public void Test2()
{
string copyToFolder = @"D:\Data\TopDown";
string outputFolder = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowTesting\Output";
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = true;
executorParameters.FolderPathForCopiedRawDataset = copyToFolder;
executorParameters.OutputFolderBase = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowTesting\Output";
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
executorParameters.WorkflowParameterFile =
@"\\proto-7\VOrbiETD01\2012_1\CPTAC_Peptidome_Test1_P1_Poroshell_03Feb12_Frodo_Poroshell300SB\MSA201202231748_Auto796395\MSAlign_Quant_Workflow_2012-07-25.xml";
executorParameters.TargetsFilePath =
@"\\proto-7\VOrbiETD01\2012_1\CPTAC_Peptidome_Test1_P1_Poroshell_03Feb12_Frodo_Poroshell300SB\MSA201202231748_Auto796395\CPTAC_Peptidome_Test1_P1_Poroshell_03Feb12_Frodo_Poroshell300SB_MSAlign_ResultTable.txt";
const string testDatasetPath =
@"\\proto-7\VOrbiETD01\2012_1\CPTAC_Peptidome_Test1_P1_Poroshell_03Feb12_Frodo_Poroshell300SB\CPTAC_Peptidome_Test1_P1_Poroshell_03Feb12_Frodo_Poroshell300SB.raw";
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
}
public void TopDownWorkflowTest1()
{
//see https://jira.pnnl.gov/jira/browse/OMCR-98
string baseFolder =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact";
const string executorParameterFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact\Parameters\topdownExecutorParameters1.xml";
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
executorParameters.ExportChromatogramData = false;
executorParameters.OutputFolderBase =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact";
const string testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Topdown_standard_testing\Test1_MSAlign_ProteusPeriIntact\RawData\Proteus_Peri_intact_ETD.raw";
string testDatasetName = RunUtilities.GetDatasetName(testDatasetPath);
string expectedResultsFilename = executorParameters.OutputFolderBase + "\\IqResults" + "\\" + testDatasetName + "_quant.txt";
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, testDatasetPath);
string proteinSeq =
@"A.VDKTNPYALMEDAAQKTFDKLKTEQPEIRKNPELLREIVQQELLPYVHIKYAGALVLGPYYRNATPAQRDAYFAAFKDYLAQVYGQALAMYEGQEYRIEPAKPFADKSNLTIRVTIIDKNGRPPVRLDFQWRKNSKTGEWQAYDMIAEGVSMITTKQNEWSDILSAKGVDGLTKQLEISAKTPITLDEKK.";
executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.Code == proteinSeq).ToList();
executor.Execute();
Assert.IsNotNull(executor.TargetedWorkflow.Run);
Console.WriteLine("Num targetedResults in Run = " + executor.TargetedWorkflow.Run.ResultCollection.MassTagResultList.Count);
Assert.IsTrue(File.Exists(expectedResultsFilename), "Results file does not exist!");
//TODO: fix _quant.txt output column headers
TopDownTargetedResultFromTextImporter importer = new TopDownTargetedResultFromTextImporter(expectedResultsFilename);
var results = importer.Import();
Assert.IsNotNull(results);
Assert.IsTrue(results.HasResults);
Assert.AreEqual(1, results.Results.Count);
//foreach (var r in results.Results)
//{
// Console.WriteLine(r.TargetID + "\t" + r.ScanLC + "\t" + r.Intensity);
//}
}
public void TopDownWorkflowFullTargetSet()
{
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = false;
executorParameters.DeleteLocalDatasetAfterProcessing = false;
executorParameters.TargetsFilePath = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Targets\fullTargetSet\Proteus_Peri_intact_ETD_MSAlign_ResultTable.Filtered05FDR.txt";
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
executorParameters.ExportChromatogramData = true;
var workflowParameters = new TopDownTargetedWorkflowParameters();
workflowParameters.AreaOfPeakToSumInDynamicSumming = 2;
workflowParameters.ChromatogramCorrelationIsPerformed = false;
workflowParameters.ChromGeneratorMode = Globals1.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
workflowParameters.ChromGenSourceDataPeakBR = 4;
workflowParameters.ChromGenSourceDataSigNoise = 3;
workflowParameters.ChromNETTolerance = 0.025;
workflowParameters.ChromPeakDetectorPeakBR = 0.1;
workflowParameters.ChromPeakDetectorSigNoise = 0.1;
workflowParameters.ChromPeakSelectorMode = Globals1.PeakSelectorMode.Smart;
workflowParameters.ChromSmootherNumPointsInSmooth = 9;
workflowParameters.MaxScansSummedInDynamicSumming = 100;
workflowParameters.MSPeakDetectorPeakBR = 1.3;
workflowParameters.MSPeakDetectorSigNoise = 2;
workflowParameters.ChromGenTolerance = 15;
workflowParameters.MSToleranceInPPM = 25;
workflowParameters.MultipleHighQualityMatchesAreAllowed = true;
workflowParameters.NumChromPeaksAllowedDuringSelection = 10;
workflowParameters.NumMSScansToSum = 5;
workflowParameters.ResultType = Globals1.ResultType.TOPDOWN_TARGETED_RESULT;
workflowParameters.SummingMode = SummingModeEnum.SUMMINGMODE_STATIC;
const string testDatasetPath =
@"\\protoapps\UserData\Fujimoto\TopDownTesting\RawData\Proteus_Peri_intact_ETD.raw";
string resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "Results");
string testDatasetName = RunUtilities.GetDatasetName(testDatasetPath);
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, workflowParameters, testDatasetPath);
executor.Execute();
Assert.IsNotNull(executor.TargetedWorkflow.Run);
Assert.IsTrue(File.Exists(expectedResultsFilename), "Results file does not exist!");
}
public void TestTargetedWorkflowExecutorMod()
{
const string executorParameterFile = @"\\protoapps\UserData\Kaipo\TopDown\test2paramsmod.xml";
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
string resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "Results");
const string testDatasetPath = @"\\protoapps\UserData\Kaipo\TopDown\test2\Proteus_Peri_intact_ETD.raw";
const string testDatasetName = "Proteus_Peri_intact_ETD";
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
// Output chrom data
var wf = executor.TargetedWorkflow as TopDownTargetedWorkflow;
Console.Write("***** chrom data *****\n");
foreach (var resultData in wf.TargetResults)
{
int id = resultData.Key;
TargetedResultBase result = resultData.Value;
double chromPeakSelected = (result.ChromPeakSelected != null) ? result.ChromPeakSelected.XValue : -1;
Console.Write("TargetID=" + id + "; ChromPeakSelected=" + chromPeakSelected + "\n");
for (int i = 0; i < result.ChromValues.Xvalues.Length; i++)
{
Console.Write(result.ChromValues.Xvalues[i] + "\t" + result.ChromValues.Yvalues[i] + "\n");
}
Console.Write("\n");
}
Console.Write("**********************\n");
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new UnlabelledTargetedResultFromTextImporter(expectedResultsFilename);
TargetedResultRepository repository = importer.Import();
Assert.AreEqual(9, repository.Results.Count);
}
public void Test1()
{
string copyToFolder = @"D:\Data\TopDown";
string outputFolder = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowTesting\Output";
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = true;
executorParameters.FolderPathForCopiedRawDataset = copyToFolder;
executorParameters.TargetsFilePath =
@"\\proto-7\VOrbiETD04\2012_1\CPTAC_Peptidome_Test2_P6-5_13Jan12_Polaroid_11-10-14\MSA201202231748_Auto796393\CPTAC_Peptidome_Test2_P6-5_13Jan12_Polaroid_11-10-14_MSAlign_ResultTable.txt";
const string testDatasetPath =
@"\\proto-7\VOrbiETD04\2012_1\CPTAC_Peptidome_Test2_P6-5_13Jan12_Polaroid_11-10-14\CPTAC_Peptidome_Test2_P6-5_13Jan12_Polaroid_11-10-14.raw";
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, testDatasetPath);
executor.Execute();
}
public void TopDownWorkflowTestNoChargeStateList()
{
//see https://jira.pnnl.gov/jira/browse/OMCR-101
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = false;
executorParameters.DeleteLocalDatasetAfterProcessing = false;
executorParameters.TargetsFilePath = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Targets\noChargeStateList\Proteus_Peri_intact_ETD_MSAlign_ResultTable.txt";
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
executorParameters.ExportChromatogramData = true;
var workflowParameters = new TopDownTargetedWorkflowParameters();
workflowParameters.AreaOfPeakToSumInDynamicSumming = 2;
workflowParameters.ChromatogramCorrelationIsPerformed = false;
workflowParameters.ChromGeneratorMode = Globals1.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
workflowParameters.ChromGenSourceDataPeakBR = 4;
workflowParameters.ChromGenSourceDataSigNoise = 3;
workflowParameters.ChromNETTolerance = 0.025;
workflowParameters.ChromPeakDetectorPeakBR = 0.1;
workflowParameters.ChromPeakDetectorSigNoise = 0.1;
workflowParameters.ChromPeakSelectorMode = Globals1.PeakSelectorMode.Smart;
workflowParameters.ChromSmootherNumPointsInSmooth = 9;
workflowParameters.MaxScansSummedInDynamicSumming = 100;
workflowParameters.MSPeakDetectorPeakBR = 1.3;
workflowParameters.MSPeakDetectorSigNoise = 2;
workflowParameters.ChromGenTolerance = 15;
workflowParameters.MSToleranceInPPM = 25;
workflowParameters.MultipleHighQualityMatchesAreAllowed = true;
workflowParameters.NumChromPeaksAllowedDuringSelection = 10;
workflowParameters.NumMSScansToSum = 5;
workflowParameters.ResultType = Globals1.ResultType.TOPDOWN_TARGETED_RESULT;
workflowParameters.SummingMode = SummingModeEnum.SUMMINGMODE_STATIC;
const string testDatasetPath =
@"\\protoapps\UserData\Fujimoto\TopDownTesting\RawData\Proteus_Peri_intact_ETD.raw";
string resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "Results");
string testDatasetName = RunUtilities.GetDatasetName(testDatasetPath);
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, workflowParameters, testDatasetPath);
executor.Execute();
/*
* var currentTarget = executor.TargetedWorkflow.Result.Target;
* Console.WriteLine("Target info:");
* Console.WriteLine(currentTarget.ID + "\t" + currentTarget.MonoIsotopicMass + "\t" + currentTarget.MZ + "\t" + currentTarget.ChargeState + "\t"+ currentTarget.EmpiricalFormula);
* Console.WriteLine("Theor profile");
* TestUtilities.DisplayIsotopicProfileData(executor.TargetedWorkflow.Result.Target.IsotopicProfile);
* TestUtilities.DisplayXYValues(executor.TargetedWorkflow.MassSpectrumXYData);
* TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
* TestUtilities.DisplayPeaks(executor.TargetedWorkflow.ChromPeaksDetected.Select(p=>(Peak)p).ToList());
*/
Assert.IsNotNull(executor.TargetedWorkflow.Run);
Console.WriteLine("Num targetedResults in Run = " + executor.TargetedWorkflow.Run.ResultCollection.MassTagResultList.Count);
Assert.IsTrue(File.Exists(expectedResultsFilename), "Results file does not exist!");
//var resultsfile = new StreamReader(@"\\protoapps\UserData\Fujimoto\TopDownTesting\Results\noChargeStateList\Proteus_Peri_intact_ETD_quant.txt");
//string line = resultsfile.ReadLine();
//line = resultsfile.ReadLine();
//string[] chargestatelist = line.Split('\t');
//Assert.AreEqual("10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22", chargestatelist[2]);
//resultsfile.Close();
}
public void TopDownWorkflowTestMissingChargeState()
{
//see https://jira.pnnl.gov/jira/browse/OMCR-102
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.CopyRawFileLocal = false;
executorParameters.DeleteLocalDatasetAfterProcessing = false;
executorParameters.TargetsFilePath = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Targets\missingChargeState\Proteus_Peri_intact_ETD_MSAlign_ResultTable.txt";
executorParameters.TargetType = Globals.TargetType.LcmsFeature;
executorParameters.ExportChromatogramData = true;
var workflowParameters = new TopDownTargetedWorkflowParameters();
workflowParameters.AreaOfPeakToSumInDynamicSumming = 2;
workflowParameters.ChromatogramCorrelationIsPerformed = false;
workflowParameters.ChromGeneratorMode = Globals1.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
workflowParameters.ChromGenSourceDataPeakBR = 4;
workflowParameters.ChromGenSourceDataSigNoise = 3;
workflowParameters.ChromNETTolerance = 0.025;
workflowParameters.ChromPeakDetectorPeakBR = 0.1;
workflowParameters.ChromPeakDetectorSigNoise = 0.1;
workflowParameters.ChromPeakSelectorMode = Globals1.PeakSelectorMode.Smart;
workflowParameters.ChromSmootherNumPointsInSmooth = 9;
workflowParameters.MaxScansSummedInDynamicSumming = 100;
workflowParameters.MSPeakDetectorPeakBR = 1.3;
workflowParameters.MSPeakDetectorSigNoise = 2;
workflowParameters.ChromGenTolerance = 15;
workflowParameters.MSToleranceInPPM = 25;
workflowParameters.MultipleHighQualityMatchesAreAllowed = true;
workflowParameters.NumChromPeaksAllowedDuringSelection = 10;
workflowParameters.NumMSScansToSum = 5;
workflowParameters.ResultType = Globals1.ResultType.TOPDOWN_TARGETED_RESULT;
workflowParameters.SummingMode = SummingModeEnum.SUMMINGMODE_STATIC;
const string testDatasetPath =
@"\\protoapps\UserData\Fujimoto\TopDownTesting\RawData\Proteus_Peri_intact_ETD.raw";
string resultsFolderLocation = executorParameters.OutputFolderBase + "\\Results";
string testDatasetName = RunUtilities.GetDatasetName(testDatasetPath);
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, workflowParameters, testDatasetPath);
string proteinSeq1 =
@"A.AENVVHHKLDGMPISEAVEINAGNNLVFLSGKVPTKKSADAPEGELASYGNTEEQTINVLEQIKTNLNNLGLDMKDVVKMQVFLVGGEENNGTMDFKGFMNGYSKFYDASKTNQLPARSAFQVAKLANPAWRVEIEVIAVRPAK.";
executor.Targets.TargetList = executor.Targets.TargetList.Where(p => (p.Code == proteinSeq1)).ToList();
executor.Execute();
Assert.IsNotNull(executor.TargetedWorkflow.Run);
Console.WriteLine("Num targetedResults in Run = " + executor.TargetedWorkflow.Run.ResultCollection.MassTagResultList.Count);
Assert.IsTrue(File.Exists(expectedResultsFilename), "Results file does not exist!");
var resultsfile = new StreamReader(@"\\protoapps\UserData\Fujimoto\TopDownTesting\Results\missingChargeState\Proteus_Peri_intact_ETD_quant.txt");
string line = resultsfile.ReadLine();
line = resultsfile.ReadLine();
string[] chargestatelist = line.Split('\t');
Assert.AreEqual("10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22", chargestatelist[2]);
resultsfile.Close();
}
public void TestTargetedWorkflowExecutor()
{
const string executorParameterFile = @"\\protoapps\UserData\Kaipo\TopDown\test2params.xml";
var executorParameters = new TopDownTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParameterFile);
string resultsFolderLocation = Path.Combine(executorParameters.OutputFolderBase, "IqResults");
const string testDatasetPath = @"\\protoapps\UserData\Kaipo\TopDown\test2\Proteus_Peri_intact_ETD.raw";
const string testDatasetName = "Proteus_Peri_intact_ETD";
string expectedResultsFilename = Path.Combine(resultsFolderLocation, testDatasetName + "_quant.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var executor = new TopDownTargetedWorkflowExecutor(executorParameters, testDatasetPath);
string proteinSeq =
@"A.VDKTNPYALMEDAAQKTFDKLKTEQPEIRKNPELLREIVQQELLPYVHIKYAGALVLGPYYRNATPAQRDAYFAAFKDYLAQVYGQALAMYEGQEYRIEPAKPFADKSNLTIRVTIIDKNGRPPVRLDFQWRKNSKTGEWQAYDMIAEGVSMITTKQNEWSDILSAKGVDGLTKQLEISAKTPITLDEKK.";
executor.Targets.TargetList = executor.Targets.TargetList.Where(p => p.Code == proteinSeq).ToList();
executor.Execute();
// Output chrom data
//var wf = executor.TargetedWorkflow as TopDownTargetedWorkflow;
//Console.Write("***** chrom data *****\n");
//foreach (var resultData in wf.TargetResults)
//{
// int id = resultData.Key;
// TargetedResultBase result = resultData.Value;
// double chromPeakSelected = (result.ChromPeakSelected != null) ? result.ChromPeakSelected.XValue : -1;
// Console.Write("TargetID=" + id + "; ChromPeakSelected=" + chromPeakSelected + "\n");
// for (int i = 0; i < result.ChromValues.Xvalues.Length; i++)
// {
// //Console.Write(result.ChromValues.Xvalues[i] + "\t" + result.ChromValues.Yvalues[i] + "\n");
// }
// //Console.Write("\n");
//}
Console.Write("**********************\n");
Assert.IsTrue(File.Exists(expectedResultsFilename));
var importer = new UnlabelledTargetedResultFromTextImporter(expectedResultsFilename);
TargetedResultRepository repository = importer.Import();
Assert.AreEqual(1, repository.Results.Count);
//// expected results as tuples in format: <target id, charge state, scan lc>
//var expectedResults = new HashSet<Tuple<long, int, int>>
//{
// new Tuple<long, int, int>(1, 8, 1583),
// new Tuple<long, int, int>(2, 23, 2643),
// new Tuple<long, int, int>(3, 21, 1853),
// new Tuple<long, int, int>(4, 14, 2303),
// new Tuple<long, int, int>(5, 17, 2339),
// new Tuple<long, int, int>(6, 26, 4630),
// new Tuple<long, int, int>(7, 26, 3583),
// new Tuple<long, int, int>(8, 7, 3709),
// new Tuple<long, int, int>(9, 42, 3439),
//};
//foreach (TargetedResultDTO result in repository.Results)
//{
// expectedResults.Remove(new Tuple<long, int, int>(result.TargetID, result.ChargeState, result.ScanLC));
//}
//Assert.IsEmpty(expectedResults);
}
