private static int Run(CommandLineSettings settings)
{
int errorCode = 0;
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Welcome to MetaMorpheus");
}
if (settings.CustomDataDirectory != null)
{
GlobalVariables.UserSpecifiedDataDir = settings.CustomDataDirectory;
}
GlobalVariables.SetUpGlobalVariables();
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(GlobalVariables.MetaMorpheusVersion);
}
try
{
settings.ValidateCommandLineSettings();
CommandLineSettings = settings;
}
catch (Exception e)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("MetaMorpheus encountered the following error:" + Environment.NewLine + e.Message);
}
errorCode = 2;
return(errorCode);
}
if (settings.GenerateDefaultTomls)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Generating default tomls at location: " + settings.OutputFolder);
}
CommandLineSettings.GenerateDefaultTaskTomls(settings.OutputFolder);
return(errorCode);
}
// set up microvignette
if (settings.RunMicroVignette)
{
// set up the spectra file
settings.Spectra.Clear();
settings.Spectra.Add(Path.Combine(GlobalVariables.DataDir, @"Data", "SmallCalibratible_Yeast.mzML"));
// set up the database
settings.Databases.Clear();
settings.Databases.Add(Path.Combine(GlobalVariables.DataDir, @"Data", "SmallYeast.fasta"));
// set up the tasks (calibration, GPTMD, search)
settings.Tasks.Clear();
CommandLineSettings.GenerateDefaultTaskTomls(settings.OutputFolder);
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "CalibrationTask.toml"));
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "GptmdTask.toml"));
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "SearchTask.toml"));
}
MetaMorpheusEngine.WarnHandler += WarnHandler;
MetaMorpheusEngine.OutProgressHandler += MyEngine_outProgressHandler;
MetaMorpheusEngine.StartingSingleEngineHander += MyEngine_startingSingleEngineHander;
MetaMorpheusEngine.FinishedSingleEngineHandler += MyEngine_finishedSingleEngineHandler;
MetaMorpheusTask.WarnHandler += WarnHandler;
MetaMorpheusTask.LogHandler += LogHandler;
MetaMorpheusTask.StartingSingleTaskHander += MyTaskEngine_startingSingleTaskHander;
MetaMorpheusTask.FinishedSingleTaskHandler += MyTaskEngine_finishedSingleTaskHandler;
MetaMorpheusTask.FinishedWritingFileHandler += MyTaskEngine_finishedWritingFileHandler;
bool containsRawFiles = settings.Spectra.Select(v => Path.GetExtension(v).ToLowerInvariant()).Any(v => v == ".raw");
if (containsRawFiles && !GlobalVariables.GlobalSettings.UserHasAgreedToThermoRawFileReaderLicence)
{
// write the Thermo RawFileReader licence agreement
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().ToLowerInvariant();
if (res == "y")
{
var newGlobalSettings = new GlobalSettings
{
UserHasAgreedToThermoRawFileReaderLicence = true,
WriteExcelCompatibleTSVs = GlobalVariables.GlobalSettings.WriteExcelCompatibleTSVs
};
Toml.WriteFile <GlobalSettings>(newGlobalSettings, Path.Combine(GlobalVariables.DataDir, @"settings.toml"));
GlobalVariables.GlobalSettings = newGlobalSettings;
}
else
{
Console.WriteLine("Thermo licence has been declined. Exiting MetaMorpheus. You can still search .mzML and .mgf files without agreeing to the Thermo licence.");
errorCode = 3;
return(errorCode);
}
}
foreach (var db in settings.Databases)
{
if (!Path.GetExtension(db).Equals(".fasta"))
{
GlobalVariables.AddMods(UsefulProteomicsDatabases.ProteinDbLoader.GetPtmListFromProteinXml(db).OfType <Modification>(), true);
// print any error messages reading the mods to the console
foreach (var error in GlobalVariables.ErrorsReadingMods)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(error);
}
}
GlobalVariables.ErrorsReadingMods.Clear();
}
}
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)>();
var tasks = settings.Tasks.ToList();
for (int i = 0; i < tasks.Count; i++)
{
var filePath = tasks[i];
var toml = Toml.ReadFile(filePath, MetaMorpheusTask.tomlConfig);
switch (toml.Get <string>("TaskType"))
{
case "Search":
var searchTask = Toml.ReadFile <SearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "SearchTask", searchTask));
break;
case "Calibrate":
var calibrationTask = Toml.ReadFile <CalibrationTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "CalibrationTask", calibrationTask));
break;
case "Gptmd":
var GptmdTask = Toml.ReadFile <GptmdTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "GptmdTask", GptmdTask));
break;
case "XLSearch":
var XlTask = Toml.ReadFile <XLSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "XLSearchTask", XlTask));
break;
case "GlycoSearch":
var GlycoTask = Toml.ReadFile <GlycoSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "GlycoSearchTask", GlycoTask));
break;
default:
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(toml.Get <string>("TaskType") + " is not a known task type! Skipping.");
}
break;
}
}
List <string> startingRawFilenameList = settings.Spectra.Select(b => Path.GetFullPath(b)).ToList();
List <DbForTask> startingXmlDbFilenameList = settings.Databases.Select(b => new DbForTask(Path.GetFullPath(b), IsContaminant(b))).ToList();
// check that experimental design is defined if normalization is enabled
var searchTasks = taskList
.Where(p => p.Item2.TaskType == MyTask.Search)
.Select(p => (SearchTask)p.Item2);
string pathToExperDesign = Directory.GetParent(startingRawFilenameList.First()).FullName;
pathToExperDesign = Path.Combine(pathToExperDesign, GlobalVariables.ExperimentalDesignFileName);
if (!File.Exists(pathToExperDesign))
{
if (searchTasks.Any(p => p.SearchParameters.Normalize))
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Experimental design file was missing! This must be defined to do normalization. Download a template from https://github.com/smith-chem-wisc/MetaMorpheus/wiki/Experimental-Design");
}
return(5);
}
}
else
{
ExperimentalDesign.ReadExperimentalDesign(pathToExperDesign, startingRawFilenameList, out var errors);
if (errors.Any())
{
if (searchTasks.Any(p => p.SearchParameters.Normalize))
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
foreach (var error in errors)
{
Console.WriteLine(error);
}
}
return(5);
}
else
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("An experimental design file was found, but an error " +
"occurred reading it. Do you wish to continue with an empty experimental design? (This will delete your experimental design file) y/n" +
"\nThe error was: " + errors.First());
var result = Console.ReadLine();
if (result.ToLowerInvariant() == "y" || result.ToLowerInvariant() == "yes")
{
File.Delete(pathToExperDesign);
}
else
{
return(5);
}
}
else
{
// just continue on if verbosity is on "none"
File.Delete(pathToExperDesign);
}
}
}
else
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Read ExperimentalDesign.tsv successfully");
}
}
}
EverythingRunnerEngine a = new EverythingRunnerEngine(taskList, startingRawFilenameList, startingXmlDbFilenameList, settings.OutputFolder);
try
{
a.Run();
}
catch (Exception e)
{
while (e.InnerException != null)
{
e = e.InnerException;
}
var message = "Run failed, Exception: " + e.Message;
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(message);
}
errorCode = 4;
}
return(errorCode);
}
private static int Run(CommandLineSettings settings)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Welcome to MetaMorpheus");
Console.WriteLine(GlobalVariables.MetaMorpheusVersion);
}
int errorCode = 0;
try
{
settings.ValidateCommandLineSettings();
CommandLineSettings = settings;
}
catch (Exception e)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("MetaMorpheus encountered the following error:" + Environment.NewLine + e.Message);
}
errorCode = 2;
return(errorCode);
}
if (settings.GenerateDefaultTomls)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine("Generating default tomls at location: " + settings.OutputFolder);
}
CommandLineSettings.GenerateDefaultTaskTomls(settings.OutputFolder);
return(errorCode);
}
// set up microvignette
if (settings.RunMicroVignette)
{
// set up the spectra file
settings.Spectra.Clear();
settings.Spectra.Add(Path.Combine(GlobalVariables.DataDir, @"Data", "SmallCalibratible_Yeast.mzML"));
// set up the database
settings.Databases.Clear();
settings.Databases.Add(Path.Combine(GlobalVariables.DataDir, @"Data", "SmallYeast.fasta"));
// set up the tasks (calibration, GPTMD, search)
settings.Tasks.Clear();
CommandLineSettings.GenerateDefaultTaskTomls(settings.OutputFolder);
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "CalibrationTask.toml"));
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "GptmdTask.toml"));
settings.Tasks.Add(Path.Combine(settings.OutputFolder, "SearchTask.toml"));
}
MetaMorpheusEngine.WarnHandler += WarnHandler;
MetaMorpheusEngine.OutProgressHandler += MyEngine_outProgressHandler;
MetaMorpheusEngine.StartingSingleEngineHander += MyEngine_startingSingleEngineHander;
MetaMorpheusEngine.FinishedSingleEngineHandler += MyEngine_finishedSingleEngineHandler;
MetaMorpheusTask.WarnHandler += WarnHandler;
MetaMorpheusTask.LogHandler += LogHandler;
MetaMorpheusTask.StartingSingleTaskHander += MyTaskEngine_startingSingleTaskHander;
MetaMorpheusTask.FinishedSingleTaskHandler += MyTaskEngine_finishedSingleTaskHandler;
MetaMorpheusTask.FinishedWritingFileHandler += MyTaskEngine_finishedWritingFileHandler;
bool containsRawFiles = settings.Spectra.Select(v => Path.GetExtension(v).ToLowerInvariant()).Any(v => v == ".raw");
if (containsRawFiles && !GlobalVariables.GlobalSettings.UserHasAgreedToThermoRawFileReaderLicence)
{
// write the Thermo RawFileReader licence agreement
Console.WriteLine(ThermoRawFileReader.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().ToLowerInvariant();
if (res == "y")
{
var newGlobalSettings = new GlobalSettings
{
UserHasAgreedToThermoRawFileReaderLicence = true,
WriteExcelCompatibleTSVs = GlobalVariables.GlobalSettings.WriteExcelCompatibleTSVs
};
Toml.WriteFile <GlobalSettings>(newGlobalSettings, Path.Combine(GlobalVariables.DataDir, @"settings.toml"));
GlobalVariables.GlobalSettings = newGlobalSettings;
}
else
{
Console.WriteLine("Thermo licence has been declined. Exiting MetaMorpheus. You can still search .mzML and .mgf files without agreeing to the Thermo licence.");
errorCode = 3;
return(errorCode);
}
}
foreach (var db in settings.Databases)
{
if (!Path.GetExtension(db).Equals(".fasta"))
{
GlobalVariables.AddMods(UsefulProteomicsDatabases.ProteinDbLoader.GetPtmListFromProteinXml(db).OfType <Modification>(), true);
// print any error messages reading the mods to the console
foreach (var error in GlobalVariables.ErrorsReadingMods)
{
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(error);
}
}
GlobalVariables.ErrorsReadingMods.Clear();
}
}
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)>();
var tasks = settings.Tasks.ToList();
for (int i = 0; i < tasks.Count; i++)
{
var filePath = tasks[i];
var toml = Toml.ReadFile(filePath, MetaMorpheusTask.tomlConfig);
switch (toml.Get <string>("TaskType"))
{
case "Search":
var searchTask = Toml.ReadFile <SearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "SearchTask", searchTask));
break;
case "Calibrate":
var calibrationTask = Toml.ReadFile <CalibrationTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "CalibrationTask", calibrationTask));
break;
case "Gptmd":
var GptmdTask = Toml.ReadFile <GptmdTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "GptmdTask", GptmdTask));
break;
case "XLSearch":
var XlTask = Toml.ReadFile <XLSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "XLSearchTask", XlTask));
break;
case "GlycoSearch":
var GlycoTask = Toml.ReadFile <GlycoSearchTask>(filePath, MetaMorpheusTask.tomlConfig);
taskList.Add(("Task" + (i + 1) + "GlycoSearchTask", GlycoTask));
break;
default:
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(toml.Get <string>("TaskType") + " is not a known task type! Skipping.");
}
break;
}
}
List <string> startingRawFilenameList = settings.Spectra.Select(b => Path.GetFullPath(b)).ToList();
List <DbForTask> startingXmlDbFilenameList = settings.Databases.Select(b => new DbForTask(Path.GetFullPath(b), IsContaminant(b))).ToList();
EverythingRunnerEngine a = new EverythingRunnerEngine(taskList, startingRawFilenameList, startingXmlDbFilenameList, settings.OutputFolder);
try
{
a.Run();
}
catch (Exception e)
{
while (e.InnerException != null)
{
e = e.InnerException;
}
var message = "Run failed, Exception: " + e.Message;
if (settings.Verbosity == CommandLineSettings.VerbosityType.minimal || settings.Verbosity == CommandLineSettings.VerbosityType.normal)
{
Console.WriteLine(message);
}
errorCode = 4;
}
return(errorCode);
}