static int DoStuff(ArgumentParser.ParseOptions opts)
{
if (!opts.ParseData & !opts.Quant & !opts.Metrics & !opts.WriteMGF & (opts.Chromatogram == null))
{
Console.WriteLine("You have not indicated what output you want (i.e. one or more of -p, -q, -m, -x, --chro). " +
"Are you sure you want to proceed? Nothing will be written to disk.");
Console.Write("(press y to proceed): ");
string proceed = Console.ReadKey().KeyChar.ToString();
Console.WriteLine();
if (proceed != "y")
{
Environment.Exit(0);
}
}
List <string> files = new List <string>();
if (opts.InputFiles.Count() > 0) // did the user give us a list of files?
{
List <string> problems = new List <string>();
files = opts.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));
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));
return(1);
}
// 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 // did the user give us a directory?
{
if (Directory.Exists(opts.InputDirectory))
{
files = Directory.GetFiles(opts.InputDirectory, "*.*", 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}", opts.InputDirectory);
return(1);
}
// 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));
}
if (opts.Quant)
{
List <string> possible = new List <string>()
{
"TMT0", "TMT2", "TMT6", "TMT10", "TMT11", "iTRAQ4", "iTRAQ8"
};
if (!possible.Contains(opts.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}", opts.LabelingReagents);
return(1);
}
}
if (opts.Chromatogram != null)
{
List <string> possible = new List <string>()
{
"1T", "2T", "3T", "1B", "2B", "3B", "1TB", "2TB", "3TB", "1TB", "2TB", "3TB"
};
if (!possible.Contains(opts.Chromatogram))
{
Console.WriteLine("ERROR: Incorrect format for --chro. See help.");
Log.Error("Invalid chromatogram argument provided: {Chro}", opts.Chromatogram);
return(1);
}
}
/*
* // is the experiment type valid?
* if (! new List<string>() { "DDA", "DIA", "PRM" }.Contains(opts.ExperimentType))
* {
* Log.Error("Experiment type of {ExpType} was passed", opts.ExperimentType);
* Console.WriteLine("Experiment type must be one of ['DDA', 'DIA', 'PRM'], not {0}", opts.ExperimentType);
* Environment.Exit(1);
* }*/
System.Diagnostics.Stopwatch singleFileTime = new System.Diagnostics.Stopwatch();
System.Diagnostics.Stopwatch totalTime = new System.Diagnostics.Stopwatch();
totalTime.Start();
WorkflowParameters parameters = new WorkflowParameters(opts);
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);
}
if (parameters.ExpType == ExperimentType.DDA)
{
WorkFlowsDDA.ParseDDA(rawFile, parameters);
}
else if (parameters.ExpType == ExperimentType.DIA)
{
WorkFlowsDIA.ParseDIA(rawFile, parameters);
}
}
singleFileTime.Stop();
Console.WriteLine("\nElapsed time: {0} s", Math.Round(Convert.ToDouble(singleFileTime.ElapsedMilliseconds) / 1000.0, 2));
singleFileTime.Reset();
}
totalTime.Stop();
Console.WriteLine("\nTime to process all {0} files: {1}", files.Count(), totalTime.Elapsed);
return(0);
}
