public void Test1()
{
string testFile =
@"\\proto-10\IMS_TOF_4\2012_3\Sarc_P22_B06_2034_23Jul12_Cheetah_11-12-23\Sarc_P22_B06_2034_23Jul12_Cheetah_11-12-23.uimf";
testFile = @"D:\Data\UIMF\Problem_datasets\Sarc_P22_B06_2034_23Jul12_Cheetah_11-12-23.uimf";
string parameterFile =
@"\\gigasax\DMS_Parameter_Files\Decon2LS\IMS_UIMF_PeakBR2_PeptideBR3_SN3_SumScans3_NoLCSum_Sat50000_2012-02-27.xml";
string expectedIsosOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_isos.csv");
string expectedScansOutput = Path.Combine(Path.GetDirectoryName(testFile), Path.GetFileNameWithoutExtension(testFile) + "_scans.csv");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
if (File.Exists(expectedScansOutput))
{
File.Delete(expectedScansOutput);
}
var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile);
workflow.Execute();
}
public void Test1()
{
Run run = new RunFactory().CreateRun(
@"\\pnl\projects\MSSHARE\Webb_Ian\no cid.UIMF");
DeconToolsParameters parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(
@"\\pnl\projects\MSSHARE\Webb_Ian\IMS_UIMF_PeakBR2_PeptideBR3_SN3_SumScans3_NoLCSum_Sat50000_2012-02-27.xml");
string expectedIsosFile = Path.Combine(run.DataSetPath, run.DatasetName + "_isos.csv");
string expectedScansFile = Path.Combine(run.DataSetPath, run.DatasetName + "_scans.csv");
string 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 workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.Execute();
}
public void scanBasedWorkflowTest1()
{
string testFile = @"D:\Data\JIRA_issues\OMCS-149_MS2_not_in_Scans\DsrC_Black_02_6Feb12_Cougar_11-10-11.raw";
string parameterFile =
@"D:\Data\JIRA_issues\OMCS-149_MS2_not_in_Scans\LTQ_Orb_USTags_MS2_THRASH_WithPeaks_Relaxed.xml";
Run run = new RunFactory().CreateRun(testFile);
var parameters = new OldDecon2LSParameters();
parameters.Load(parameterFile);
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.OldDecon2LsParameters.HornTransformParameters.UseScanRange = true;
workflow.OldDecon2LsParameters.HornTransformParameters.MinScan = 25;
workflow.OldDecon2LsParameters.HornTransformParameters.MaxScan = 35;
workflow.ExportData = true;
workflow.Execute();
// foreach (var isosResult in run.ResultCollection.ResultList)
// {
// isosResult.Display();
// }
}
public void saturatedFixingTest2()
{
string uimfFile =
@"D:\Data\UIMF\Sarc_Main_Study_Controls\Sarc_P08_A01_0673_21Nov11_Cheetah_11-09-03.uimf";
Run run = new RunFactory().CreateRun(uimfFile);
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(@"\\gigasax\DMS_Parameter_Files\Decon2LS\IMS_UIMF_PeakBR4_PeptideBR4_SN3_SumScans3_NoLCSum_Sat50000_2012-01-30.xml");
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 397;
parameters.MSGeneratorParameters.MaxLCScan = 408;
parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "uimf_saturation_repair";
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.ExportData = true;
var sw = new Stopwatch();
sw.Start();
workflow.Execute();
return;
sw.Stop();
var distinctItems = run.ResultCollection.ResultList.GroupBy(x => x.MSFeatureID).Select(y => y.First()).ToList();
int minFrame = parameters.MSGeneratorParameters.MinLCScan;
int maxFrame = parameters.MSGeneratorParameters.MaxLCScan;
int minScan = 102;
int maxScan = 125;
double targetMass = 1642.85958;
int chargestate = 4;
double tolerance = 0.3;
var featureData =
(from n in distinctItems
where (Math.Abs(n.IsotopicProfile.MonoIsotopicMass - targetMass)) < tolerance &&
n.IsotopicProfile.ChargeState == chargestate
select n).Select <IsosResult, UIMFIsosResult>(r => (UIMFIsosResult)r).ToList();
OutputFeatureIntensityData(featureData, minFrame, maxFrame, maxScan, minScan);
MathUtils mathUtils = new MathUtils();
var monoMasses = (from n in featureData select n.IsotopicProfile.MonoIsotopicMass).ToList();
var massVariance = MathUtils.GetStDev(monoMasses);
Console.WriteLine("Mass variance = " + massVariance);
Console.WriteLine("Time taken = " + sw.ElapsedMilliseconds);
}
public void TempSaturationFixingTestOnYehiaBSAData()
{
var uimfFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\BSA_30N2_30ms_gate_10tof_Padjust_0000.UIMF";
var run = new RunFactory().CreateRun(uimfFile);
var parameters = new DeconToolsParameters();
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 4;
parameters.PeakDetectorParameters.SignalToNoiseThreshold = 3;
parameters.ThrashParameters.MaxFit = 0.6;
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 2;
parameters.MSGeneratorParameters.MaxLCScan = 2;
parameters.MSGeneratorParameters.UseMZRange = true;
parameters.MSGeneratorParameters.MinMZ = 652;
parameters.MSGeneratorParameters.MaxMZ = 657;
parameters.MSGeneratorParameters.SumSpectraAcrossLC = true;
parameters.MSGeneratorParameters.SumSpectraAcrossIms = true;
parameters.MSGeneratorParameters.NumLCScansToSum = 1;
parameters.MSGeneratorParameters.NumImsScansToSum = 7;
parameters.MiscMSProcessingParameters.UseZeroFilling = true;
parameters.ThrashParameters.MinIntensityForDeletion = 10;
parameters.MiscMSProcessingParameters.SaturationThreshold = 6000;
parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "uimf_saturation_repair";
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
//workflow.ExportData = false;
workflow.Execute();
}
public void scanBasedWorkflowTest1()
{
string testFile = @"D:\Data\UIMF\Problem_datasets\DsrC_Black_02_6Feb12_Cougar_11-10-11.raw";
string parameterFile = @"D:\Data\UIMF\Problem_datasets\LTQ_Orb_USTags_MS2_THRASH_WithPeaks_Relaxed.xml";
Run run = new RunFactory().CreateRun(testFile);
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(parameterFile);
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.NewDeconToolsParameters.MSGeneratorParameters.UseLCScanRange = true;
workflow.NewDeconToolsParameters.MSGeneratorParameters.MinLCScan = 1;
workflow.NewDeconToolsParameters.MSGeneratorParameters.MaxLCScan = 5;
workflow.ExportData = true;
workflow.Execute();
// foreach (var isosResult in run.ResultCollection.ResultList)
// {
// isosResult.Display();
// }
}
public void saturatedFixingTest3()
{
var uimfFile = @"D:\Data\UIMF\Sarc_Main_Study_Controls\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf";
var run = new RunFactory().CreateRun(uimfFile);
var parameters = new DeconToolsParameters();
parameters.LoadFromOldDeconToolsParameterFile(
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\ParameterFiles\IMS_UIMF_PeakBR2_PeptideBR3_SN3_SumScans3_NoLCSum_Sat50000_2012-02-27_frames_180_195.xml");
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 394;
parameters.MSGeneratorParameters.MaxLCScan = 404;
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.ExportData = false;
var sw = new Stopwatch();
sw.Start();
workflow.Execute();
//return;
sw.Stop();
var distinctItems = run.ResultCollection.ResultList.GroupBy(x => x.MSFeatureID).Select(y => y.First()).ToList();
var minFrame = parameters.MSGeneratorParameters.MinLCScan;
var maxFrame = parameters.MSGeneratorParameters.MaxLCScan;
var minScan = 102;
var maxScan = 127;
var targetMass = 1059.55169;
var chargestate = 2;
var tolerance = 0.3;
var featureData =
(from n in distinctItems
where (Math.Abs(n.IsotopicProfile.MonoIsotopicMass - targetMass)) < tolerance &&
n.IsotopicProfile.ChargeState == chargestate
select n).Select <IsosResult, UIMFIsosResult>(r => (UIMFIsosResult)r).ToList();
OutputFeatureIntensityData(featureData, minFrame, maxFrame, maxScan, minScan);
var mathUtils = new MathUtils();
var monoMasses = (from n in featureData select n.IsotopicProfile.MonoIsotopicMass).ToList();
var massVariance = MathUtils.GetStDev(monoMasses);
Console.WriteLine("Mass variance = " + massVariance);
Console.WriteLine("Time taken = " + sw.ElapsedMilliseconds);
}
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));
}
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 ProblemTesting()
{
var parameterFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\DeconMSn\ParameterFiles\DeconMSn_LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_scans6000_6050.xml";
var rawdataFile = @"D:\Data\DeconMSn_testing\CPTAC_CompRef_test_iTRAQ_NiNTA_08_17Jan13_Frodo_12-12-50.raw";
var workflow = ScanBasedWorkflow.CreateWorkflow(rawdataFile, parameterFile);
workflow.Execute();
}
public void WorkflowTypeIsWrongTest1()
{
var uimfFile = @"D:\Data\UIMF\Sarc_Main_Study_Controls\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf";
var run = new RunFactory().CreateRun(uimfFile);
var parameters = new DeconToolsParameters();
parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "incorrectTextProblem";
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
}
void bw_DoWork(object sender, DoWorkEventArgs e)
{
var bw = (BackgroundWorker)sender;
try
{
//This mode was requested by Julia Laskin.
//This mode detects peaks in each dataset and merges the output
if (_parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName.ToLower() == "run_merging_with_peak_export")
{
var workflow = new RunMergingPeakExportingWorkflow(_parameters, _inputFileList, _outputPath, bw);
workflow.Execute();
}
else
{
foreach (var file in _inputFileList)
{
_currentFile = file;
var workflow = ScanBasedWorkflow.CreateWorkflow(file, _parameterFileName, _outputPath, bw);
workflow.Execute();
}
}
}
catch (COMException ex)
{
// bool isFile = RunUtilities.RunIsFileOrFolder(_currentFile);
var errorMessage =
"A 'COMException' has occurred. This can happen when the vendor library has not been installed.\n\n";
errorMessage +=
"If you are trying to read Thermo .raw files, please install Thermo's MSFileReader library. ";
errorMessage += "To do so, Google 'thermo msfilereader' and you should find it. If not, contact us.\n\n";
errorMessage += "Full error details below:\n";
errorMessage += ex.Message;
MessageBox.Show(errorMessage, "COMError occurred");
}
catch (Exception ex)
{
MessageBox.Show(ex.Message + Environment.NewLine + Environment.NewLine + "**NOTE: see log file for additional details.");
}
if (bw.CancellationPending)
{
e.Cancel = true;
}
}
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 createScanSetTests()
{
int testScan1 = 6005;
var run = new RunFactory().CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
ScanBasedWorkflow workflow = new ScanBasedWorkflow(run);
workflow.NumScansSummed = 3;
workflow.SetScanSet(testScan1);
Assert.AreEqual(3, workflow.scanSetSelected.IndexValues.Count);
}
public void getRunInfoTest1()
{
var run = new RunFactory().CreateRun(_testdatafile);
Console.WriteLine(TestUtilities.DisplayRunInformation(run));
OldDecon2LSParameters parameters = new OldDecon2LSParameters();
parameters.PeakProcessorParameters.WritePeaksToTextFile = true;
ScanBasedWorkflow workflow = ScanBasedWorkflow.CreateWorkflow(run, new OldDecon2LSParameters());
workflow.Execute();
}
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 WorkflowTypeIsCorrectTest1()
{
var uimfFile = @"D:\Data\UIMF\Sarc_Main_Study_Controls\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf";
var run = new RunFactory().CreateRun(uimfFile);
var parameters = new DeconToolsParameters();
parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "standard";
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
Assert.IsTrue(workflow is IMSScanBasedWorkflow);
parameters.ScanBasedWorkflowParameters.ScanBasedWorkflowName = "uimf_saturation_repair";
workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
Assert.IsTrue(workflow is SaturationIMSScanBasedWorkflow);
}
public void WorkflowTestUsingParameterFile_Sum5_Test1()
{
var parameterFile =
@"C:\Users\d3x720\Documents\Data\QCShew\DeconMSn_LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_LCSum5.xml";
var localTestFile =
@"C:\Users\d3x720\Documents\Data\QCShew\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var outputFolder = @"C:\Users\d3x720\Documents\Data\QCShew\Output";
var workflow = ScanBasedWorkflow.CreateWorkflow(localTestFile, parameterFile, outputFolder);
workflow.Execute();
}
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 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 ProcessBruker9T()
{
var testFile = FileRefs.RawDataMSFiles.Bruker9TStandardFile2;
var dirInfo = new DirectoryInfo(testFile);
var datasetName = dirInfo.Name;
var expectedIsosOutput = Path.Combine(testFile, datasetName + "_isos.csv");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, FileRefs.ParameterFiles.Bruker9T_Scans1000_1010ParamFile);
workflow.Execute();
Assert.That(File.Exists(expectedIsosOutput));
}
public void processYAFMSFile1()
{
var testFile = FileRefs.RawDataMSFiles.YAFMSStandardFile2;
var parameterFile = FileRefs.ParameterFiles.YAFMSParameterFileScans4000_4050;
var dirInfo = new DirectoryInfo(testFile);
var datasetName = dirInfo.Name;
var expectedIsosOutput = Path.Combine(testFile, datasetName + "_isos.csv");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, parameterFile);
workflow.Execute();
//Assert.That(File.Exists(expectedIsosOutput));
}
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 ProcessBruker12TSolarixFile1()
{
var testFile = FileRefs.RawDataMSFiles.BrukerSolarix12TFile1;
var dirInfo = new DirectoryInfo(testFile);
var datasetName = dirInfo.Name;
var expectedIsosOutput = Path.Combine(FileRefs.RawDataMSFiles.BrukerSolarix12TFile1, datasetName + "_isos.csv");
if (File.Exists(expectedIsosOutput))
{
File.Delete(expectedIsosOutput);
}
var run = new RunFactory().CreateRun(testFile);
var workflow = ScanBasedWorkflow.CreateWorkflow(testFile, FileRefs.ParameterFiles.Bruker12TSolarixScans4_8ParamFile);
workflow.Execute();
Assert.That(File.Exists(expectedIsosOutput));
}
public void noFixingTest1()
{
var uimfFile = @"D:\Data\UIMF\Sarc_Main_Study_Controls\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf";
var run = new RunFactory().CreateRun(uimfFile);
var parameters = new DeconToolsParameters();
parameters.PeakDetectorParameters.PeakToBackgroundRatio = 4;
parameters.PeakDetectorParameters.SignalToNoiseThreshold = 3;
parameters.MSGeneratorParameters.UseLCScanRange = true;
parameters.MSGeneratorParameters.MinLCScan = 180;
parameters.MSGeneratorParameters.MaxLCScan = 180;
parameters.MSGeneratorParameters.SumSpectraAcrossLC = true;
parameters.MSGeneratorParameters.SumSpectraAcrossIms = true;
parameters.MSGeneratorParameters.NumLCScansToSum = 1;
parameters.MSGeneratorParameters.NumImsScansToSum = 3;
var workflow = ScanBasedWorkflow.CreateWorkflow(run, parameters);
workflow.Execute();
}
public void WorkflowTestUsingParameterFile1()
{
var parameterFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\DeconMSn\ParameterFiles\DeconMSn_LTQ_Orb_SN2_PeakBR1pt3_PeptideBR1_scans6000_6050.xml";
var rawdataFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var outputFolder = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\DeconMSn\Output";
var datasetName = RunUtilities.GetDatasetName(rawdataFile);
var expectedResultsFile1 = Path.Combine(outputFolder, datasetName + ".mgf");
var expectedResultsFile2 = Path.Combine(outputFolder, datasetName + "_DeconMSn_log.txt");
var expectedResultsFile3 = Path.Combine(outputFolder, 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 = ScanBasedWorkflow.CreateWorkflow(rawdataFile, parameterFile, outputFolder);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedResultsFile1));
Assert.IsTrue(File.Exists(expectedResultsFile2));
Assert.IsTrue(File.Exists(expectedResultsFile3));
}
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));
}
