static int DoStuff(ArgumentParser.ExampleOptions opts)
{
if (opts.DisplayModifications)
{
Examples.ExampleMods();
}
if (opts.InterfaceExamples)
{
Examples.CommandLineUsage();
}
return(0);
}
static int Run(Dictionary <string, object> opts)
{
if ((bool)opts["ExampleCommands"] == true)
{
Examples.CommandLineUsage();
Environment.Exit(0);
}
if ((bool)opts["ExampleModifications"] == true)
{
Examples.ExampleMods();
Environment.Exit(0);
}
List <string> files = new List <string>();
QcDataCollection qcDataCollection = new QcDataCollection();
WorkflowParameters parameters = new WorkflowParameters(opts);
if (parameters.InputFiles != null) // did the user give us a list of files?
{
List <string> problems = new List <string>();
files = parameters.InputFiles.ToList();
// check if the list provided contains only .raw files
foreach (string file in files)
{
if (!file.EndsWith(".raw", StringComparison.OrdinalIgnoreCase))
{
problems.Add(file);
}
}
if (problems.Count() == 1)
{
Console.WriteLine("\nERROR: {0} does not appear to be a .raw file. Invoke '>RawTools --help' if you need help.", problems.ElementAt(0));
Log.Error("Invalid file provided: {0}", problems.ElementAt(0));
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
if (problems.Count() > 1)
{
Console.WriteLine("\nERROR: The following {0} files do not appear to be .raw files. Invoke '>RawTools --help' if you need help." +
"\n\n{1}", problems.Count(), String.Join("\n", problems));
Log.Error("Invalid files provided: {0}", String.Join(" ", problems));
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
files = RawFileInfo.RemoveInAcquistionFiles(files);
// if the file location(s) are relative, we need to get the absolute path to them
files.EnsureAbsolutePaths();
Log.Information("Files to be processed, provided as list: {0}", String.Join(" ", files));
}
else if (!String.IsNullOrEmpty(parameters.RawFileDirectory)) // did the user give us a directory?
{
// if QC is being done, use the QC method snf get the qc data collection at the same time
if (parameters.QcParams.QcDirectory != null)
{
(files, qcDataCollection) = QcWorkflow.GetFileListAndQcFile(parameters, parameters.IncludeSubdirectories);
}
// if not, the parse method
else if (Directory.Exists(parameters.RawFileDirectory))
{
files = Directory.GetFiles(parameters.RawFileDirectory, "*.*", SearchOption.TopDirectoryOnly)
.Where(s => s.EndsWith(".raw", StringComparison.OrdinalIgnoreCase)).ToList();
}
else
{
Console.WriteLine("ERROR: The provided directory does not appear to be valid.");
Log.Error("Invalid directory provided: {0}", parameters.RawFileDirectory);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
files = RawFileInfo.RemoveInAcquistionFiles(files);
// if the file location(s) are relative, we need to get the absolute path to them
files.EnsureAbsolutePaths();
Log.Information("Files to be processed, provided as directory: {0}", String.Join(" ", files));
}
else
{
Console.WriteLine("ERROR: At least one of the following arguments is required: -f, -d");
Log.Error("No raw files or directory specified.");
return(1);
}
if (parameters.ParseParams.Quant)
{
List <string> possible = new List <string>()
{
"TMT0", "TMT2", "TMT6", "TMT10", "TMT11", "iTRAQ4", "iTRAQ8"
};
if (!possible.Contains(parameters.ParseParams.LabelingReagents))
{
Console.WriteLine("ERROR: For quantification, the labeling reagent must be one of {TMT0, TMT2, TMT6, TMT10, TMT11, iTRAQ4, iTRAQ8}");
Log.Error("Invalid labeling reagent provided: {0}", parameters.ParseParams.LabelingReagents);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
}
if (parameters.ParseParams.Chromatogram != null)
{
List <string> possible = new List <string>()
{
"1", "2", "3", "T", "B"
};
foreach (var x in parameters.ParseParams.Chromatogram)
{
if (!possible.Contains(x.ToString()))
{
Console.WriteLine("ERROR: Incorrect format for -chro. See help.");
Log.Error("Invalid chromatogram argument provided: {Chro}", parameters.ParseParams.Chromatogram);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
}
}
System.Diagnostics.Stopwatch singleFileTime = new System.Diagnostics.Stopwatch();
System.Diagnostics.Stopwatch totalTime = new System.Diagnostics.Stopwatch();
totalTime.Start();
foreach (string file in files)
{
singleFileTime.Start();
Console.WriteLine("\nProcessing: {0}\n", file);
//using (IRawDataPlus rawFile = RawFileReaderFactory.ReadFile(fileName:file))
using (IRawFileThreadManager rawFile = RawFileReaderFactory.CreateThreadManager(file))
{
if (parameters.ParseParams.OutputDirectory == null)
{
parameters.ParseParams.OutputDirectory = Path.GetDirectoryName(file);
}
WorkFlowsDDA.UniversalDDA(rawFile, parameters, qcDataCollection);
}
singleFileTime.Stop();
Console.WriteLine("\nElapsed time: {0} s", Math.Round(Convert.ToDouble(singleFileTime.ElapsedMilliseconds) / 1000.0, 2));
singleFileTime.Reset();
}
if (parameters.LogDump)
{
Write.LogDump.WriteToDisk(parameters);
}
totalTime.Stop();
Console.WriteLine("\nTime to process all {0} files: {1}", files.Count(), totalTime.Elapsed);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(0);
}