private void RunFlashLfq()
{
// read IDs
var ids = new List <Identification>();
foreach (var identFile in identFilesForDataGrid)
{
ids = ids.Concat(PsmReader.ReadPsms(identFile.FilePath, false, spectraFileInfo)).ToList();
}
// run FlashLFQ engine
try
{
flashLfqEngine = new FlashLFQEngine(
allIdentifications: ids,
normalize: flashLfqEngine.Normalize,
ppmTolerance: flashLfqEngine.PpmTolerance,
isotopeTolerancePpm: flashLfqEngine.IsotopePpmTolerance,
matchBetweenRuns: flashLfqEngine.MatchBetweenRuns,
matchBetweenRunsPpmTolerance: flashLfqEngine.MbrPpmTolerance,
integrate: flashLfqEngine.Integrate,
numIsotopesRequired: flashLfqEngine.NumIsotopesRequired,
idSpecificChargeState: flashLfqEngine.IdSpecificChargeState,
requireMonoisotopicMass: flashLfqEngine.RequireMonoisotopicMass,
silent: false,
optionalPeriodicTablePath: null,
maxMbrWindow: flashLfqEngine.MbrRtWindow,
advancedProteinQuant: flashLfqEngine.AdvancedProteinQuant);
results = flashLfqEngine.Run();
}
catch (Exception ex)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
}
// write output
try
{
OutputWriter.WriteOutput(Directory.GetParent(spectraFileInfo.First().FullFilePathWithExtension).FullName, results, outputFolderPath);
}
catch (Exception ex)
{
MessageBox.Show("Could not write FlashLFQ output: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
}
}
public static void TestPercolatorErrorHandling()
{
string search = "Percolator";
string psmFilename = "BadPercolatorSmallCalibratableYeast.txt";
string myDirectory = Path.Combine(TestContext.CurrentContext.TestDirectory, "SampleFiles");
string pathOfIdentificationFile = Path.Combine(myDirectory, search, psmFilename);
string pathOfMzml = Path.Combine(myDirectory, "SmallCalibratible_Yeast.mzML");
SpectraFileInfo sfi = new SpectraFileInfo(pathOfMzml, "A", 1, 1, 1);
List <Identification> ids = PsmReader.ReadPsms(pathOfIdentificationFile, false, new List <SpectraFileInfo> {
sfi
});
//would like better assertion with message but can't get it to return exception message...
Assert.IsEmpty(ids);
}
public void TestPercolatorReadPsmsGetsRTsFromFileHeader()
{
string search = "Percolator";
string psmFilename = "percolatorTestData.txt";
var myDirectory = Path.Combine(TestContext.CurrentContext.TestDirectory, "SampleFiles", search);
var pathOfIdentificationFile = Path.Combine(myDirectory, psmFilename);
var pathOfMzml = Path.Combine(myDirectory, "percolatorMzml.mzML");
Assert.That(File.Exists(pathOfIdentificationFile));
Assert.That(File.Exists(pathOfMzml));
SpectraFileInfo sfi = new SpectraFileInfo(pathOfMzml, "A", 1, 1, 1);
List <double> expectedRetentionTimes = new List <double> {
7.54, 7.54, 7.56, 7.58, 7.61, 7.63
};
List <Identification> ids = PsmReader.ReadPsms(pathOfIdentificationFile, true, new List <SpectraFileInfo> {
sfi
});
Assert.AreEqual(6, ids.Count);
List <double> actualRetentionTimes = ids.Select(t => Math.Round(t.Ms2RetentionTimeInMinutes, 2)).ToList();
foreach (double rt in actualRetentionTimes)
{
Assert.IsTrue(Double.IsFinite(rt));
}
CollectionAssert.AreEquivalent(expectedRetentionTimes, actualRetentionTimes);
List <int> proteinGroupCounts = new List <int> {
11, 6, 3, 2, 15, 3
};
CollectionAssert.AreEquivalent(proteinGroupCounts, ids.Select(i => i.ProteinGroups.Count).ToList());
}
/// <summary>
/// Runs the FlashLFQ engine with the user's defined spectra files, ID files, and FlashLFQ
/// settings.
/// </summary>
private void RunFlashLfq()
{
// read IDs
var ids = new List <Identification>();
try
{
foreach (var identFile in idFiles)
{
ids = ids.Concat(PsmReader.ReadPsms(identFile.FilePath, false, spectraFiles.Select(p => p.SpectraFileInfo).ToList())).ToList();
}
}
catch (Exception e)
{
string errorReportPath = Directory.GetParent(spectraFiles.First().FilePath).FullName;
if (outputFolderPath != null)
{
errorReportPath = outputFolderPath;
}
try
{
OutputWriter.WriteErrorReport(e, Directory.GetParent(spectraFiles.First().FilePath).FullName,
outputFolderPath);
}
catch (Exception ex2)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + e.Message +
".\nThe error report could not be written: " + ex2.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
MessageBox.Show("FlashLFQ could not read the PSM file: " + e.Message +
".\nError report written to " + errorReportPath, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
if (!ids.Any())
{
MessageBox.Show("No peptide IDs for the specified spectra files were found! " +
"Check to make sure the spectra file names match between the ID file and the spectra files",
"Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
// run FlashLFQ engine
try
{
flashLfqEngine = FlashLfqSettings.CreateEngineWithSettings(settings, ids);
results = flashLfqEngine.Run();
}
catch (Exception ex)
{
string errorReportPath = Directory.GetParent(spectraFiles.First().FilePath).FullName;
if (outputFolderPath != null)
{
errorReportPath = outputFolderPath;
}
try
{
OutputWriter.WriteErrorReport(ex, Directory.GetParent(spectraFiles.First().FilePath).FullName,
outputFolderPath);
}
catch (Exception ex2)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message +
".\nThe error report could not be written: " + ex2.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message +
".\nError report written to " + errorReportPath, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
// write output
if (results != null)
{
try
{
OutputWriter.WriteOutput(Directory.GetParent(spectraFiles.First().FilePath).FullName, results, flashLfqEngine.Silent,
outputFolderPath);
}
catch (Exception ex)
{
MessageBox.Show("Could not write FlashLFQ output: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
}
}
private void RunFlashLfq()
{
// read IDs
var ids = new List <Identification>();
try
{
foreach (var identFile in identFilesForDataGrid)
{
ids = ids.Concat(PsmReader.ReadPsms(identFile.FilePath, false, spectraFileInfo)).ToList();
}
}
catch (Exception e)
{
string errorReportPath = Directory.GetParent(spectraFileInfo.First().FullFilePathWithExtension).FullName;
if (outputFolderPath != null)
{
errorReportPath = outputFolderPath;
}
try
{
OutputWriter.WriteErrorReport(e, Directory.GetParent(spectraFileInfo.First().FullFilePathWithExtension).FullName,
outputFolderPath);
}
catch (Exception ex2)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + e.Message +
".\nThe error report could not be written: " + ex2.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
MessageBox.Show("FlashLFQ could not read the PSM file: " + e.Message +
".\nError report written to " + errorReportPath, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
if (!ids.Any())
{
MessageBox.Show("No peptide IDs for the specified spectra files were found! " +
"Check to make sure the spectra file names match between the ID file and the spectra files",
"Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
// run FlashLFQ engine
try
{
flashLfqEngine = new FlashLfqEngine(
allIdentifications: ids,
normalize: flashLfqEngine.Normalize,
ppmTolerance: flashLfqEngine.PpmTolerance,
isotopeTolerancePpm: flashLfqEngine.IsotopePpmTolerance,
matchBetweenRuns: flashLfqEngine.MatchBetweenRuns,
matchBetweenRunsPpmTolerance: flashLfqEngine.MbrPpmTolerance,
integrate: flashLfqEngine.Integrate,
numIsotopesRequired: flashLfqEngine.NumIsotopesRequired,
idSpecificChargeState: flashLfqEngine.IdSpecificChargeState,
requireMonoisotopicMass: flashLfqEngine.RequireMonoisotopicMass,
silent: false,
optionalPeriodicTablePath: null,
maxMbrWindow: flashLfqEngine.MbrRtWindow,
advancedProteinQuant: flashLfqEngine.AdvancedProteinQuant);
results = flashLfqEngine.Run();
}
catch (Exception ex)
{
string errorReportPath = Directory.GetParent(spectraFileInfo.First().FullFilePathWithExtension).FullName;
if (outputFolderPath != null)
{
errorReportPath = outputFolderPath;
}
try
{
OutputWriter.WriteErrorReport(ex, Directory.GetParent(spectraFileInfo.First().FullFilePathWithExtension).FullName,
outputFolderPath);
}
catch (Exception ex2)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message +
".\nThe error report could not be written: " + ex2.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message +
".\nError report written to " + errorReportPath, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
// write output
if (results != null)
{
try
{
OutputWriter.WriteOutput(Directory.GetParent(spectraFileInfo.First().FullFilePathWithExtension).FullName, results,
outputFolderPath);
}
catch (Exception ex)
{
MessageBox.Show("Could not write FlashLFQ output: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
}
}
/// <summary>
/// Runs the FlashLFQ engine with the user's defined spectra files, ID files, and FlashLFQ
/// settings.
/// </summary>
private void RunFlashLfq()
{
// read IDs
var ids = new List <Identification>();
try
{
foreach (var identFile in idFiles)
{
ids = ids.Concat(PsmReader.ReadPsms(identFile.FilePath, false, spectraFiles.Select(p => p.SpectraFileInfo).ToList())).ToList();
}
}
catch (Exception e)
{
string errorReportPath = Directory.GetParent(spectraFiles.First().FilePath).FullName;
if (outputFolderPath != null)
{
errorReportPath = outputFolderPath;
}
try
{
OutputWriter.WriteErrorReport(e, Directory.GetParent(spectraFiles.First().FilePath).FullName,
outputFolderPath);
}
catch (Exception ex2)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + e.Message +
".\nThe error report could not be written: " + ex2.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
MessageBox.Show("FlashLFQ could not read the PSM file: " + e.Message +
".\nError report written to " + errorReportPath, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
if (!ids.Any())
{
MessageBox.Show("No peptide IDs for the specified spectra files were found! " +
"Check to make sure the spectra file names match between the ID file and the spectra files",
"Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
if (ids.Any(p => p.Ms2RetentionTimeInMinutes > 500))
{
var res = MessageBox.Show("It seems that some of the retention times in the PSM file(s) are in seconds and not minutes; FlashLFQ requires the RT to be in minutes. " +
"Continue with the FlashLFQ run? (only click yes if the RTs are actually in minutes)",
"Error", MessageBoxButton.YesNo, MessageBoxImage.Hand);
if (res == MessageBoxResult.No)
{
return;
}
}
// run FlashLFQ engine
try
{
flashLfqEngine = FlashLfqSettings.CreateEngineWithSettings(settings, ids);
results = flashLfqEngine.Run();
}
catch (Exception ex)
{
string errorReportPath = Directory.GetParent(spectraFiles.First().FilePath).FullName;
if (outputFolderPath != null)
{
errorReportPath = outputFolderPath;
}
try
{
OutputWriter.WriteErrorReport(ex, Directory.GetParent(spectraFiles.First().FilePath).FullName,
outputFolderPath);
}
catch (Exception ex2)
{
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message +
".\nThe error report could not be written: " + ex2.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
MessageBox.Show("FlashLFQ has crashed with the following error: " + ex.Message +
".\nError report written to " + errorReportPath, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
// write output
if (results != null)
{
try
{
OutputWriter.WriteOutput(Directory.GetParent(spectraFiles.First().FilePath).FullName, results, flashLfqEngine.Silent,
outputFolderPath);
MessageBox.Show("Run complete");
}
catch (Exception ex)
{
MessageBox.Show("Could not write FlashLFQ output: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Hand);
return;
}
}
}
