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");
}
}
}
/// <summary>
/// Handles adding a file (spectra or ID file). The source can be by drag+drop or through
/// clicking one of the "Add" buttons.
/// </summary>
private void AddAFile(string filePath)
{
string filename = Path.GetFileName(filePath);
string theExtension = Path.GetExtension(filename).ToLowerInvariant();
if (theExtension == ".raw")
{
var licenceAgreement = LicenceAgreementSettings.ReadLicenceSettings();
if (!licenceAgreement.HasAcceptedThermoLicence)
{
var thermoLicenceWindow = new ThermoLicenceAgreementWindow();
thermoLicenceWindow.LicenceText.AppendText(ThermoRawFileReader.ThermoRawFileReaderLicence.ThermoLicenceText);
var dialogResult = thermoLicenceWindow.ShowDialog();
if (dialogResult.HasValue && dialogResult.Value == true)
{
try
{
licenceAgreement.AcceptLicenceAndWrite();
}
catch (Exception e)
{
MessageBox.Show(e.Message);
}
}
else
{
return;
}
}
}
switch (theExtension)
{
case ".raw":
case ".mzml":
List <int> existingDefaultSampleNumbers = spectraFiles.Where(p => p.Condition == DefaultCondition)
.Select(p => p.Sample)
.Distinct()
.OrderBy(p => p).ToList();
int sampleNumber = 1;
for (int i = 1; i < int.MaxValue; i++)
{
if (!existingDefaultSampleNumbers.Contains(i))
{
sampleNumber = i;
break;
}
}
SpectraFileForDataGrid spectraFile = new SpectraFileForDataGrid(filePath, DefaultCondition, sampleNumber, 1, 1);
if (!spectraFiles.Select(f => f.FilePath).Contains(spectraFile.FilePath))
{
CheckForExistingExperimentalDesignFile(spectraFile);
spectraFiles.Add(spectraFile);
DragAndDropHelperLabelSpectraFiles.Visibility = Visibility.Hidden;
}
if (string.IsNullOrEmpty(OutputFolderTextBox.Text))
{
var pathOfFirstSpectraFile = Path.GetDirectoryName(spectraFiles.First().FilePath);
OutputFolderTextBox.Text = Path.Combine(pathOfFirstSpectraFile, @"FlashLFQ_$DATETIME");
}
break;
case ".txt":
case ".tsv":
case ".psmtsv":
case ".tabular":
IdentificationFileForDataGrid identFile = new IdentificationFileForDataGrid(filePath);
if (!idFiles.Select(f => f.FilePath).Contains(identFile.FilePath) && !identFile.FileName.Equals("ExperimentalDesign.tsv"))
{
bool valid = ValidateIdentificationFile(identFile);
if (valid)
{
idFiles.Add(identFile);
DragAndDropHelperLabelIdFiles.Visibility = Visibility.Hidden;
}
}
break;
default:
//TODO: change this to popup
AddNotification("Unrecognized file type: " + theExtension);
break;
}
}
