private static void Run(FlashLfqSettings settings)
{
try
{
settings.ValidateCommandLineSettings();
}
catch (Exception e)
{
if (!settings.Silent)
{
Console.WriteLine("Error: " + e.Message);
}
return;
}
// check to see if experimental design file exists
string assumedPathToExpDesign = Path.Combine(settings.SpectraFileRepository, "ExperimentalDesign.tsv");
if ((settings.Normalize || settings.BayesianProteinQuant) && !File.Exists(assumedPathToExpDesign))
{
if (!settings.Silent)
{
Console.WriteLine("Could not find experimental design file " +
"(required for normalization and Bayesian statistical analysis): " + assumedPathToExpDesign);
}
return;
}
// set up spectra file info
List <SpectraFileInfo> spectraFileInfos = new List <SpectraFileInfo>();
List <string> filePaths = Directory.GetFiles(settings.SpectraFileRepository)
.Where(f => acceptedSpectrumFileFormats.Contains(Path.GetExtension(f).ToLowerInvariant())).ToList();
// check for duplicate file names (agnostic of file extension)
foreach (var fileName in filePaths.GroupBy(p => Path.GetFileNameWithoutExtension(p)))
{
if (fileName.Count() > 1)
{
var types = fileName.Select(p => Path.GetFileNameWithoutExtension(p)).Distinct();
if (!settings.Silent)
{
Console.WriteLine("Multiple spectra files with the same name were detected (maybe " + string.Join(" and ", types) + "?). " +
"Please remove or rename duplicate files from the spectra file directory.");
}
return;
}
}
if (settings.PrintThermoLicenceViaCommandLine)
{
Console.WriteLine(ThermoRawFileReaderLicence.ThermoLicenceText);
return;
}
// check thermo licence agreement
if (filePaths.Select(v => Path.GetExtension(v).ToLowerInvariant()).Any(f => f == ".raw"))
{
var licenceAgreement = LicenceAgreementSettings.ReadLicenceSettings();
if (!licenceAgreement.HasAcceptedThermoLicence)
{
if (settings.AcceptThermoLicenceViaCommandLine)
{
if (!settings.ReadOnlyFileSystem)
{
licenceAgreement.AcceptLicenceAndWrite();
}
}
else
{
// decided to write this even if it's on silent mode...
Console.WriteLine(ThermoRawFileReaderLicence.ThermoLicenceText);
Console.WriteLine("\nIn order to search Thermo .raw files, you must agree to the above terms. Do you agree to the above terms? y/n\n");
string res = Console.ReadLine();
if (res.ToLowerInvariant() == "y")
{
try
{
if (!settings.ReadOnlyFileSystem)
{
licenceAgreement.AcceptLicenceAndWrite();
}
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
}
else
{
Console.WriteLine("Thermo licence has been declined. Exiting FlashLFQ. You can still search .mzML and .mgf files without agreeing to the Thermo licence.");
return;
}
}
}
}
if (File.Exists(assumedPathToExpDesign))
{
var experimentalDesign = File.ReadAllLines(assumedPathToExpDesign)
.ToDictionary(v => v.Split('\t')[0], v => v);
foreach (var file in filePaths)
{
string filename = Path.GetFileNameWithoutExtension(file);
var expDesignForThisFile = experimentalDesign[filename];
var split = expDesignForThisFile.Split('\t');
string condition = split[1];
int biorep = int.Parse(split[2]);
int fraction = int.Parse(split[3]);
int techrep = int.Parse(split[4]);
// experimental design info passed in here for each spectra file
spectraFileInfos.Add(new SpectraFileInfo(fullFilePathWithExtension: file,
condition: condition,
biorep: biorep - 1,
fraction: fraction - 1,
techrep: techrep - 1));
}
}
else
{
for (int i = 0; i < filePaths.Count; i++)
{
var file = filePaths[i];
spectraFileInfos.Add(new SpectraFileInfo(fullFilePathWithExtension: file,
condition: "Default",
biorep: i,
fraction: 0,
techrep: 0));
}
}
// check the validity of the settings and experimental design
try
{
settings.ValidateSettings(spectraFileInfos);
}
catch (Exception e)
{
if (!settings.Silent)
{
Console.WriteLine("Error: " + e.Message);
}
return;
}
// set up IDs
List <Identification> ids;
try
{
ids = PsmReader.ReadPsms(settings.PsmIdentificationPath, settings.Silent, spectraFileInfos);
}
catch (Exception e)
{
Console.WriteLine("Problem reading PSMs: " + e.Message);
return;
}
if (ids.Any())
{
if (!settings.Silent)
{
Console.WriteLine("Setup is OK; read in " + ids.Count + " identifications; starting FlashLFQ engine");
}
// write FlashLFQ settings to a file
if (!Directory.Exists(settings.OutputPath))
{
Directory.CreateDirectory(settings.OutputPath);
}
Nett.Toml.WriteFile(settings, Path.Combine(settings.OutputPath, "FlashLfqSettings.toml"));
// make engine with desired settings
FlashLfqEngine engine = null;
FlashLfqResults results = null;
try
{
engine = FlashLfqSettings.CreateEngineWithSettings(settings, ids);
// run
results = engine.Run();
}
catch (Exception ex)
{
string errorReportPath = Directory.GetParent(filePaths.First()).FullName;
if (settings.OutputPath != null)
{
errorReportPath = settings.OutputPath;
}
if (!settings.Silent)
{
Console.WriteLine("FlashLFQ has crashed with the following error: " + ex.Message +
".\nError report written to " + errorReportPath);
}
OutputWriter.WriteErrorReport(ex, Directory.GetParent(filePaths.First()).FullName, settings.OutputPath);
}
// output
if (results != null)
{
try
{
OutputWriter.WriteOutput(settings.PsmIdentificationPath, results, settings.Silent, settings.OutputPath);
}
catch (Exception ex)
{
if (!settings.Silent)
{
Console.WriteLine("Could not write FlashLFQ output: " + ex.Message);
}
}
}
}
else
{
if (!settings.Silent)
{
Console.WriteLine("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");
}
}
}
private void ParseSettings()
{
// check for ID/spectra files
if (!spectraFiles.Any())
{
throw new Exception("You need to add at least one spectra file!");
}
if (!idFiles.Any())
{
throw new Exception("You need to add at least one identification file!");
}
// fold-change cutoff
if (!double.TryParse(FoldChangeCutoffManualTextBox.Text, NumberStyles.Number, CultureInfo.InvariantCulture, out double foldChangeCutoff))
{
throw new Exception("The fold-change cutoff must be a decimal number");
}
settings.ProteinQuantFoldChangeCutoff = double.Parse(FoldChangeCutoffManualTextBox.Text, CultureInfo.InvariantCulture);
// ppm tolerance
if (double.TryParse(ppmToleranceTextBox.Text, NumberStyles.Number, CultureInfo.InvariantCulture, out double ppmTolerance))
{
settings.PpmTolerance = ppmTolerance;
}
else
{
throw new Exception("The PPM tolerance must be a decimal number");
}
settings.Normalize = normalizeCheckbox.IsChecked.Value;
settings.MatchBetweenRuns = mbrCheckbox.IsChecked.Value;
settings.UseSharedPeptidesForProteinQuant = sharedPeptideCheckbox.IsChecked.Value;
settings.BayesianProteinQuant = bayesianCheckbox.IsChecked.Value;
settings.Integrate = integrateCheckBox.IsChecked.Value;
settings.IdSpecificChargeState = precursorIdOnlyCheckbox.IsChecked.Value;
settings.ProteinQuantBaseCondition = (string)ControlConditionComboBox.SelectedItem;
settings.RequireMsmsIdInCondition = requireMsmsIdInConditionCheckbox.IsChecked.Value;
// isotope PPM tolerance
if (double.TryParse(isotopePpmToleranceTextBox.Text, NumberStyles.Number, CultureInfo.InvariantCulture, out double isotopePpmTolerance))
{
settings.IsotopePpmTolerance = isotopePpmTolerance;
}
else
{
throw new Exception("The isotope PPM tolerance must be a decimal number");
}
// num isotopes required
if (int.TryParse(numIsotopesRequiredTextBox.Text, NumberStyles.Integer, CultureInfo.InvariantCulture, out int numIsotopesRequired))
{
settings.NumIsotopesRequired = numIsotopesRequired;
}
else
{
throw new Exception("The number of isotopes required must be an integer");
}
// mcmc iterations
if (int.TryParse(mcmcIterationsTextBox.Text, out int McmcSteps))
{
settings.McmcSteps = McmcSteps;
}
else
{
throw new Exception("The number of MCMC iterations must be an integer");
}
// random seed
if (int.TryParse(mcmcRandomSeedTextBox.Text, NumberStyles.Integer, CultureInfo.InvariantCulture, out int randomSeed))
{
settings.RandomSeed = randomSeed;
}
else
{
throw new Exception("The random seed must be an integer");
}
// MBR time tolerance
if (double.TryParse(mbrRtWindowTextBox.Text, NumberStyles.Number, CultureInfo.InvariantCulture, out double MbrRtWindow))
{
settings.MbrRtWindow = MbrRtWindow;
}
else
{
throw new Exception("The MBR time window must be a decimal number");
}
settings.ValidateSettings(spectraFiles.Select(p => p.SpectraFileInfo).ToList());
}