public void WorkflowTesting2_SumLC5()
{
var localTestFile =
@"C:\Users\d3x720\Documents\Data\QCShew\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var parameters = new DeconToolsParameters();
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 6012;
parameters.MSGeneratorParameters.MaxLCScan = 6019;
parameters.MSGeneratorParameters.SumSpectraAcrossLC = true;
parameters.MSGeneratorParameters.NumLCScansToSum = 5;
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 1.3;
parameters.PeakDetectorParameters.SignalToNoiseThreshold = 2;
parameters.PeakDetectorParameters.IsDataThresholded = true;
parameters.ThrashParameters.MinIntensityForScore = 1;
parameters.ThrashParameters.MinMSFeatureToBackgroundRatio = 1;
var run = new RunFactory().CreateRun(localTestFile);
var workflow = new DeconMSnWorkflow(parameters, run);
workflow.Execute();
}
public void LowIntensityButGoodFeatureTest1()
{
var rawDataFile = @"D:\Data\DeconMSn_testing\QC_Shew_13_01_pt5_b_23Jan13_Cougar_12-02-27.raw";
var parameters = new DeconToolsParameters();
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 20593;
parameters.MSGeneratorParameters.MaxLCScan = 20598;
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 1.3;
parameters.PeakDetectorParameters.SignalToNoiseThreshold = 2;
parameters.PeakDetectorParameters.IsDataThresholded = true;
parameters.ThrashParameters.MinIntensityForScore = 1;
parameters.ThrashParameters.MinMSFeatureToBackgroundRatio = 1;
var run = new RunFactory().CreateRun(rawDataFile);
var workflow = new DeconMSnWorkflow(parameters, run);
workflow.NumMaxAttemptsAtLowIntensitySpecies = 4;
workflow.Execute();
}
public void WorkflowTest1()
{
var parameters = new DeconToolsParameters();
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 6005;
parameters.MSGeneratorParameters.MaxLCScan = 6012;
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 1.3;
parameters.PeakDetectorParameters.SignalToNoiseThreshold = 2;
parameters.PeakDetectorParameters.IsDataThresholded = true;
parameters.ThrashParameters.MinIntensityForScore = 1;
parameters.ThrashParameters.MinMSFeatureToBackgroundRatio = 1;
var run = new RunFactory().CreateRun(testFile1);
var expectedResultsFile1 = Path.Combine(run.DataSetPath, run.DatasetName + ".mgf");
var expectedResultsFile2 = Path.Combine(run.DataSetPath, run.DatasetName + "_DeconMSn_log.txt");
var expectedResultsFile3 = Path.Combine(run.DataSetPath, run.DatasetName + "_profile.txt");
if (File.Exists(expectedResultsFile1))
{
File.Delete(expectedResultsFile1);
}
if (File.Exists(expectedResultsFile2))
{
File.Delete(expectedResultsFile2);
}
if (File.Exists(expectedResultsFile3))
{
File.Delete(expectedResultsFile3);
}
var workflow = new DeconMSnWorkflow(parameters, run);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedResultsFile1));
Assert.IsTrue(File.Exists(expectedResultsFile2));
Assert.IsTrue(File.Exists(expectedResultsFile3));
}