public void TestIndexedMzML()
{
// Get temp path for writing the test mzML
var tempFilePath = Path.GetTempPath();
Console.WriteLine(tempFilePath);
var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/small.RAW");
var parseInput = new ParseInput(testRawFile, null, tempFilePath, OutputFormat.IndexMzML);
RawFileParser.Parse(parseInput);
// Deserialize the mzML file
var xmlSerializer = new XmlSerializer(typeof(indexedmzML));
var testMzMl = (indexedmzML)xmlSerializer.Deserialize(new FileStream(
Path.Combine(tempFilePath, "small.mzML"), FileMode.Open, FileAccess.Read, FileShare.ReadWrite));
Assert.AreEqual("48", testMzMl.mzML.run.spectrumList.count);
Assert.AreEqual(48, testMzMl.mzML.run.spectrumList.spectrum.Length);
Assert.AreEqual("1", testMzMl.mzML.run.chromatogramList.count);
Assert.AreEqual(1, testMzMl.mzML.run.chromatogramList.chromatogram.Length);
Assert.AreEqual(2, testMzMl.indexList.index.Length);
Assert.AreEqual("spectrum", testMzMl.indexList.index[0].name.ToString());
Assert.AreEqual(48, testMzMl.indexList.index[0].offset.Length);
Assert.AreEqual("chromatogram", testMzMl.indexList.index[1].name.ToString());
Assert.AreEqual(1, testMzMl.indexList.index[1].offset.Length);
}
public void TestProfileMzml()
{
// Get temp path for writing the test mzML
var tempFilePath = Path.GetTempPath();
var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/small.RAW");
var parseInput = new ParseInput(testRawFile, null, tempFilePath, OutputFormat.MzML);
parseInput.NoPeakPicking = true;
RawFileParser.Parse(parseInput);
// Deserialize the mzML file
var xmlSerializer = new XmlSerializer(typeof(mzMLType));
var testMzMl = (mzMLType)xmlSerializer.Deserialize(new FileStream(
Path.Combine(tempFilePath, "small.mzML"), FileMode.Open, FileAccess.Read, FileShare.ReadWrite));
Assert.AreEqual("48", testMzMl.run.spectrumList.count);
Assert.AreEqual(48, testMzMl.run.spectrumList.spectrum.Length);
Assert.AreEqual("1", testMzMl.run.chromatogramList.count);
Assert.AreEqual(1, testMzMl.run.chromatogramList.chromatogram.Length);
Assert.AreEqual(48, testMzMl.run.chromatogramList.chromatogram[0].defaultArrayLength);
}
public void TestMzML_MS2()
{
// Get temp path for writing the test mzML
var tempFilePath = Path.GetTempPath();
var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/small2.RAW");
var parseInput = new ParseInput(testRawFile, null, tempFilePath, OutputFormat.MzML);
RawFileParser.Parse(parseInput);
// Deserialize the mzML file
var xmlSerializer = new XmlSerializer(typeof(mzMLType));
var testMzMl = (mzMLType)xmlSerializer.Deserialize(new FileStream(
Path.Combine(tempFilePath, "small2.mzML"), FileMode.Open, FileAccess.Read, FileShare.ReadWrite));
Assert.AreEqual(95, testMzMl.run.spectrumList.spectrum.Length);
var precursor = testMzMl.run.spectrumList.spectrum[16].precursorList.precursor[0].selectedIonList.selectedIon[0];
var selectedMz = Double.Parse(precursor.cvParam.Where(cv => cv.accession == "MS:1000744").First().value);
Assert.IsTrue(selectedMz - 604.7592 < 0.001);
var selectedZ = int.Parse(precursor.cvParam.Where(cv => cv.accession == "MS:1000041").First().value);
Assert.AreEqual(selectedZ, 2);
//var selectedI = Double.Parse(precursor.cvParam.Where(cv => cv.accession == "MS:1000042").First().value);
//Assert.IsTrue(selectedI - 10073 < 1);
Assert.AreEqual(95, testMzMl.run.chromatogramList.chromatogram[0].defaultArrayLength);
}
public void TestFolderMgfs()
{
// Get temp path for writing the test MGF
var tempFilePath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
Directory.CreateDirectory(tempFilePath);
var testRawFolder = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/TestFolderMgfs");
var parseInput = new ParseInput(null, testRawFolder, tempFilePath, OutputFormat.MGF);
RawFileParser.Parse(parseInput);
var numFiles = Directory.GetFiles(tempFilePath, "*.mgf");
Assert.AreEqual(numFiles.Length, 2);
var mgfData = Mgf.LoadAllStaticData(Path.Combine(tempFilePath, "small1.mgf"));
Assert.AreEqual(34, mgfData.NumSpectra);
var mgfData2 = Mgf.LoadAllStaticData(Path.Combine(tempFilePath, "small2.mgf"));
Assert.AreEqual(34, mgfData2.NumSpectra);
Directory.Delete(tempFilePath, true);
}
public void TestMgf()
{
// Get temp path for writing the test MGF
var tempFilePath = Path.GetTempPath();
var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/small.RAW");
var parseInput = new ParseInput(testRawFile, null, tempFilePath, OutputFormat.MGF);
RawFileParser.Parse(parseInput);
var mgfData = Mgf.LoadAllStaticData(Path.Combine(tempFilePath, "small.mgf"));
Assert.AreEqual(34, mgfData.NumSpectra);
}
public void TestMgf()
{
// Get temp path for writing the test MGF
var tempFilePath = Path.GetTempPath();
var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"small.RAW");
var parseInput = new ParseInput(testRawFile, tempFilePath, null, OutputFormat.MGF);
RawFileParser.Parse(parseInput);
// Do this for the mzLib library issue
var tempFileName = Path.GetTempPath() + "elements.dat";
Loaders.LoadElements(tempFileName);
var mgfData = Mgf.LoadAllStaticData(Path.Combine(tempFilePath, "small.mgf"));
Assert.AreEqual(34, mgfData.NumSpectra);
}
public void TestMzml()
{
// Get temp path for writing the test mzML
var tempFilePath = Path.GetTempPath();
var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"small.RAW");
var parseInput = new ParseInput(testRawFile, tempFilePath, OutputFormat.Mzml, false, MetadataFormat.NON, false,
"coll", "run", "sub");
RawFileParser.Parse(parseInput);
// Deserialize the mzML file
var xmlSerializer = new XmlSerializer(typeof(mzMLType));
var testMzMl = (mzMLType)xmlSerializer.Deserialize(new FileStream(
Path.Combine(tempFilePath, "small.mzML"), FileMode.Open, FileAccess.Read, FileShare.ReadWrite));
Assert.AreEqual("48", testMzMl.run.spectrumList.count);
Assert.AreEqual(48, testMzMl.run.spectrumList.spectrum.Length);
Assert.AreEqual("1", testMzMl.run.chromatogramList.count);
Assert.AreEqual(1, testMzMl.run.chromatogramList.chromatogram.Length);
}
public void TestMgf()
{
// Get temp path for writing the test MGF
var tempFilePath = Path.GetTempPath();
var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"small.RAW");
var parseInput = new ParseInput(testRawFile, tempFilePath, OutputFormat.Mgf, false, MetadataFormat.NON, false,
"coll",
"run", "sub");
RawFileParser.Parse(parseInput);
// Do this for the mzLib library issue
var tempFileName = Path.GetTempPath() + "elements.dat";
UsefulProteomicsDatabases.Loaders.LoadElements(tempFileName);
var mgfData = Mgf.LoadAllStaticData(Path.Combine(tempFilePath, "small.mgf"));
Assert.AreEqual(34, mgfData.NumSpectra);
Assert.IsEmpty(mgfData.GetMS1Scans());
}