static int Main(string[] args)
{
var options = new IqConsoleOptions();
var datasetList = new List <string>();
if (!CommandLine.Parser.Default.ParseArguments(args, options))
{
return(-1);
}
var inputFile = options.InputFile;
var inputFileIsAListOfDatasets = inputFile.ToLower().EndsWith(".txt");
if (inputFileIsAListOfDatasets)
{
using (var reader = new StreamReader(inputFile))
{
while (reader.Peek() != -1)
{
var datsetName = reader.ReadLine();
datasetList.Add(datsetName);
}
}
}
else
{
datasetList.Add(options.InputFile);
}
var numDatasets = datasetList.Count;
var datasetCounter = 0;
foreach (var dataset in datasetList)
{
datasetCounter++;
var datasetNameContainsPath = dataset.Contains(@"\");
string currentDatasetPath;
if (datasetNameContainsPath)
{
currentDatasetPath = dataset;
}
else
{
if (string.IsNullOrEmpty(options.TemporaryWorkingFolder))
{
IqLogger.Log.Fatal("Trying to grab .raw file from DMS, but no temporary working folder was declared. Use option -f. ");
break;
}
if (string.IsNullOrEmpty(options.OutputFolder))
{
options.OutputFolder = options.TemporaryWorkingFolder;
}
var datasetutil = new DatasetUtilities();
//TODO: figure out how to do this while supporting other file types
currentDatasetPath = Path.Combine(datasetutil.GetDatasetPath(dataset), dataset + ".raw");
if (currentDatasetPath.ToLower().Contains("purged"))
{
currentDatasetPath = Path.Combine(datasetutil.GetDatasetPathArchived(dataset), dataset + ".raw");
}
}
if (!File.Exists(currentDatasetPath))
{
IqLogger.Log.Fatal("!!!!!!!!! Dataset not found! Dataset path = " + currentDatasetPath);
return(-2);
}
if (string.IsNullOrEmpty(options.OutputFolder))
{
options.OutputFolder = RunUtilities.GetDatasetParentFolder(currentDatasetPath);
}
var executorParameters = GetExecutorParameters(options);
IqLogger.Log.Info("IQ analyzing dataset " + datasetCounter + " of " + numDatasets + ". Dataset = " + dataset);
if (options.UseOldIq)
{
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters,
currentDatasetPath);
//executor.Targets.TargetList = executor.Targets.TargetList.Take(10).ToList();
executor.MsgfFdrScoreCutoff = 0.1;
executor.Execute();
}
else
{
var run = new RunFactory().CreateRun(currentDatasetPath);
var executor = new IqExecutor(executorParameters, run);
executor.LoadAndInitializeTargets(executorParameters.TargetsFilePath);
executor.SetupMassAndNetAlignment();
executor.DoAlignment();
foreach (var iqTarget in executor.Targets)
{
TargetedWorkflowParameters workflowParameters = new O16O18WorkflowParameters();
if (iqTarget.ElutionTimeTheor > 0.7 || iqTarget.ElutionTimeTheor < 0.15)
{
//TODO: remove the hard-coded value
workflowParameters.ChromNETTolerance = 0.1;
}
else
{
//TODO: remove the hard-coded value
workflowParameters.ChromNETTolerance = 0.025;
}
if (run.MassAlignmentInfo != null && run.MassAlignmentInfo.StdevPpmShiftData > 0)
{
workflowParameters.ChromGenTolerance = run.MassAlignmentInfo.StdevPpmShiftData * 3;
}
//define workflows for parentTarget and childTargets
// Note: this is currently hard-coded to user O16O18IqWorkflow
var parentWorkflow = new ChromPeakDeciderIqWorkflow(run, workflowParameters);
var childWorkflow = new O16O18IqWorkflow(run, workflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, iqTarget);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, iqTarget);
}
executor.Execute();
run.Dispose();
}
}
return(0);
}
private static BasicTargetedWorkflowExecutorParameters GetExecutorParameters(IqConsoleOptions options)
{
var executorParameters = new BasicTargetedWorkflowExecutorParameters
{
TargetsFilePath = options.TargetFile,
OutputFolderBase = options.OutputFolder,
TargetedAlignmentIsPerformed = options.IsAlignmentPerformed,
WorkflowParameterFile = options.WorkflowParameterFile,
TargetedAlignmentWorkflowParameterFile = options.AlignmentParameterFile,
IsMassAlignmentPerformed = options.IsMassAlignmentPerformed,
IsNetAlignmentPerformed = options.IsNetAlignmentPerformed,
ReferenceTargetsFilePath = options.ReferenceTargetFile,
TargetType = options.UseInputScan
? Globals.TargetType.LcmsFeature
: Globals.TargetType.DatabaseTarget
};
if (!string.IsNullOrEmpty(options.TemporaryWorkingFolder))
{
executorParameters.CopyRawFileLocal = true;
executorParameters.FolderPathForCopiedRawDataset = options.TemporaryWorkingFolder;
executorParameters.DeleteLocalDatasetAfterProcessing = true;
}
if (!string.IsNullOrWhiteSpace(options.WorkflowParameterFile))
{
// Load workflow parameter file to update the options
var parameterList = LoadParameters(options.WorkflowParameterFile);
executorParameters.CopyRawFileLocal = GetParameter(parameterList, "CopyRawFileLocal", executorParameters.CopyRawFileLocal);
executorParameters.DeleteLocalDatasetAfterProcessing = GetParameter(parameterList, "DeleteLocalDatasetAfterProcessing", executorParameters.DeleteLocalDatasetAfterProcessing);
// Skip: FileContainingDatasetPaths
executorParameters.FolderPathForCopiedRawDataset = GetParameter(parameterList, "FolderPathForCopiedRawDataset", executorParameters.FolderPathForCopiedRawDataset);
// Skip: LoggingFolder
executorParameters.TargetsFilePath = GetParameter(parameterList, "TargetsFilePath", executorParameters.TargetsFilePath);
var targetType = GetParameter(parameterList, "TargetType", "DatabaseTarget");
if (string.Equals(targetType, "LcmsFeature", StringComparison.CurrentCultureIgnoreCase))
{
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
}
if (string.Equals(targetType, "DatabaseTarget", StringComparison.CurrentCultureIgnoreCase))
{
executorParameters.TargetType = Globals.TargetType.DatabaseTarget;
}
executorParameters.OutputFolderBase = GetParameter(parameterList, "ResultsFolder", executorParameters.OutputFolderBase);
executorParameters.WorkflowParameterFile = GetParameter(parameterList, "WorkflowParameterFile", executorParameters.WorkflowParameterFile);
// ToDo: Use this: <WorkflowType>TopDownTargetedWorkflowExecutor1</WorkflowType>
executorParameters.IsMassAlignmentPerformed = GetParameter(parameterList, "IsMassAlignmentPerformed", executorParameters.IsMassAlignmentPerformed);
executorParameters.IsNetAlignmentPerformed = GetParameter(parameterList, "IsNetAlignmentPerformed", executorParameters.IsNetAlignmentPerformed);
executorParameters.ReferenceTargetsFilePath = GetParameter(parameterList, "ReferenceTargetFile", executorParameters.ReferenceTargetsFilePath);
}
return(executorParameters);
}
