Пример #1
0
        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.CreateSettings();

            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);
        }
Пример #2
0
        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.CreateSettings();

            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);
        }
Пример #3
0
        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();
        }
Пример #4
0
        public void deconToolsFiltersAreBeingReadIn_test1(string settingsFileName)
        {
            var methodName = MethodBase.GetCurrentMethod().Name;

            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();

            Assert.AreEqual(12, Settings.DeconToolsFilterList.Count);
        }
Пример #5
0
        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();
        }
Пример #6
0
        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.CreateSettings();

            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 folder 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");

            Assert.AreEqual(2046, 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");
            }
        }
Пример #7
0
        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);
                }

                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.CreateSettings();

                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 fit = " + Settings.FitMax);
                    Logger.Log(" Maximum i_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.Log("Exception while processing: " + ex.Message);
                System.Threading.Thread.Sleep(1500);
                return(-11);
            }
            finally
            {
                Logger.CloseLog();
            }
        }