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Standardize file extensions
1 parent 82ff97c commit ca35579

4 files changed

Lines changed: 146 additions & 8 deletions

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‎ThermoRawFileParserTest/Data/ExtensionTest.tsv‎

Lines changed: 23 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,23 @@
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Format Gzip UserInput FileOutput
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MGF FALSE rawfile rawfile.mgf
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MGF FALSE rawfile. rawfile.mgf
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MGF FALSE rawfile.mgf rawfile.mgf
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MGF FALSE rawfile.MGF rawfile.mgf
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MGF FALSE rawfile.. rawfile.mgf
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MGF TRUE rawfile.mgf.gz rawfile.mgf.gz
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MGF TRUE rawfile rawfile.mgf.gz
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MGF TRUE rawfile.. rawfile.mgf.gz
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MGF TRUE rawfile.mgf.GZ rawfile.mgf.gz
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MGF TRUE rawfile.mgf rawfile.mgf.gz
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MGF TRUE rawfile.MGF. rawfile.mgf.gz
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mzML FALSE rawfile rawfile.mzML
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mzML FALSE rawfile. rawfile.mzML
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mzML FALSE rawfile.mgf rawfile.mgf.mzML
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mzML FALSE rawfile.MzML rawfile.mzML
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mzML FALSE rawfile.. rawfile.mzML
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mzML TRUE rawfile.mzML.gz rawfile.mzML.gz
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mzML TRUE rawfile rawfile.mzML.gz
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mzML TRUE rawfile.. rawfile.mzML.gz
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mzML TRUE rawfile.mzml.GZ rawfile.mzML.gz
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mzML TRUE rawfile.mzML rawfile.mzML.gz
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mzML TRUE rawfile.MZml. rawfile.mzML.gz

‎ThermoRawFileParserTest/ThermoRawFileParserTest.csproj‎

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Original file line numberDiff line numberDiff line change
@@ -187,6 +187,9 @@
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</ItemGroup>
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<ItemGroup>
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<None Include="app.config" />
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<None Include="Data\ExtensionTest.tsv">
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<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
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</None>
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<None Include="Data\TestFolderMgfs\small1.RAW">
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<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
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</None>

‎ThermoRawFileParserTest/WriterTests.cs‎

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Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@
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using MzLibUtil;
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using NUnit.Framework;
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using ThermoRawFileParser;
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using ThermoRawFileParser.Writer;
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using ThermoRawFileParser.Writer.MzML;
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using UsefulProteomicsDatabases;
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@@ -16,6 +17,97 @@ namespace ThermoRawFileParserTest
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[TestFixture]
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public class WriterTests
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{
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[Test]
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public void TestExtensionsNull()
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{
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// Get temp path for writing the test files
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var tempFilePath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
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Directory.CreateDirectory(tempFilePath);
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var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/small.RAW");
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var parseInput = new ParseInput();
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parseInput.RawFilePath = testRawFile;
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parseInput.OutputDirectory = tempFilePath;
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//empty filename
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parseInput.OutputFormat = OutputFormat.MGF;
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RawFileParser.Parse(parseInput);
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Assert.IsTrue(File.Exists(Path.Combine(tempFilePath, "small.mgf")));
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parseInput.OutputFormat = OutputFormat.MzML;
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RawFileParser.Parse(parseInput);
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Assert.IsTrue(File.Exists(Path.Combine(tempFilePath, "small.mzML")));
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File.Delete(Path.Combine(tempFilePath, "small.mzML"));
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parseInput.OutputFormat = OutputFormat.IndexMzML;
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RawFileParser.Parse(parseInput);
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Assert.IsTrue(File.Exists(Path.Combine(tempFilePath, "small.mzML")));
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parseInput.Gzip = true;
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RawFileParser.Parse(parseInput);
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Assert.IsTrue(File.Exists(Path.Combine(tempFilePath, "small.mzML.gz")));
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File.Delete(Path.Combine(tempFilePath, "small.mzML.gz"));
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parseInput.OutputFormat = OutputFormat.MGF;
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RawFileParser.Parse(parseInput);
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Assert.IsTrue(File.Exists(Path.Combine(tempFilePath, "small.mgf.gz")));
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parseInput.OutputFormat = OutputFormat.MzML;
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RawFileParser.Parse(parseInput);
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Assert.IsTrue(File.Exists(Path.Combine(tempFilePath, "small.mzML.gz")));
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Directory.Delete(tempFilePath, true);
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}
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[Test]
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public void TestExtensionsFull()
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{
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// Get temp path for writing the test files
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var tempFilePath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
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Directory.CreateDirectory(tempFilePath);
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var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/small.RAW");
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var parseInput = new ParseInput();
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parseInput.RawFilePath = testRawFile;
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List<OutputFormat> formats = new List<OutputFormat>();
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string userInput;
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string expectedOutput;
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foreach (string line in File.ReadLines(Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/ExtensionTest.tsv")).Skip(1))
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{
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string[] words = line.Split('\t');
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switch (words[0].ToLower())
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{
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case "mgf": formats = new List<OutputFormat> { OutputFormat.MGF }; break;
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case "mzml": formats = new List<OutputFormat> { OutputFormat.MzML, OutputFormat.IndexMzML }; break;
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}
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switch (words[1].ToLower())
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{
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case "true": parseInput.Gzip = true; break;
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default: parseInput.Gzip = false; break;
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}
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userInput = words[2];
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expectedOutput = words[3];
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parseInput.OutputFile = Path.Combine(tempFilePath, userInput);
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foreach (var format in formats)
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{
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parseInput.OutputFormat = format;
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RawFileParser.Parse(parseInput);
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Assert.IsTrue(File.Exists(Path.Combine(tempFilePath, expectedOutput)));
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File.Delete(Path.Combine(tempFilePath, expectedOutput));
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}
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}
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Directory.Delete(tempFilePath, true);
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}
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[Test]
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public void TestMgf()
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{

‎Writer/SpectrumWriter.cs‎

Lines changed: 28 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -70,7 +70,7 @@ protected void ConfigureWriter(string extension)
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if (ParseInput.OutputFile == null)
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{
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var fullExtension = ParseInput.Gzip ? extension + ".gzip" : extension;
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var fullExtension = ParseInput.Gzip ? extension + ".gz" : extension;
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if (!ParseInput.Gzip || ParseInput.OutputFormat == OutputFormat.IndexMzML)
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{
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Writer = File.CreateText(ParseInput.OutputDirectory + "//" +
@@ -87,25 +87,45 @@ protected void ConfigureWriter(string extension)
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}
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else
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{
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var fileName = NormalizeFileName(ParseInput.OutputFile, extension, ParseInput.Gzip);
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if (!ParseInput.Gzip || ParseInput.OutputFormat == OutputFormat.IndexMzML)
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{
92-
Writer = File.CreateText(ParseInput.OutputFile);
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Writer = File.CreateText(fileName);
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}
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else
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{
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var fileName = ParseInput.OutputFile;
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if (ParseInput.Gzip && !Path.GetExtension(fileName).Equals(".gzip"))
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{
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fileName = ParseInput.OutputFile + ".gzip";
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}
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var fileStream = File.Create(fileName);
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var compress = new GZipStream(fileStream, CompressionMode.Compress);
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Writer = new StreamWriter(compress);
105100
}
106101
}
107102
}
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104+
private string NormalizeFileName(string outputFile, string extension, bool gzip)
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{
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string result = outputFile;
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string tail = "";
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109+
string[] extensions;
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if (ParseInput.Gzip)
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extensions = new string[] { ".gz", extension };
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else
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extensions = new string[] { extension };
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result = result.TrimEnd('.');
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foreach (var ext in extensions)
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{
119+
if (result.ToLower().EndsWith(ext.ToLower()))
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result = result.Substring(0, result.Length - ext.Length);
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tail = ext + tail;
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result = result.TrimEnd('.');
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}
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return result + tail;
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}
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/// <summary>
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/// Construct the spectrum title.
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/// </summary>

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