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");
}
}
}
public static void Main(string[] args)
{
// parameters
List <string> acceptedSpectrumFileFormats = new List <string> {
".RAW", ".MZML"
};
// setup parameters
var p = new FluentCommandLineParser <ApplicationArguments>();
p.SetupHelp("?", "help")
.Callback(text => Console.WriteLine(
"Valid arguments:\n" +
"--idt [string|identification file path (TSV format)]\n" +
"--rep [string|directory containing spectrum data files]\n" +
"--out [string|output directory]\n" +
"--ppm [double|ppm tolerance]\n" +
"--iso [double|isotopic distribution tolerance in ppm]\n" +
"--sil [bool|silent mode]\n" +
"--int [bool|integrate features]\n" +
"--mbr [bool|match between runs]\n" +
"--mrt [double|maximum MBR window in minutes]\n" +
"--chg [bool|use only precursor charge state]\n" +
"--rmm [bool|require observed monoisotopic mass peak]\n" +
"--nis [int|number of isotopes required to be observed]\n" +
"--nor [bool|normalize intensity results]\n" +
"--pro [bool|advanced protein quantification]\n"
));
p.Setup(arg => arg.PsmInputPath) // PSMs file
.As("idt").
Required();
p.Setup(arg => arg.RawFilesPath) // spectrum files
.As("rep").
Required();
p.Setup(arg => arg.OutputPath) // output path
.As("out");
p.Setup(arg => arg.PpmTolerance) // ppm tolerance
.As("ppm");
p.Setup(arg => arg.IsotopePpmTolerance) // isotope ppm tolerance
.As("iso");
p.Setup(arg => arg.Silent) // do not display output messages
.As("sil");
p.Setup(arg => arg.Integrate) // integrate
.As("int");
p.Setup(arg => arg.MatchBetweenRuns) // match between runs
.As("mbr");
p.Setup(arg => arg.MbrRtWindow) // maximum match-between-runs window in minutes
.As("mrt");
p.Setup(arg => arg.IdSpecificChargeState) // only use PSM-identified charge states
.As("chg");
p.Setup(arg => arg.RequireMonoisotopicMass) // require observation of monoisotopic peak
.As("rmm");
p.Setup(arg => arg.NumIsotopesRequired) // num of isotopes required
.As("nis");
p.Setup(arg => arg.Normalize) // normalize
.As("nor");
p.Setup(arg => arg.AdvancedProteinQuant) // advanced protein quant
.As("pro");
// args are OK - run FlashLFQ
if (!p.Parse(args).HasErrors&& p.Object.PsmInputPath != null)
{
if (!File.Exists(p.Object.PsmInputPath))
{
if (!p.Object.Silent)
{
Console.WriteLine("Could not locate identification file " + p.Object.PsmInputPath);
}
return;
}
if (!Directory.Exists(p.Object.RawFilesPath))
{
if (!p.Object.Silent)
{
Console.WriteLine("Could not locate folder " + p.Object.RawFilesPath);
}
return;
}
string assumedPathToExpDesign = Path.Combine(p.Object.RawFilesPath, "ExperimentalDesign.tsv");
if (p.Object.Normalize && !File.Exists(assumedPathToExpDesign))
{
if (!p.Object.Silent)
{
Console.WriteLine("Could not find experimental design file (required for normalization): " + assumedPathToExpDesign);
}
return;
}
// set up spectra file info
// get experimental design info for normalization
List <SpectraFileInfo> spectraFileInfos = new List <SpectraFileInfo>();
IEnumerable <string> files = Directory.GetFiles(p.Object.RawFilesPath)
.Where(f => acceptedSpectrumFileFormats.Contains(Path.GetExtension(f).ToUpperInvariant()));
if (p.Object.Normalize)
{
var experimentalDesign = File.ReadAllLines(assumedPathToExpDesign)
.ToDictionary(v => v.Split('\t')[0], v => v);
foreach (var file in files)
{
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
{
foreach (var file in files)
{
spectraFileInfos.Add(new SpectraFileInfo(fullFilePathWithExtension: file,
condition: "",
biorep: 0,
fraction: 0,
techrep: 0));
}
}
// set up IDs
List <Identification> ids;
try
{
ids = PsmReader.ReadPsms(p.Object.PsmInputPath, p.Object.Silent, spectraFileInfos);
}
catch (Exception e)
{
Console.WriteLine("Problem reading PSMs: " + e.Message);
return;
}
if (ids.Any())
{
if (!p.Object.Silent)
{
Console.WriteLine("Setup is OK; read in " + ids.Count + " identifications; starting FlashLFQ engine");
}
// make engine with desired settings
FlashLfqEngine engine = null;
FlashLfqResults results = null;
try
{
engine = new FlashLfqEngine(
allIdentifications: ids,
normalize: p.Object.Normalize,
ppmTolerance: p.Object.PpmTolerance,
isotopeTolerancePpm: p.Object.IsotopePpmTolerance,
matchBetweenRuns: p.Object.MatchBetweenRuns,
matchBetweenRunsPpmTolerance: p.Object.MbrPpmTolerance,
integrate: p.Object.Integrate,
numIsotopesRequired: p.Object.NumIsotopesRequired,
idSpecificChargeState: p.Object.IdSpecificChargeState,
requireMonoisotopicMass: p.Object.RequireMonoisotopicMass,
silent: p.Object.Silent,
optionalPeriodicTablePath: null,
maxMbrWindow: p.Object.MbrRtWindow,
advancedProteinQuant: p.Object.AdvancedProteinQuant);
// run
results = engine.Run();
}
catch (Exception ex)
{
string errorReportPath = Directory.GetParent(files.First()).FullName;
if (p.Object.OutputPath != null)
{
errorReportPath = p.Object.OutputPath;
}
if (!p.Object.Silent)
{
Console.WriteLine("FlashLFQ has crashed with the following error: " + ex.Message +
".\nError report written to " + errorReportPath);
}
OutputWriter.WriteErrorReport(ex, Directory.GetParent(files.First()).FullName, p.Object.OutputPath);
}
// output
if (results != null)
{
try
{
OutputWriter.WriteOutput(p.Object.PsmInputPath, results, p.Object.OutputPath);
}
catch (Exception ex)
{
if (!p.Object.Silent)
{
Console.WriteLine("Could not write FlashLFQ output: " + ex.Message);
}
}
}
}
else
{
if (!p.Object.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");
}
}
}
else if (p.Parse(args).HasErrors == false && p.Object.PsmInputPath == null)
{
// no errors - just requesting help?
}
else
{
Console.WriteLine("Invalid arguments - type \"--help\" for valid arguments");
}
}
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;
}
// 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;
}
}
}
/// <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;
}
}
}