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");
}
}
static int Main(string[] args)
{
try
{
if (args.Length < 1)
{
PrintUsage();
return(-1);
}
if (args[0].ToUpper().Equals("/X"))
{
Settings.PrintExampleSettings();
return(0);
}
if (args[0].ToUpper().Equals("/Y"))
{
Settings.PrintExampleDeconToolsFilterFile();
return(0);
}
// Uncomment this to prevent selecting text at the console from pausing program execution
//
// var handle = Process.GetCurrentProcess().MainWindowHandle;
// SetConsoleMode(handle, ENABLE_EXTENDED_FLAGS);
var assembly = Assembly.GetExecutingAssembly();
var assemblyVersion = assembly.GetName().Version.ToString();
var iniFilePath = ProcessFileLocation(args[0]);
var iniFile = new FileInfo(iniFilePath);
if (!iniFile.Exists)
{
Logger.Log("Error: Ini file not found at " + iniFilePath);
System.Threading.Thread.Sleep(1500);
return(-2);
}
var iniReader = new IniReader(iniFile.FullName);
iniReader.UpdateSettings();
Logger.Log("LCMSFeatureFinder Version " + assemblyVersion);
Logger.Log("Loading settings from INI file: " + iniFile.FullName);
Logger.Log("Data Filters - ");
Logger.Log(" Minimum LC scan = " + Settings.ScanLCMin);
Logger.Log(" Maximum LC scan = " + Settings.ScanLCMax);
Logger.Log(" Minimum IMS scan = " + Settings.ScanIMSMin);
Logger.Log(" Maximum IMS scan = " + Settings.ScanIMSMax);
if (Settings.FilterUsingHardCodedFilters)
{
Logger.Log(" Filtering using charge/abundance/fitScore/i_score table from file: " + Settings.DeconToolsFilterFileName);
}
else
{
Logger.Log(" Maximum isotopic fit score = " + Settings.FitMax);
Logger.Log(" Maximum i_score (interference score) = " + Settings.InterferenceScoreMax);
Logger.Log(" Minimum intensity = " + Settings.IntensityMin);
}
if (Settings.FilterFlaggedData)
{
Logger.Log(" Filtering out flagged data");
}
Logger.Log(" Mono mass start = " + Settings.MassMonoisotopicStart);
Logger.Log(" Mono mass end = " + Settings.MassMonoisotopicEnd);
var isosFile = GetSourceFile(Settings.InputDirectory, Settings.InputFileName);
if (!isosFile.Exists)
{
Logger.Log("Error: Isos file not found at " + isosFile.FullName);
System.Threading.Thread.Sleep(1500);
return(-3);
}
var dataType = PeekAtIsosFile(isosFile.FullName);
if (dataType < 0)
{
Logger.Log("Unknown type of Isos file. Exiting.");
System.Threading.Thread.Sleep(1500);
return(-4);
}
var uimfFile = GetSourceFile(Settings.InputDirectory, FileUtil.GetUimfFileForIsosFile(Settings.InputFileName));
if (Settings.UseConformationDetection && !uimfFile.Exists && dataType != LC_DATA)
{
Logger.Log("Error: UIMF file not found at " + uimfFile.FullName);
System.Threading.Thread.Sleep(1500);
return(-7);
}
var isosReader = new IsosReader(isosFile.FullName, Settings.OutputDirectory);
if (dataType == LC_DATA || Settings.IgnoreIMSDriftTime)
{
Logger.Log("Total number of MS Features in _isos.csv file = " + isosReader.NumOfUnfilteredMSFeatures);
Logger.Log("Total number of MS Features we'll consider = " + isosReader.MSFeatureList.Count);
Logger.Log("LC data processing is not currently implemented. Exiting...");
//RunLCMSFeatureFinder(isosReader);
Logger.Log("Aborted!");
System.Threading.Thread.Sleep(1500);
return(-5);
}
if (dataType != IMS_DATA)
{
Logger.Log("Unsupported data type. Exiting...");
Logger.Log("Aborted!");
System.Threading.Thread.Sleep(1500);
return(-6);
}
Logger.Log("Processing LC-IMS-MS Data...");
var success = RunLCIMSMSFeatureFinder(isosReader);
if (success)
{
Logger.Log("Finished!");
System.Threading.Thread.Sleep(750);
return(0);
}
Logger.Log("Processing error; check the log messages");
System.Threading.Thread.Sleep(1500);
return(-10);
}
catch (Exception ex)
{
Logger.LogError("Exception while processing", ex);
System.Threading.Thread.Sleep(1500);
return(-11);
}
finally
{
Logger.CloseLog();
}
}