protected virtual void SetupLogging()
{
string loggingFolder;
if (string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase))
{
loggingFolder = RunUtilities.GetDatasetParentFolder(DatasetPath);
}
else
{
loggingFolder = Path.Combine(ExecutorParameters.OutputFolderBase, "Logs");
}
try
{
if (!Directory.Exists(loggingFolder))
{
Directory.CreateDirectory(loggingFolder);
}
}
catch (Exception ex)
{
throw new System.IO.IOException("Trying to set up logging folder but there was a critical error. Details:\n\n" + ex.Message, ex);
}
_loggingFileName = Path.Combine(loggingFolder, RunUtilities.GetDatasetName(DatasetPath) + "_log.txt");
}
protected void SetupAlignment()
{
string alignmentFolder;
if (string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase))
{
alignmentFolder = Path.Combine(RunUtilities.GetDatasetParentFolder(DatasetPath), "AlignmentInfo");
}
else
{
alignmentFolder = Path.Combine(ExecutorParameters.OutputFolderBase, "AlignmentInfo");
}
if (!Directory.Exists(alignmentFolder))
{
Directory.CreateDirectory(alignmentFolder);
}
_alignmentFolder = alignmentFolder;
}
protected override string GetOutputFileName()
{
string resultsFolder;
if (string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase))
{
resultsFolder = RunUtilities.GetDatasetParentFolder(DatasetPath);
}
else
{
resultsFolder = Path.Combine(ExecutorParameters.OutputFolderBase, "IqResults");
}
if (!Directory.Exists(resultsFolder))
{
Directory.CreateDirectory(resultsFolder);
}
return(Path.Combine(resultsFolder, Run.DatasetName + "_quant.txt"));
}
public new void InitializeWorkflow()
{
_resultsFolder = string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase) ? RunUtilities.GetDatasetParentFolder(DatasetPath) : GetResultsFolder(ExecutorParameters.OutputFolderBase);
MassTagsForTargetedAlignment = GetMassTagTargets(GetTargetFilePathForIqAlignment());
var targetsFilePathIsEmpty = (String.IsNullOrEmpty(ExecutorParameters.TargetsFilePath));
var currentTargetsFilePath = targetsFilePathIsEmpty ? TryFindTargetsForCurrentDataset() : ExecutorParameters.TargetsFilePath;
Targets = CreateTargets(ExecutorParameters.TargetType, currentTargetsFilePath);
if (ExecutorParameters.TargetType == Globals.TargetType.LcmsFeature)
{
UpdateTargetMissingInfo();
}
if (_workflowParameters == null)
{
_workflowParameters = WorkflowParameters.CreateParameters(ExecutorParameters.WorkflowParameterFile);
_workflowParameters.LoadParameters(ExecutorParameters.WorkflowParameterFile);
}
if (ExecutorParameters.TargetedAlignmentIsPerformed)
{
if (string.IsNullOrEmpty(ExecutorParameters.TargetedAlignmentWorkflowParameterFile))
{
throw new FileNotFoundException(
"Cannot initialize workflow. TargetedAlignment is requested but TargetedAlignmentWorkflowParameter file is not found. Check path for the 'TargetedAlignmentWorkflowParameterFile' ");
}
TargetedAlignmentWorkflowParameters = new TargetedAlignerWorkflowParameters();
TargetedAlignmentWorkflowParameters.LoadParameters(ExecutorParameters.TargetedAlignmentWorkflowParameterFile);
}
TargetedWorkflow = TargetedWorkflow.CreateWorkflow(_workflowParameters);
}
public void InitializeWorkflow()
{
if (string.IsNullOrEmpty(ExecutorParameters.OutputFolderBase))
{
_resultsFolder = RunUtilities.GetDatasetParentFolder(DatasetPath);
}
else
{
_resultsFolder = GetResultsFolder(ExecutorParameters.OutputFolderBase);
}
if (ExecutorParameters.TargetedAlignmentIsPerformed)
{
MassTagsForTargetedAlignment = GetMassTagTargets(GetTargetFilePathForIqAlignment());
}
var targetsFilePathIsEmpty = (String.IsNullOrEmpty(ExecutorParameters.TargetsFilePath));
string currentTargetsFilePath;
if (targetsFilePathIsEmpty)
{
currentTargetsFilePath = TryFindTargetsForCurrentDataset(); //check for a _targets file specifically associated with dataset
}
else
{
currentTargetsFilePath = ExecutorParameters.TargetsFilePath;
}
Targets = CreateTargets(ExecutorParameters.TargetType, currentTargetsFilePath);
Check.Ensure(Targets != null && Targets.TargetList.Count > 0,
"Target massTags is empty (or all peptides contain unknown modifications). Check the path to the massTag data file.");
IqLogger.Log.Info("Total targets loaded= " + Targets.TargetList.Count);
if (ExecutorParameters.TargetType == Globals.TargetType.LcmsFeature)
{
UpdateTargetMissingInfo();
}
if (TargetedWorkflow == null)
{
if (_workflowParameters == null)
{
_workflowParameters = WorkflowParameters.CreateParameters(ExecutorParameters.WorkflowParameterFile);
_workflowParameters.LoadParameters(ExecutorParameters.WorkflowParameterFile);
}
TargetedWorkflow = TargetedWorkflow.CreateWorkflow(_workflowParameters);
}
else
{
_workflowParameters = TargetedWorkflow.WorkflowParameters;
}
if (ExecutorParameters.TargetedAlignmentIsPerformed)
{
if (string.IsNullOrEmpty(ExecutorParameters.TargetedAlignmentWorkflowParameterFile))
{
throw new FileNotFoundException(
"Cannot initialize workflow. TargetedAlignment is requested but TargetedAlignmentWorkflowParameter file is not found. Check path for the 'TargetedAlignmentWorkflowParameterFile' ");
}
TargetedAlignmentWorkflowParameters = new TargetedAlignerWorkflowParameters();
TargetedAlignmentWorkflowParameters.LoadParameters(ExecutorParameters.TargetedAlignmentWorkflowParameterFile);
}
}
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);
}