public void traditionalMSFeatureDataProcessingTest1()
{
var sourceIsosFile =
@"\\protoapps\UserData\Slysz\Data\Redmine_Issues\Issue947_saturationTesting\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31_mass860_noRepair_isos.csv";
var copiedIsosFileName = @"\\protoapps\UserData\Slysz\Data\Redmine_Issues\Issue947_saturationTesting\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31_isos.csv";
File.Copy(sourceIsosFile, copiedIsosFileName, true);
var testFile =
@"\\protoapps\UserData\Slysz\Data\Redmine_Issues\Issue947_saturationTesting\FF_IMS4Filters_NoFlags_20ppm_Min3Pts_4MaxLCGap_NoDaCorr_ConfDtn_2011-05-16_issue947.ini";
var iniReader = new IniReader(testFile);
iniReader.UpdateSettings();
var isosReader = new IsosReader(Settings.InputFileName, Settings.OutputDirectory);
var controller = new LCIMSMSFeatureFinderController(isosReader);
controller.Execute();
Assert.AreEqual(2, controller.LcImsMsFeatures.Count());
var testFeature1 = (from n in controller.LcImsMsFeatures where n.Charge == 2 select n).FirstOrDefault();
Assert.IsNotNull(testFeature1);
DisplayFeatureStats(testFeature1);
}
public void nonSaturatedLowIntensityProcessingTest1()
{
var sourceIsosFile =
@"\\protoapps\UserData\Slysz\Data\Redmine_Issues\Issue947_saturationTesting\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31_lowIntensityCase860_repaired_isos.csv";
var copiedIsosFileName = @"\\protoapps\UserData\Slysz\Data\Redmine_Issues\Issue947_saturationTesting\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31_isos.csv";
File.Copy(sourceIsosFile, copiedIsosFileName, true);
var testFile =
@"\\protoapps\UserData\Slysz\Data\Redmine_Issues\Issue947_saturationTesting\FF_IMS4Filters_NoFlags_20ppm_Min3Pts_4MaxLCGap_NoDaCorr_ConfDtn_2011-05-16_issue947.ini";
var iniReader = new IniReader(testFile);
iniReader.UpdateSettings();
var isosReader = new IsosReader(Settings.InputFileName, Settings.OutputDirectory);
var controller = new LCIMSMSFeatureFinderController(isosReader);
controller.Execute();
Assert.AreEqual(2, controller.LcImsMsFeatures.Count());
var testFeature1 = controller.LcImsMsFeatures.ElementAt(1);
Assert.IsNotNull(testFeature1);
Assert.AreEqual(20, testFeature1.GetMemberCount());
Assert.AreEqual(0, testFeature1.GetSaturatedMemberCount());
DisplayFeatureStats(testFeature1);
}
public void standardFile_conformationDetection_test1()
{
var testfile = @"\\protoapps\UserData\Slysz\Standard_Testing\LCMSFeatureFinder\UIMF\Parameter_Files\FF_IMS_UseHardCodedFilters_NoFlags_20ppm_Min3Pts_4MaxLCGap_NoDaCorr_ConfDtn_2011-03-21.ini";
var iniReader = new IniReader(testfile);
iniReader.CreateSettings();
var isosReader = new IsosReader(Settings.InputFileName, Settings.OutputDirectory);
var controller = new LCIMSMSFeatureFinderController(isosReader);
controller.Execute();
}
/// <summary>
/// Runs the necessary steps for LC-IMS-MS Feature Finding.
/// </summary>
/// <param name="isosReader">The IsosReader object</param>
private static bool RunLCIMSMSFeatureFinder(IsosReader isosReader)
{
try
{
var controller = new LCIMSMSFeatureFinderController(isosReader);
controller.Execute();
return(true);
}
catch (Exception ex)
{
Logger.LogError("Exception in RunLCIMSMSFeatureFinder", ex);
return(false);
}
}
/// <summary>
/// Runs the necessary steps for LC-IMS-MS Feature Finding.
/// </summary>
/// <param name="isosReader">The IsosReader object</param>
private static bool RunLCIMSMSFeatureFinder(IsosReader isosReader)
{
try
{
var controller = new LCIMSMSFeatureFinderController(isosReader);
controller.Execute();
return(true);
}
catch (Exception e)
{
Logger.Log(e.Message);
Logger.Log(e.StackTrace);
return(false);
}
}
public void deconToolsfiltersAreBeingAppliedTest(string settingsFileName)
{
var methodName = MethodBase.GetCurrentMethod().Name;
// FF_IMS4Filters_NoFlags_20ppm_Min3Pts_4MaxLCGap_NoDaCorr_ConfDtn_2011-05-16.ini references
// Sarc_MS2_90_6Apr11_Cheetah_11-02-19_inverse_isos.csv and DeconToolsIsosFilters_IMS4_2011-04-28.txt in folder
// \\proto-2\UnitTest_Files\DeconTools_TestFiles\LCMSFeatureFinder
var iniFile = Test.GetTestFile(methodName, settingsFileName);
if (!iniFile.Exists)
{
Assert.Ignore("Skipping test " + methodName + " since file not found: " + iniFile.FullName);
}
Console.WriteLine("Reading settings in " + iniFile.FullName);
var iniReader = new IniReader(iniFile.FullName);
iniReader.CreateSettings();
if (string.IsNullOrWhiteSpace(Settings.InputDirectory) && iniFile.Directory != null)
{
Settings.InputDirectory = iniFile.Directory.FullName;
}
var isosFilePath = Path.Combine(Settings.InputDirectory, Settings.InputFileName);
var isosFile = new FileInfo(isosFilePath);
if (!isosFile.Exists)
{
Assert.Ignore("Skipping test " + methodName + " since file not found: " + isosFile.FullName);
}
var isosReader = new IsosReader(isosFilePath, Settings.OutputDirectory);
var controller = new LCIMSMSFeatureFinderController(isosReader);
controller.Execute();
}
public void RunFeatureFinder(string settingsFileName)
{
var methodName = MethodBase.GetCurrentMethod().Name;
// This Ini file references file Sarc_MS2_90_6Apr11_Cheetah_11-02-19_Excerpt_isos.csv
var iniFile = GetTestFile(methodName, settingsFileName);
if (!iniFile.Exists)
{
Assert.Ignore("Skipping test " + methodName + " since file not found: " + iniFile.FullName);
}
Console.WriteLine("Reading settings in " + iniFile.FullName);
var iniReader = new IniReader(iniFile.FullName);
iniReader.UpdateSettings();
if (string.IsNullOrWhiteSpace(Settings.InputDirectory) && iniFile.Directory != null)
{
Settings.InputDirectory = iniFile.Directory.FullName;
}
if (!string.IsNullOrWhiteSpace(Settings.DeconToolsFilterFileName) && !File.Exists(Settings.DeconToolsFilterFileName) && iniFile.Directory != null)
{
var updatedPath = Path.Combine(iniFile.Directory.FullName, Path.GetFileName(Settings.DeconToolsFilterFileName));
Settings.DeconToolsFilterFileName = updatedPath;
}
var isosFilePath = Path.Combine(Settings.InputDirectory, Settings.InputFileName);
var isosFile = new FileInfo(isosFilePath);
if (!isosFile.Exists)
{
Assert.Ignore("Skipping test " + methodName + " since file not found: " + isosFile.FullName);
}
if (isosFile.Directory == null)
{
Assert.Ignore("Skipping test " + methodName + " since cannot determine the parent directory of: " + isosFile.FullName);
}
Console.WriteLine("Processing " + isosFile.FullName);
if (string.IsNullOrWhiteSpace(Settings.OutputDirectory))
{
Settings.OutputDirectory = isosFile.Directory.FullName;
}
Console.WriteLine("Writing results to " + Settings.OutputDirectory);
var isosReader = new IsosReader(isosFile.FullName, Settings.OutputDirectory);
var featuresFilePath = Path.Combine(Settings.OutputDirectory, isosFile.Name.Replace("_isos.csv", "_LCMSFeatures.txt"));
var filteredIsosFilePath = Path.Combine(Settings.OutputDirectory, isosFile.Name.Replace("_isos.csv", "_Filtered_isos.csv"));
var featuresFile = new FileInfo(featuresFilePath);
var filteredIsos = new FileInfo(filteredIsosFilePath);
if (!featuresFile.Exists)
{
featuresFile.Delete();
}
if (!filteredIsos.Exists)
{
filteredIsos.Delete();
}
var controller = new LCIMSMSFeatureFinderController(isosReader);
controller.Execute();
featuresFile.Refresh();
filteredIsos.Refresh();
if (!featuresFile.Exists)
{
Assert.Fail("LCMSFeatures file not found at " + featuresFile.FullName);
}
if (!filteredIsos.Exists)
{
Assert.Fail("_Filtered_isos.csv file not found at " + filteredIsos.FullName);
}
var lcmsFeatureCount = 0;
var filteredIsosCount = 0;
var lcmsFeaturesHeaderLine = string.Empty;
var filteredIsosHeaderLine = string.Empty;
using (var featuresFileReader = new StreamReader(new FileStream(featuresFile.FullName, FileMode.Open, FileAccess.Read, FileShare.ReadWrite)))
{
if (!featuresFileReader.EndOfStream)
{
lcmsFeaturesHeaderLine = featuresFileReader.ReadLine();
}
while (!featuresFileReader.EndOfStream)
{
var dataLine = featuresFileReader.ReadLine();
if (string.IsNullOrWhiteSpace(dataLine))
{
continue;
}
lcmsFeatureCount++;
}
Console.WriteLine("{0} data lines in {1}", lcmsFeatureCount, featuresFile.Name);
}
using (var filteredIsosReader = new StreamReader(new FileStream(filteredIsos.FullName, FileMode.Open, FileAccess.Read, FileShare.ReadWrite)))
{
if (!filteredIsosReader.EndOfStream)
{
filteredIsosHeaderLine = filteredIsosReader.ReadLine();
}
while (!filteredIsosReader.EndOfStream)
{
var dataLine = filteredIsosReader.ReadLine();
if (string.IsNullOrWhiteSpace(dataLine))
{
continue;
}
filteredIsosCount++;
}
Console.WriteLine("{0} data lines in {1}", filteredIsosCount, filteredIsos.Name);
}
Assert.AreEqual(lcmsFeatureCount, filteredIsosCount, "Mismatch between number of LC-IMS-MS features and Filtered_Isos data points");
// Old value: 2046
// Value in March 2020: 2204
Assert.AreEqual(2204, lcmsFeatureCount, "Unexpected number of LC-IMS-features");
if (lcmsFeaturesHeaderLine == null || !lcmsFeaturesHeaderLine.StartsWith("Feature_Index"))
{
Assert.Fail("LCMSFeatures file header line does not start with Feature_Index");
}
if (filteredIsosHeaderLine == null || !filteredIsosHeaderLine.StartsWith("msfeature_id"))
{
Assert.Fail("LCMSFeatures file header line does not start with msfeature_id");
}
}
