, MetadataFormat.NONE,
44-
null, null, null, null, false);
43+
var parseInput = new ParseInput(testRawFile, tempFilePath, null, OutputFormat.MzML, false, MetadataFormat.NONE,
44+
null, null, null, null, false, false);
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4646
RawFileParser.Parse(parseInput);
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@@ -66,9 +66,9 @@ public void TestIndexedMzML()
6666
Console.WriteLine(tempFilePath);
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var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"small.RAW");
69-
var parseInput = new ParseInput(testRawFile, tempFilePath, OutputFormat.IndexMzML, false,
69+
var parseInput = new ParseInput(testRawFile, tempFilePath, null, OutputFormat.IndexMzML, false,
7070
MetadataFormat.NONE,
71-
null, null, null, null, false);
71+
null, null, null, null, false, false);
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7373
RawFileParser.Parse(parseInput);
7474

‎Writer/SpectrumWriter.cs‎

Lines changed: 24 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -39,18 +39,34 @@ protected SpectrumWriter(ParseInput parseInput)
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/// <param name="extension">The extension of the output file</param>
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protected void ConfigureWriter(string extension)
4141
{
42-
var fullExtension = ParseInput.Gzip ? extension + ".gzip" : extension;
43-
if (!ParseInput.Gzip || ParseInput.OutputFormat == OutputFormat.IndexMzML)
42+
if (ParseInput.OutputFile == null)
4443
{
45-
Writer = File.CreateText(ParseInput.OutputDirectory + "//" + ParseInput.RawFileNameWithoutExtension +
46-
extension);
44+
var fullExtension = ParseInput.Gzip ? extension + ".gzip" : extension;
45+
if (!ParseInput.Gzip || ParseInput.OutputFormat == OutputFormat.IndexMzML)
46+
{
47+
Writer = File.CreateText(ParseInput.OutputDirectory + "//" + ParseInput.RawFileNameWithoutExtension +
48+
extension);
49+
}
50+
else
51+
{
52+
var fileStream = File.Create(ParseInput.OutputDirectory + "//" + ParseInput.RawFileNameWithoutExtension + fullExtension);
53+
var compress = new GZipStream(fileStream, CompressionMode.Compress);
54+
Writer = new StreamWriter(compress);
55+
}
4756
}
4857
else
4958
{
50-
var fileStream = File.Create(ParseInput.OutputDirectory + "//" +
51-
ParseInput.RawFileNameWithoutExtension + fullExtension);
52-
var compress = new GZipStream(fileStream, CompressionMode.Compress);
53-
Writer = new StreamWriter(compress);
59+
if (!ParseInput.Gzip || ParseInput.OutputFormat == OutputFormat.IndexMzML)
60+
{
61+
Writer = File.CreateText(ParseInput.OutputFile);
62+
}
63+
else
64+
{
65+
var fileName = ParseInput.Gzip ? ParseInput.OutputFile + ".gzip" : ParseInput.OutputFile;
66+
var fileStream = File.Create(fileName);
67+
var compress = new GZipStream(fileStream, CompressionMode.Compress);
68+
Writer = new StreamWriter(compress);
69+
}
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}
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}
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‎packages/System.Text.Encoding.CodePages.4.0.1/.signature.p7s‎

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‎packages/System.Text.Encoding.CodePages.4.0.1/System.Text.Encoding.CodePages.4.0.1.nupkg‎

1.54 MB
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