public void importPartialUIMFData_test1()
{
var startFrame = 801;
var stopFrame = 801;
var testMSFeatureFile = FileRefs.RawDataBasePath + @"\Output\35min_QC_Shew_Formic_4T_1.8_500_20_30ms_fr1950_0000_Frames800_802_isos.csv";
var importer = new IsosImporter(testMSFeatureFile, Backend.Globals.MSFileType.PNNL_UIMF, startFrame, stopFrame);
var results = new List <IsosResult>();
results = importer.Import();
Assert.AreEqual(1533, results.Count);
var testResult = (UIMFIsosResult)results[0];
Assert.AreEqual(801, testResult.ScanSet.PrimaryScanNumber);
Assert.AreEqual(208, testResult.IMSScanSet.PrimaryScanNumber);
Assert.AreEqual(2, testResult.IsotopicProfile.ChargeState);
Assert.AreEqual(2135, testResult.IntensityAggregate);
Assert.AreEqual(402.220489501953m, (decimal)testResult.IsotopicProfile.GetMZ());
Assert.AreEqual(0.0619m, (decimal)testResult.IsotopicProfile.Score);
Assert.AreEqual(0.38938m, (decimal)testResult.InterferenceScore);
TestUtilities.DisplayMSFeatures(results);
}
public void outputToText_xcaliburData_Test1()
{
var exportedFile = exportedMSFeaturesToTextFileFromOrbitrapFile1;
if (File.Exists(exportedFile))
{
File.Delete(exportedFile);
}
//create run and get some results
var run = TestDataCreationUtilities.CreateResultsFromThreeScansOfStandardOrbitrapData();
var isosExporter = new DeconTools.Backend.FileIO.MSFeatureToTextFileExporterBasic(exportedFile);
isosExporter.ExportResults(run.ResultCollection.ResultList);
Assert.AreEqual(true, File.Exists(exportedFile));
var importer = new IsosImporter(exportedFile, run.MSFileType);
var results = importer.Import();
Assert.IsTrue(results != null);
Assert.IsTrue(results.Count > 300);
//TODO: need to check if '388' is good or not
//Assert.AreEqual(388, results.Count);
}
public void TraditionalWorkflowTestOrbitrapData_useThrashV1_test2()
{
var parameterFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\LTQ_Orb\LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_Thrash_scan6000_9000 - oldThrash.xml";
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv");
var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv");
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedIsosFile))
{
File.Delete(expectedIsosFile);
}
if (File.Exists(expectedScansFile))
{
File.Delete(expectedScansFile);
}
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(parameterFile);
//parameters.MSGeneratorParameters.MinLCScan = 6005;
//parameters.MSGeneratorParameters.MaxLCScan = 6005;
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created.");
Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created.");
Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created.");
var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType);
var isos = isosImporter.Import();
Assert.AreEqual(186, isos.Count);
var peakImporter = new PeakImporterFromText(expectedPeaksFile);
var peaklist = new List <MSPeakResult>();
peakImporter.ImportPeaks(peaklist);
Assert.AreEqual(809, peaklist.Count);
var sumIntensities = isos.Select(p => p.IntensityAggregate).Sum();
//Assert.AreEqual(263499300d, Math.Round(sumIntensities));
var sumPeakIntensities = peaklist.Select(p => p.Height).Sum();
//Assert.AreEqual(605170496.0f, sumPeakIntensities);
}
public void ProcessOrbitrapData1()
{
var testFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile;
var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv");
var expectedPeaksFileOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_peaks.txt");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
if (File.Exists(expectedPeaksFileOutput))
{
File.Delete(expectedPeaksFileOutput);
}
var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile);
var stopwatch = new Stopwatch();
stopwatch.Start();
workflow.Execute();
stopwatch.Stop();
var typicalTimeInSeconds = 11.0;
var currentTimeInSeconds = Math.Round(stopwatch.ElapsedMilliseconds / (double)1000, 1);
Console.WriteLine("Typical processing time (sec)= " + typicalTimeInSeconds);
Console.WriteLine("Current Processing time (sec) = " + currentTimeInSeconds);
var percentDiff = (currentTimeInSeconds - typicalTimeInSeconds) / typicalTimeInSeconds * 100;
Assert.IsTrue(percentDiff < 20, "Processing failed time test. Too slow.");
Assert.That(File.Exists(expectedIsosOutput));
Assert.That(File.Exists(expectedPeaksFileOutput));
Console.WriteLine(percentDiff);
var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.Finnigan);
var results = new List <IsosResult>();
results = importer.Import();
//TestUtilities.DisplayMSFeatures(results);
//Assert.AreEqual(1340, results.Count);
//Assert.AreEqual(2006580356, results.Sum(p => p.IntensityAggregate));
}
private List <IsosResult> readInIsos(string canonIsosFilename, DeconTools.Backend.Globals.MSFileType filetype)
{
List <IsosResult> results = new List <IsosResult>();
IsosImporter importer = new IsosImporter(canonIsosFilename, filetype);
importer.Import(results);
return(results);
}
public void NegativeIonModeDeisotoping_useThrashV1()
{
var parameterFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\LTQ_Orb\LTQ_Orb_SN2_PeakBR2_PeptideBR1_NegIon_Thrash_Sum3.xml";
var testFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\NegativeIonMode\AC2_Neg_highpH_14Apr13_Sauron_13-04-03.raw";
var run = new RunFactory().CreateRun(testFile);
var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv");
var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv");
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedIsosFile))
{
File.Delete(expectedIsosFile);
}
if (File.Exists(expectedScansFile))
{
File.Delete(expectedScansFile);
}
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(parameterFile);
parameters.ScanBasedWorkflowParameters.DeconvolutionType = Globals.DeconvolutionType.ThrashV1;
parameters.MSGeneratorParameters.MinLCScan = 4100;
parameters.MSGeneratorParameters.MaxLCScan = 4100;
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created.");
Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created.");
Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created.");
var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType);
var isos = isosImporter.Import();
var testIso =
(from n in isos where n.IsotopicProfile.MonoPeakMZ > 744 && n.IsotopicProfile.MonoPeakMZ < 749 select n).FirstOrDefault();
Assert.IsNotNull(testIso, "Test iso not found.");
Console.WriteLine("monomass= " + testIso.IsotopicProfile.MonoIsotopicMass);
Assert.AreEqual(1491.32852m, (decimal)Math.Round(testIso.IsotopicProfile.MonoIsotopicMass, 5));
}
public void TraditionalWorkflowTestOrbitrapData_usingNewThrash()
{
var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile;
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv");
var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv");
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedIsosFile))
{
File.Delete(expectedIsosFile);
}
if (File.Exists(expectedScansFile))
{
File.Delete(expectedScansFile);
}
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var allPeaksFilepath = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_peaksFULL.txt";
File.Copy(allPeaksFilepath, allPeaksFilepath.Replace("FULL", ""));
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(parameterFile);
parameters.ScanBasedWorkflowParameters.DeconvolutionType = Globals.DeconvolutionType.ThrashV2;
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 6000; // run.GetMinPossibleLCScanNum();
parameters.MSGeneratorParameters.MaxLCScan = 6050; // run.GetMaxPossibleLCScanNum();
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created.");
Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created.");
Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created.");
var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType);
var isos = isosImporter.Import();
//Assert.AreEqual(186, isos.Count);
//TODO: still report
Console.WriteLine("Num MSfeatures = " + isos.Count);
var sumIntensities = isos.Select(p => p.IntensityAggregate).Sum();
// Assert.AreEqual(266185816d, Math.Round(sumIntensities));
}
public void TraditionalWorkflowTestOrbitrapData_DetectPeaksOnly()
{
var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile;
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv");
var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv");
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedIsosFile))
{
File.Delete(expectedIsosFile);
}
if (File.Exists(expectedScansFile))
{
File.Delete(expectedScansFile);
}
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(parameterFile);
parameters.ScanBasedWorkflowParameters.DeconvolutionType = Globals.DeconvolutionType.None;
parameters.MSGeneratorParameters.MinLCScan = 6005;
parameters.MSGeneratorParameters.MaxLCScan = 6005;
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created.");
Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created.");
Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created.");
var peakImporter = new PeakImporterFromText(expectedPeaksFile);
var peaklist = new List <MSPeakResult>();
peakImporter.ImportPeaks(peaklist);
Assert.AreEqual(809, peaklist.Count);
var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType);
var isos = isosImporter.Import();
Assert.AreEqual(0, isos.Count);
}
public void xcaliburResultsTest1()
{
List <IsosResult> results = new List <IsosResult>();
IsosImporter importer = new IsosImporter(xcaliburIsosResults1, DeconTools.Backend.Globals.MSFileType.Finnigan);
importer.Import(results);
List <IsosResult> flaggedResults = (from n in results where n.Flags.Count > 0 select n).ToList();
Assert.AreEqual(119, flaggedResults.Count);
}
public void uimfResultsTest1()
{
List <IsosResult> results = new List <IsosResult>();
IsosImporter importer = new IsosImporter(uimfIsosResults1, DeconTools.Backend.Globals.MSFileType.PNNL_UIMF);
importer.Import(results);
List <IsosResult> flaggedResults = (from n in results where n.Flags.Count > 0 select n).ToList();
Assert.AreEqual(3177, results.Count);
Assert.AreEqual(1253, flaggedResults.Count);
}
public void processOrbitrapData_outputMS2_and_peaks_test1()
{
var testFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var parameterFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\LTQ_Orb\LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_Thrash_scans6000_6050_MS2.xml";
var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv");
var expectedScansOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_scans.csv");
var expectedPeaksFileOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_peaks.txt");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
if (File.Exists(expectedScansOutput))
{
File.Delete(expectedScansOutput);
}
if (File.Exists(expectedPeaksFileOutput))
{
File.Delete(expectedPeaksFileOutput);
}
var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile);
workflow.Execute();
Assert.That(File.Exists(expectedIsosOutput));
Assert.That(File.Exists(expectedScansOutput));
Assert.That(File.Exists(expectedPeaksFileOutput));
var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.Finnigan);
var results = new List <IsosResult>();
results = importer.Import();
// TestUtilities.DisplayMSFeatures(results);
//Assert.AreEqual(1340, results.Count);
//Assert.AreEqual(2006580356, results.Sum(p => p.IntensityAggregate));
}
public void TraditionalWorkflowTestOrbitrapData_InformedThrash()
{
var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile;
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv");
var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv");
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedIsosFile))
{
File.Delete(expectedIsosFile);
}
if (File.Exists(expectedScansFile))
{
File.Delete(expectedScansFile);
}
//if (File.Exists(expectedPeaksFile)) File.Delete(expectedPeaksFile);
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(parameterFile);
parameters.ScanBasedWorkflowParameters.DeconvolutionType = Globals.DeconvolutionType.ThrashV2;
parameters.MSGeneratorParameters.MinLCScan = 6005;
parameters.MSGeneratorParameters.MaxLCScan = 6050;
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created.");
Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created.");
Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created.");
var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType);
var isos = isosImporter.Import();
Assert.AreEqual(1287, isos.Count);
var sumIntensities = isos.Select(p => p.IntensityAggregate).Sum();
Assert.AreEqual(1974438598m, (decimal)Math.Round(sumIntensities));
// Expected: 1973657234m
// But was: 1974438598m
}
public void CompareOldAndNew2()
{
var newResultsFile =
@"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\Standard_Testing\DeconTools\Orbitrap\Test_Results\Version_1.0.XX_Jan6_AfterThrashRefining\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_isos.csv";
var oldResultsFile =
@"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\Standard_Testing\DeconTools\Orbitrap\Test_Results\Version_1.0.4745_Dec28_AfterThrashRefactor\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_isos.csv";
var importer = new IsosImporter(newResultsFile, Globals.MSFileType.Finnigan);
var newResults = importer.Import();
importer = new IsosImporter(oldResultsFile, Globals.MSFileType.Finnigan);
var oldResults = importer.Import();
//newResults = newResults.Where(p => p.ScanSet.PrimaryScanNumber == 6005).ToList();
//oldResults = oldResults.Where(p => p.ScanSet.PrimaryScanNumber == 6005).ToList();
var sharedIsos = new List <IsosResult>();
var uniqueToNew = new List <IsosResult>();
var uniqueToOld = new List <IsosResult>();
GetComparisons(newResults, oldResults, sharedIsos, uniqueToNew, uniqueToOld);
Console.WriteLine("Summary----------------------------");
Console.WriteLine("Shared =\t" + sharedIsos.Count);
Console.WriteLine("Unique to new =\t" + uniqueToNew.Count);
Console.WriteLine("Unique to old =\t" + uniqueToOld.Count);
Console.WriteLine("\n--------------Common to new and Old ------------------");
TestUtilities.DisplayMSFeatures(sharedIsos);
Console.WriteLine("\n--------------Unique to new ------------------");
TestUtilities.DisplayMSFeatures(uniqueToNew);
var outputFilename = @"D:\temp\exportedIsos.csv";
var exporter = IsosExporterFactory.CreateIsosExporter(Globals.ResultType.BASIC_TRADITIONAL_RESULT, Globals.ExporterType.Text, outputFilename);
exporter.ExportIsosResults(uniqueToNew);
Console.WriteLine("\n--------------Unique to old ------------------");
TestUtilities.DisplayMSFeatures(uniqueToOld);
}
public void processUIMFContainingMSMS()
{
var testFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\MSMS_Testing\PepMix_MSMS_4msSA.UIMF";
var run = new RunFactory().CreateRun(testFile);
var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
var parameters = new DeconToolsParameters();
parameters.MSGeneratorParameters.NumLCScansToSum = 3;
parameters.MSGeneratorParameters.NumImsScansToSum = 9;
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 4;
parameters.MiscMSProcessingParameters.UseZeroFilling = true;
parameters.ScanBasedWorkflowParameters.ProcessMS2 = true;
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.SumSpectraAcrossLC = true;
parameters.MSGeneratorParameters.MinLCScan = 1; //min frame
parameters.MSGeneratorParameters.MaxLCScan = 15; //max frame
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.Execute();
var results = new List <IsosResult>();
Assert.That(File.Exists(expectedIsosOutput));
var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.PNNL_UIMF);
results = importer.Import();
//TestUtilities.DisplayMSFeatures(results);
//Assert.AreEqual(36078, results.Count);
//Assert.AreEqual(1224247916, (int)results.Sum(p => p.IntensityAggregate));
}
public void importOrbitrapData_test1()
{
var testMSFeatureFile = FileRefs.RawDataBasePath + @"\Output\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_Scans6000_6050_isos.csv";
var importer = new IsosImporter(testMSFeatureFile, Backend.Globals.MSFileType.Finnigan);
var results = new List <IsosResult>();
results = importer.Import();
Assert.AreEqual(1340, results.Count);
var testResult = results[0];
Assert.AreEqual(6005, testResult.ScanSet.PrimaryScanNumber);
Assert.AreEqual(2, testResult.IsotopicProfile.ChargeState);
Assert.AreEqual(13084442, testResult.IntensityAggregate);
Assert.AreEqual(481.274108886719m, (decimal)testResult.IsotopicProfile.GetMZ());
Assert.AreEqual(0.0101m, (decimal)testResult.IsotopicProfile.Score);
Assert.AreEqual(0.10352m, (decimal)testResult.InterferenceScore);
}
public void LoadResults(string isosTextFile, Globals.MSFileType fileType, int minVal, int maxVal)
{
var fileExists = false;
try
{
fileExists = File.Exists(isosTextFile);
}
catch (Exception)
{
// Ignore exceptions
}
Check.Require(fileExists, "IsosResultUtilities cannot open input file");
var importer = new IsosImporter(isosTextFile, fileType, minVal, maxVal);
var isosResults = importer.Import();
Results = isosResults;
}
public void ProcessMZ5File()
{
var testFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\mzXML\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.mz5";
var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile;
var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv");
var expectedPeaksFileOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_peaks.txt");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
if (File.Exists(expectedPeaksFileOutput))
{
File.Delete(expectedPeaksFileOutput);
}
var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile);
workflow.Execute();
Assert.That(File.Exists(expectedIsosOutput));
Assert.That(File.Exists(expectedPeaksFileOutput));
var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.Finnigan);
var results = new List <IsosResult>();
results = importer.Import();
TestUtilities.DisplayMSFeatures(results);
Assert.AreEqual(1340, results.Count);
Assert.AreEqual(2006580356, results.Sum(p => p.IntensityAggregate));
}
public void LoadResults(string isosTextFile, Globals.MSFileType fileType)
{
var fileExists = false;
try
{
fileExists = System.IO.File.Exists(isosTextFile);
}
catch (Exception)
{
}
Check.Require(fileExists, "IsosResultUtilities cannot open input file");
var isosResults = new List <IsosResult>();
var importer = new IsosImporter(isosTextFile, fileType);
isosResults = importer.Import();
this.results = isosResults;
}
public void importUIMFData_test1()
{
var testMSFeatureFile = FileRefs.RawDataBasePath + @"\Output\35min_QC_Shew_Formic_4T_1.8_500_20_30ms_fr1950_0000_Frames800_802_isos.csv";
var importer = new IsosImporter(testMSFeatureFile, Backend.Globals.MSFileType.PNNL_UIMF);
var results = new List <IsosResult>();
results = importer.Import();
Assert.AreEqual(4709, results.Count);
var testResult = (UIMFIsosResult)results[0];
Assert.AreEqual(800, testResult.ScanSet.PrimaryScanNumber);
Assert.AreEqual(207, testResult.IMSScanSet.PrimaryScanNumber);
Assert.AreEqual(2, testResult.IsotopicProfile.ChargeState);
Assert.AreEqual(1318, testResult.IntensityAggregate);
Assert.AreEqual(402.731689453125m, (decimal)testResult.IsotopicProfile.GetMZ());
Assert.AreEqual(0.0735m, (decimal)testResult.IsotopicProfile.Score);
Assert.AreEqual(0.66701m, (decimal)testResult.InterferenceScore);
}
public void processUIMF_Frames800_802_SumAllIMSScansPerFrame()
{
var testFile = FileRefs.RawDataMSFiles.UIMFStdFile3;
var parameterFile = Path.Combine(FileRefs.RawDataBasePath, "ParameterFiles", "UIMF_frames_peakBR7_800-802_OneSpectrumPerFrame.xml");
var run = new RunFactory().CreateRun(testFile);
var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
var parameters = new DeconToolsParameters();
parameters.MSGeneratorParameters.MinLCScan = 800;
parameters.MSGeneratorParameters.MaxLCScan = 802;
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.SumAllSpectra = true;
parameters.MiscMSProcessingParameters.UseZeroFilling = true;
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.Execute();
var results = new List <IsosResult>();
Assert.That(File.Exists(expectedIsosOutput));
var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.PNNL_UIMF);
results = importer.Import();
//TestUtilities.DisplayMSFeatures(results);
//Assert.AreEqual(189, results.Count);
//Assert.AreEqual(62294623, (int)results.Sum(p => p.IntensityAggregate));
}
public void ProcessAgilentCentroidedFile()
{
var testFile =
@"\\protoapps\UserData\Nikola\DDD_Milk\D6.1.forExpRepAnal_3.14.2012.d";
var parameterFile = @"\\protoapps\UserData\Nikola\DDD_Milk\agilTOF_Normal_SavGolSmooth_2007-08-16_DEFAULT.xml";
var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile);
workflow.Execute();
//return;
string expectedIsosOutput = null;
var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.Finnigan);
var results = new List <IsosResult>();
results = importer.Import();
TestUtilities.DisplayMSFeatures(results);
Assert.AreEqual(1340, results.Count);
Assert.AreEqual(2006580356, results.Sum(p => p.IsotopicProfile.IntensityMostAbundant));
}
public void processUIMF_demultiplexedUIMF()
{
var testFile = FileRefs.RawDataMSFiles.UIMFStdFile3;
//string parameterFile = Path.Combine(FileRefs.RawDataBasePath, "ParameterFiles", "IMS_UIMF_PeakBR4_PeptideBR4_SN3_SumScans3_NoLCSum_Frame_500-501.xml");
var parameterFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\IMS\IMS_UIMF_PeakBR4_PeptideBR4_SN3_SumScans3_NoLCSum_Frame_500-501.xml";
var expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv");
var expectedScansOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_scans.csv");
var expectedPeaksOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_peaks.txt");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
if (File.Exists(expectedScansOutput))
{
File.Delete(expectedScansOutput);
}
if (File.Exists(expectedPeaksOutput))
{
File.Delete(expectedPeaksOutput);
}
var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile);
workflow.NewDeconToolsParameters.ScanBasedWorkflowParameters.ExportPeakData = true;
workflow.Execute();
var results = new List <IsosResult>();
Assert.That(File.Exists(expectedIsosOutput));
Assert.That(File.Exists(expectedScansOutput));
Assert.That(File.Exists(expectedPeaksOutput));
var importer = new IsosImporter(expectedIsosOutput, Globals.MSFileType.PNNL_UIMF);
results = importer.Import();
var scansFileLineCounter = 0;
using (var sr = new StreamReader(expectedScansOutput))
{
sr.ReadLine();
while (sr.Peek() != -1)
{
sr.ReadLine();
scansFileLineCounter++;
}
}
Assert.AreEqual(2, scansFileLineCounter);
// Assert.AreEqual(1573, results.Count);
Assert.IsTrue(results.Sum(p => p.IntensityAggregate) > 1e6);
//Assert.AreEqual(109217766, results.Sum(p => p.IntensityAggregate));
var testResult1 = results[0] as UIMFIsosResult;
//Assert.AreEqual(9.476, (decimal)testResult1.DriftTime);
}
public void TraditionalWorkflowTestOrbitrapData1()
{
var parameterFile = FileRefs.ParameterFiles.Orbitrap_Scans6000_6050ParamFile;
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv");
var expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv");
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedIsosFile))
{
File.Delete(expectedIsosFile);
}
if (File.Exists(expectedScansFile))
{
File.Delete(expectedScansFile);
}
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(parameterFile);
parameters.ScanBasedWorkflowParameters.DeconvolutionType = Globals.DeconvolutionType.ThrashV1;
parameters.MSGeneratorParameters.MinLCScan = 6005;
parameters.MSGeneratorParameters.MaxLCScan = 6005;
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedIsosFile), "Isos file was not created.");
Assert.IsTrue(File.Exists(expectedScansFile), "Scans file was not created.");
Assert.IsTrue(File.Exists(expectedPeaksFile), "Peaks file was not created.");
var isosImporter = new IsosImporter(expectedIsosFile, run.MSFileType);
var isos = isosImporter.Import();
Assert.AreEqual(186, isos.Count);
var peakImporter = new PeakImporterFromText(expectedPeaksFile);
var peaklist = new List <MSPeakResult>();
peakImporter.ImportPeaks(peaklist);
Assert.AreEqual(809, peaklist.Count);
var sumIntensities = isos.Select(p => p.IntensityAggregate).Sum();
Assert.AreEqual(266185816d, Math.Round(sumIntensities));
var sumPeakIntensities = peaklist.Select(p => p.Height).Sum();
Assert.AreEqual(605170496.0f, sumPeakIntensities);
}
