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); }
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); }
public static void DoQc(WorkflowParameters parameters) { //QcDataCollectionDDA qcDataCollection; dynamic qcDataCollection; string dataDirectory = parameters.RawFileDirectory; string qcDirectory = parameters.QcParams.QcDirectory; string qcSearchDataDirecotry = parameters.QcParams.QcSearchDataDirectory; List <string> fileList = new List <string>(); string qcFile = Path.Combine(qcDirectory, "QC.xml"); (fileList, qcDataCollection) = GetFileListAndQcFile(parameters); foreach (string fileName in fileList) { Console.WriteLine("\nProcessing {0}", fileName); if (!RawFileInfo.CheckIfValid(fileName)) { continue; } // okay, it is probably a real raw file, let's do the QC // check if the raw file already exists in the QC data with a different name if (CheckIfFilePresentInQcCollection(fileName, qcDataCollection)) { Log.Information("A file with the same creation date and time as {File} already exists in the QC data", fileName); Console.WriteLine("A file with the same creation date and time as {File} already exists in the QC data. Skipping to next file.", fileName); continue; } IRawFileThreadManager rawFileThreadManager = RawFileReaderFactory.CreateThreadManager(fileName); if (parameters.ExpType == ExperimentType.DDA) { WorkFlowsDDA.QcDDA(rawFileThreadManager, parameters); } //else if (parameters.ExpType == ExperimentType.DIA) //{ // WorkFlowsDIA.QcDIA(rawFileThreadManager, parameters); //} /* * using (IRawDataPlus rawFile = RawFileReaderFactory.ReadFile(fileName)) * { * rawFile.SelectInstrument(Device.MS, 1); * * if (parameters.ExpType == ExperimentType.DDA) * { * WorkFlowsDDA.QcDDA(rawFile, parameters); * } * else if (parameters.ExpType == ExperimentType.DIA) * { * WorkFlowsDIA.QcDIA(rawFile, parameters); * } * }*/ Log.Information("QC finished: {File}", fileName); } Log.Information("QC of all files completed"); Console.WriteLine("QC of all files completed!"); }