public void Test1()
{
TargetedWorkflowParameters o16o18workflowParameters = new O16O18WorkflowParameters();
var parentWorkflow = new O16O18IqWorkflow(o16o18workflowParameters);
TargetedWorkflowParameters workflowParameters = new BasicTargetedWorkflowParameters();
var childWorkflow = new BasicIqWorkflow(workflowParameters);
IqTarget parentTarget = new IqChargeStateTarget();
IqTarget childTarget1 = new IqChargeStateTarget();
IqTarget childTarget2 = new IqChargeStateTarget();
IqTarget childTarget3 = new IqChargeStateTarget();
parentTarget.AddTarget(childTarget1);
parentTarget.AddTarget(childTarget2);
parentTarget.AddTarget(childTarget3);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, parentTarget);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, parentTarget);
Assert.IsNotNull(parentTarget.ChildTargets().First().Workflow);
var childTargets = parentTarget.ChildTargets();
foreach (var childTarget in childTargets)
{
Assert.IsTrue(childTarget.Workflow is BasicIqWorkflow);
}
Assert.IsTrue(parentTarget.Workflow is O16O18IqWorkflow);
}
public void testVladsData()
{
var testFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\RawData\Alz_P01_A01_097_26Apr12_Roc_12-03-15.RAW";
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\O16O18_standard_testing\Test1_VladAlz\Targets\MT_Human_ALZ_O18_P836\MassTags_PMT2_First60.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndAlignRun(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24653;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.MSToleranceInPPM = 10;
parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromatogramCorrelationIsPerformed = true;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as O16O18TargetedResultObject;
Assert.IsTrue(workflow.Success);
Assert.IsFalse(result.FailedResult);
result.DisplayToConsole();
Console.WriteLine("Correlation between 016 and O18(double label)= " + result.ChromCorrO16O18DoubleLabel);
Assert.IsTrue(result.ChromCorrO16O18DoubleLabel > 0);
Console.WriteLine("theor monomass= \t" + result.Target.MonoIsotopicMass);
Console.WriteLine("monomass= \t" + result.IsotopicProfile.MonoIsotopicMass);
Console.WriteLine("ppmError before= \t" + result.MassErrorBeforeAlignment);
Console.WriteLine("ppmError after= \t" + result.MassErrorAfterAlignment);
}
public void ChromCorrelatorTest1()
{
var rawFilename = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw";
var run = new RunFactory().CreateRun(rawFilename);
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new IqExecutor(executorBaseParameters, run);
executor.LoadChromData(run);
var workflowAssigner = new IqWorkflowAssigner();
TargetedWorkflowParameters workflowParameters = new O16O18WorkflowParameters();
IqWorkflow workflow = new O16O18IqWorkflow(run, workflowParameters);
IqTarget iqTarget = new IqChargeStateTarget();
iqTarget.EmpiricalFormula = "C58H100N18O20";
iqTarget.Code = "GAAQNIIPASTGAAK";
iqTarget.ID = 1093;
iqTarget.ChargeState = 0;
var iqTargetList = new List <IqTarget>();
iqTargetList.Add(iqTarget);
var utilities = new IqTargetUtilities();
utilities.CreateChildTargets(iqTargetList);
workflowAssigner.AssignWorkflowToParent(workflow, iqTargetList);
workflowAssigner.AssignWorkflowToChildren(workflow, iqTargetList);
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
foreach (var target in iqTarget.ChildTargets())
{
utilities.UpdateTargetMissingInfo(target);
target.TheorIsotopicProfile = theorFeatureGenerator.GenerateTheorProfile(target.EmpiricalFormula, target.ChargeState);
}
foreach (var childTarget in iqTarget.ChildTargets())
{
var result = childTarget.CreateResult();
var correlator = new O16O18ChromCorrelator(7, 0.1, 20, Globals.ToleranceUnit.PPM);
var corrData = correlator.CorrelateData(run, result, 5700, 6500);
var corrDataItem1 = corrData.CorrelationDataItems.First();
Console.WriteLine("z= \t" + childTarget.ChargeState + "\tCorrelationData (slope,intercept,rsquared)= \t" + corrDataItem1);
}
}
public void findSingleMassTag_test1()
{
var testFile = @"D:\Data\O16O18\Weijun\TechTest_O18_02\TechTest_O18_02_RunA_10Dec09_Doc_09-11-08.RAW";
var massTagFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2011\O16O18_TargetedProcessing\Targets\MassTags_MousePlasma_1709_allChargeStates_nonRedundant.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 6643962;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.1;
parameters.MSToleranceInPPM = 10;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Assert.IsNotNull(result);
result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
Assert.AreEqual(6865, result.ScanSet.PrimaryScanNumber);
}
public void Test1()
{
var testFile = @"\\protoapps\UserData\Slysz\Data\O16O18\BSA\BSA_18O_99_8Jan11_Falcon_10-12-09.RAW";
var massTagFile =
@"\\protoapps\UserData\Slysz\Data\O16O18\BSA\Targets\BSAmassTags_MinimalInfo_withScans.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 3;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.2;
parameters.MSToleranceInPPM = 10;
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.MostIntense;
parameters.ChromGeneratorMode = DeconTools.Backend.Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
parameters.ChromSmootherNumPointsInSmooth = 31;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
Assert.IsTrue(workflow.Result.Target.ScanLCTarget > 0);
Assert.IsNotNull(workflow.ChromPeakSelected);
Assert.AreEqual(10622, (int)workflow.ChromPeakSelected.XValue);
Console.WriteLine("ChromPeak scan value = " + workflow.ChromPeakSelected.XValue);
}
public void checkO16O18ChromGenMode_test1()
{
//
var testFile = @"D:\Data\O16O18\Weijun\TechTest_O18_02\TechTest_O18_02_RunA_10Dec09_Doc_09-11-08.RAW";
var massTagFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2011\O16O18_TargetedProcessing\Targets\MassTags_MousePlasma_1709_allChargeStates_nonRedundant.txt";
var peakTestFile = testFile.Replace(".RAW", "_peaks.txt");
var run = RunUtilities.CreateAndLoadPeaks(testFile, peakTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 20746149;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new O16O18WorkflowParameters();
parameters.ChromNETTolerance = 0.1;
parameters.MSToleranceInPPM = 10;
parameters.ChromGeneratorMode = DeconTools.Backend.Globals.ChromatogramGeneratorMode.O16O18_THREE_MONOPEAKS;
parameters.ChromPeakDetectorPeakBR = 1;
var workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
result.DisplayToConsole();
// Assert.AreEqual(3498, result.ScanSet.PrimaryScanNumber);
Console.WriteLine("O16O18 ChromMode PeaksWithinTol = " + result.NumChromPeaksWithinTolerance);
Console.WriteLine("O16O18 ChromMode HQPeaksWithinTol = " + result.NumQualityChromPeaks);
//foreach (var item in workflow.ChromPeaksDetected)
//{
// Console.WriteLine("peak\t" + item.XValue.ToString("0.0") + "\t" + item.Height.ToString("0"));
//}
// TestUtilities.DisplayXYValues(workflow.ChromatogramXYData);
parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
workflow = new O16O18Workflow(run, parameters);
workflow.Execute();
result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Console.WriteLine("MonoChromMode PeaksWithinTol = " + result.NumChromPeaksWithinTolerance);
Console.WriteLine("O16O18 ChromMode HQPeaksWithinTol = " + result.NumQualityChromPeaks);
// TestUtilities.DisplayXYValues(workflow.ChromatogramXYData);
//foreach (var item in workflow.ChromPeaksDetected)
//{
// Console.WriteLine("peak\t" + item.XValue.ToString("0.0") + "\t" + item.Height.ToString("0"));
//}
result.DisplayToConsole();
}
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);
}
