public static void CalibrationTestLowRes()
{
CalibrationTask calibrationTask = new CalibrationTask();
EngineLayer.CommonParameters CommonParameters = new EngineLayer.CommonParameters
(dissociationType: MassSpectrometry.DissociationType.LowCID,
scoreCutoff: 1);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestCalibrationLow");
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\sliced_b6.mzML");
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\LowResSnip_B6_mouse_11700_117500.xml.gz");
Directory.CreateDirectory(outputFolder);
calibrationTask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, new List <string> {
myFile
}, "test");
Assert.That(File.Exists(Path.Combine(outputFolder, @"sliced_b6-calib.mzML")));
Assert.That(File.Exists(Path.Combine(outputFolder, @"sliced_b6-calib.toml")));
var lines = File.ReadAllLines(Path.Combine(outputFolder, @"sliced_b6-calib.toml"));
var tolerance = Regex.Match(lines[0], @"\d+\.\d*").Value;
var tolerance1 = Regex.Match(lines[1], @"\d+\.\d*").Value;
Assert.That(double.TryParse(tolerance, out double tol) == true);
Assert.That(double.TryParse(tolerance1, out double tol1) == true);
Assert.That(lines[0].Contains("PrecursorMassTolerance"));
Assert.That(lines[1].Contains("ProductMassTolerance"));
Directory.Delete(outputFolder, true);
Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"Task Settings"), true);
}
public static void ExperimentalDesignCalibrationTest(string originalFileName)
{
CalibrationTask calibrationTask = new CalibrationTask();
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestCalibration");
string myFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\" + originalFileName);
File.Copy(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"), myFile, true);
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta");
string experimentalDesignFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\ExperimentalDesign.tsv");
Directory.CreateDirectory(outputFolder);
using (StreamWriter output = new StreamWriter(experimentalDesignFilePath))
{
output.WriteLine("FileName\tCondition\tBiorep\tFraction\tTechrep");
output.WriteLine(Path.GetFileNameWithoutExtension(myFile) + "\t" + "condition" + "\t" + "1" + "\t" + "1" + "\t" + "1");
}
calibrationTask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, new List <string> {
myFile
}, "test");
var expDesignPath = Path.Combine(outputFolder, @"ExperimentalDesign.tsv");
var expDesign = File.ReadAllLines(expDesignPath);
string expectedCalibratedFileName = Path.GetFileNameWithoutExtension(myFile) + "-calib.mzML";
string expectedTomlName = Path.GetFileNameWithoutExtension(myFile) + "-calib.toml";
Assert.That(expDesign[1].Contains(Path.GetFileNameWithoutExtension(expectedCalibratedFileName)));
Assert.That(File.Exists(Path.Combine(outputFolder, myFile)));
Assert.That(File.Exists(Path.Combine(outputFolder, expectedTomlName)));
var lines = File.ReadAllLines(Path.Combine(outputFolder, expectedTomlName));
var tolerance = Regex.Match(lines[0], @"\d+\.\d*").Value;
var tolerance1 = Regex.Match(lines[1], @"\d+\.\d*").Value;
Assert.That(double.TryParse(tolerance, out double tol) == true);
Assert.That(double.TryParse(tolerance1, out double tol1) == true);
Assert.That(lines[0].Contains("PrecursorMassTolerance"));
Assert.That(lines[1].Contains("ProductMassTolerance"));
File.Delete(experimentalDesignFilePath);
File.Delete(myFile);
Directory.Delete(outputFolder, true);
Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"Task Settings"), true);
}
public static void ExperimentalDesignCalibrationTest(string nonCalibratedFile)
{
// set up directories
string unitTestFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"ExperimentalDesignCalibrationTest");
string outputFolder = Path.Combine(unitTestFolder, @"TaskOutput");
Directory.CreateDirectory(unitTestFolder);
Directory.CreateDirectory(outputFolder);
// set up original spectra file (input to calibration)
string nonCalibratedFilePath = Path.Combine(unitTestFolder, nonCalibratedFile);
File.Copy(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"), nonCalibratedFilePath, true);
// protein db
string myDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta");
// set up original experimental design (input to calibration)
SpectraFileInfo fileInfo = new SpectraFileInfo(nonCalibratedFilePath, "condition", 0, 0, 0);
var experimentalDesignFilePath = ExperimentalDesign.WriteExperimentalDesignToFile(new List <SpectraFileInfo> {
fileInfo
});
// run calibration
CalibrationTask calibrationTask = new CalibrationTask();
calibrationTask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(myDatabase, false)
}, new List <string> {
nonCalibratedFilePath
}, "test");
// test new experimental design written by calibration
var newExpDesignPath = Path.Combine(outputFolder, @"ExperimentalDesign.tsv");
string expectedCalibratedFileName = Path.GetFileNameWithoutExtension(nonCalibratedFilePath) + "-calib.mzML";
var expectedCalibratedFilePath = Path.Combine(outputFolder, expectedCalibratedFileName);
var newExperDesign = ExperimentalDesign.ReadExperimentalDesign(newExpDesignPath, new List <string> {
expectedCalibratedFilePath
}, out var errors);
Assert.That(!errors.Any());
Assert.That(newExperDesign.Count == 1);
// test file-specific toml written by calibration w/ suggested ppm tolerances
string expectedTomlName = Path.GetFileNameWithoutExtension(nonCalibratedFilePath) + "-calib.toml";
Assert.That(File.Exists(Path.Combine(outputFolder, expectedTomlName)));
var lines = File.ReadAllLines(Path.Combine(outputFolder, expectedTomlName));
var tolerance = Regex.Match(lines[0], @"\d+\.\d*").Value;
var tolerance1 = Regex.Match(lines[1], @"\d+\.\d*").Value;
Assert.That(double.TryParse(tolerance, out double tol) == true);
Assert.That(double.TryParse(tolerance1, out double tol1) == true);
Assert.That(lines[0].Contains("PrecursorMassTolerance"));
Assert.That(lines[1].Contains("ProductMassTolerance"));
// check that calibrated .mzML exists
Assert.That(File.Exists(Path.Combine(outputFolder, expectedCalibratedFilePath)));
// clean up
Directory.Delete(unitTestFolder, true);
}
