public void doAlignmentTest1()
{
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt";
UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
TargetedResultRepository repo = importer.Import();
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
MassTagCollection mtc = new MassTagCollection();
MassTagFromTextFileImporter mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
NETAndMassAligner aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.MassTagList);
aligner.Execute(run);
Assert.IsNotNull(run.AlignmentInfo);
Assert.IsNotNull(run.AlignmentInfo.marrNETFncTimeInput);
Assert.AreEqual(2273.0f, run.AlignmentInfo.marrNETFncTimeInput[0]);
float testScan = 6005;
float testNET1 = run.AlignmentInfo.GetNETFromTime(testScan);
Assert.AreEqual(0.3253423m, (decimal)testNET1);
}
public void ExportNET_andMass_AlignmentDataTest1()
{
var exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt");
var exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt");
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
aligner.Execute(run);
var exporter = new NETAlignmentInfoToTextExporter(exportNETFilename);
exporter.ExportAlignmentInfo(run.AlignmentInfo);
var massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename);
massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo);
}
public void test1()
{
var mtc = new TargetCollection();
var massTagImporter = new MassTagFromTextFileImporter(massTagTestFile1);
mtc = massTagImporter.Import();
Assert.AreNotEqual(null, mtc.TargetList);
Assert.AreEqual(101, mtc.TargetList.Count);
var testMassTag = (PeptideTarget)mtc.TargetList[0];
Assert.AreEqual("AVAFGEALRPEFK", testMassTag.Code);
Assert.AreEqual(2, testMassTag.ChargeState);
Assert.AreEqual(0.3649905m, (decimal)testMassTag.NormalizedElutionTime);
Assert.AreEqual("C67H103N17O18", testMassTag.EmpiricalFormula);
Assert.AreEqual(872, testMassTag.RefID);
Assert.AreEqual("ABA80002 SHMT serine hydroxymethyltransferase", testMassTag.ProteinDescription);
Assert.AreEqual(1433.766629m, (decimal)testMassTag.MonoIsotopicMass);
Assert.AreEqual(717.8905912m, (decimal)testMassTag.MZ);
Assert.AreEqual(75, testMassTag.ObsCount);
Assert.AreEqual(4225609, testMassTag.ID);
}
public void SetMassTags(string massTagFilename)
{
var importer = new MassTagFromTextFileImporter(massTagFilename);
var mtc = importer.Import();
MassTagList = mtc.TargetList;
}
public void cannotFindMassTag_test1()
{
//
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 26523;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 1 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.IsNull(result.IsotopicProfile);
Assert.IsNull(result.ScanSet);
Assert.IsNull(result.ChromPeakSelected);
Assert.IsTrue(result.FailedResult);
Assert.AreEqual(DeconTools.Backend.Globals.TargetedResultFailureType.ChrompeakNotFoundWithinTolerances, result.FailureType);
}
public void ExportNET_andMass_AlignmentDataTest1()
{
string exportNETFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedNETAlignmentInfo1.txt");
string exportMassFilename = Path.Combine(FileRefs.OutputFolderPath, "exportedMassAlignmentInfo1.txt");
RunFactory rf = new RunFactory();
Run run = rf.CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
string deconToolsResultFile = @"D:\Temp\output7\targetedFeatures.txt";
UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
TargetedResultRepository repo = importer.Import();
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
MassTagCollection mtc = new MassTagCollection();
MassTagFromTextFileImporter mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
NETAndMassAligner aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.MassTagList);
aligner.Execute(run);
NETAlignmentInfoToTextExporter exporter = new NETAlignmentInfoToTextExporter(exportNETFilename);
exporter.ExportAlignmentInfo(run.AlignmentInfo);
MassAlignmentInfoToTextExporter massInfoexporter = new MassAlignmentInfoToTextExporter(exportMassFilename);
massInfoexporter.ExportAlignmentInfo(run.AlignmentInfo);
}
public void doAlignmentTest1()
{
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var deconToolsResultFile = Path.Combine(FileRefs.ImportedData, "QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_targetedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(deconToolsResultFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_allMassTags.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
aligner.Execute(run);
float testScan = 6005;
var testNET1 = run.NetAlignmentInfo.GetNETValueForScan((int)testScan);
//note - this is Multialign's
Assert.AreEqual(0.3253423m, (decimal)testNET1);
}
public void exportMassTagsToTextFile_Test1()
{
//first, import some data
var mtc = new TargetCollection();
var massTagTestFile1 = "..\\..\\..\\TestFiles\\FileIOTests\\top40MassTags.txt";
var massTagImporter = new MassTagFromTextFileImporter(massTagTestFile1);
mtc = massTagImporter.Import();
//second, export it
//but first delete any existing output file
if (File.Exists(testOutput1))
{
File.Delete(testOutput1);
}
var exporter = new MassTagTextFileExporter(testOutput1);
exporter.ExportResults(mtc.TargetList);
var fi = new FileInfo(testOutput1);
Assert.IsTrue(fi.Exists);
//Assert.AreEqual(13716, fi.Length);
}
public void SetMassTags(string massTagFilename)
{
MassTagFromTextFileImporter importer = new MassTagFromTextFileImporter(massTagFilename);
MassTagCollection mtc = importer.Import();
MassTagList = mtc.MassTagList;
}
public void tempUpdateLCMSFeaturesWithEmpiricalFormulaTest1()
{
var testLCMSFile1 =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_allWithIDs_LCMSFeatures.txt";
var massTagFileName =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_MassTags.txt";
var importer =
new LcmsTargetFromFeaturesFileImporter(testLCMSFile1);
var features = importer.Import();
var mtImporter = new MassTagFromTextFileImporter(massTagFileName);
var massTags = mtImporter.Import();
massTags.TargetList = (from n in massTags.TargetList
group n by new
{
n.ID,
n.ChargeState
}
into grp
select grp.First()).ToList();
var massTagIDList = features.TargetList.Select(p => (long)((LcmsFeatureTarget)p).FeatureToMassTagID).ToList();
var outputLCMSFeaturesFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_withEmpFormulas_LCMSFeatures.txt";
using (var writer = new StreamWriter(outputLCMSFeaturesFile))
{
var headerLine = "TargetID\tScan\tMonoIsotopicMass\tChargeState\tMatchedMassTagID\tEmpiricalFormula";
writer.WriteLine(headerLine);
foreach (var targetBase in features.TargetList)
{
UpdateTargetsUsingMassTagInfo(massTagIDList, features, massTags);
var stringBuilder = new StringBuilder();
stringBuilder.Append(targetBase.ID);
stringBuilder.Append("\t");
stringBuilder.Append(targetBase.ScanLCTarget);
stringBuilder.Append("\t");
stringBuilder.Append(targetBase.MonoIsotopicMass);
stringBuilder.Append("\t");
stringBuilder.Append(targetBase.ChargeState);
stringBuilder.Append("\t");
stringBuilder.Append(((LcmsFeatureTarget)targetBase).FeatureToMassTagID);
stringBuilder.Append("\t");
stringBuilder.Append(targetBase.EmpiricalFormula);
writer.WriteLine(stringBuilder.ToString());
}
}
}
public void unlabelled_data_TFFTest1()
{
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_first10.txt";
var masstagImporter = new MassTagFromTextFileImporter(massTagFile);
var massTagColl = masstagImporter.Import();
var mt24702_charge3 = (from n in massTagColl.TargetList where n.ID == 24702 && n.ChargeState == 3 select n).First();
var mt24702_charge4 = (from n in massTagColl.TargetList where n.ID == 24702 && n.ChargeState == 4 select n).First();
}
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 findFeatureIn_dataset_with_bad_massCalibration_test1()
{
//mass error in this dataset is typically ~50ppm.
var datasetFile = @"D:\Data\Orbitrap\Subissue01\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24.RAW";
var massTagFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\MassTags\QCShew_Formic_MassTags_Bin10_first10.txt";
var workflowParameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\UnlabelledTargeted_WorkflowParameters_noSum.xml";
var run = RunUtilities.CreateAndLoadPeaks(datasetFile, datasetFile.Replace(".RAW", "_peaks.txt"));
RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
Assert.IsTrue(run.MassIsAligned);
Assert.IsTrue(run.NETIsAligned);
var parameters = new BasicTargetedWorkflowParameters();
parameters.LoadParameters(workflowParameterFile);
var workflow = new BasicTargetedWorkflow(parameters);
workflow.Run = run;
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var mt1 = (from n in mtc.TargetList where n.ID == 24702 && n.ChargeState == 4 select n).First();
run.CurrentMassTag = mt1;
workflow.Execute();
var repo = new TargetedResultRepository();
repo.AddResult(workflow.Result);
Console.WriteLine("theor mono mass = " + mt1.MonoIsotopicMass);
Console.WriteLine("theorMZ = " + mt1.MZ);
Console.WriteLine("theorNET = " + mt1.NormalizedElutionTime);
Console.WriteLine("obsScan = " + repo.Results[0].ScanLC);
Console.WriteLine("obsNET = " + repo.Results[0].NET);
Console.WriteLine("NETError = " + repo.Results[0].NETError);
Console.WriteLine("obsMZ = " + repo.Results[0].MonoMZ);
Console.WriteLine("monoMass = " + repo.Results[0].MonoMass);
Console.WriteLine("obsMonoMassCalibrated = " + repo.Results[0].MonoMassCalibrated);
Console.WriteLine("MassErrorBeforeAlignment = " + (mt1.MZ - repo.Results[0].MonoMZ) / mt1.MZ * 1e6);
Console.WriteLine("MassErrorAfterAlignment = " + repo.Results[0].MassErrorBeforeCalibration);
}
public void ComparePeakFitterVsAreaFitter()
{
var massTagFile1 = Path.Combine(FileRefs.RawDataBasePath, "TargetedWorkflowStandards", "QCShew_peptidesWithObsCountGreaterThan1000.txt");
//load target
var masstagImporter = new MassTagFromTextFileImporter(massTagFile1);
var targets = masstagImporter.Import().TargetList;
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var scanSet = new ScanSet(9575);
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
var selectedTarget = targets.First(p => p.ID == 635428 && p.ChargeState == 3);
var theorFeatureGen = new JoshTheorFeatureGenerator(Backend.Globals.LabellingType.NONE, 0.005);
theorFeatureGen.GenerateTheorFeature(selectedTarget);
var peakForFWHM = run.PeakList.First(p => p.XValue > 768.38 && p.XValue < 768.39);
var theorXYdata =
TheorXYDataCalculationUtilities.GetTheoreticalIsotopicProfileXYData(selectedTarget.IsotopicProfile,
peakForFWHM.Width);
theorXYdata.NormalizeYData();
var areaFitter = new AreaFitter();
var areaFitScore = areaFitter.GetFit(theorXYdata, run.XYData, 0.1);
var peakLeastSquaresFitter = new PeakLeastSquaresFitter();
var peakBasedFitScore = peakLeastSquaresFitter.GetFit(new List <Peak>(selectedTarget.IsotopicProfile.Peaklist), run.PeakList, 0.1, 25);
Console.WriteLine("fit score based on XYData = " + areaFitScore);
Console.WriteLine("fit score based on Peaks= " + peakBasedFitScore);
Assert.IsTrue(peakBasedFitScore < 0.1);
}
public void loadLCMSFeatures_and_massTags()
{
var lcmsfeaturesFile =
@"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2012\C12C13YellowStone\2011_02_20_SIPPER_workflow_standards\Yellow_C13_070_23Mar10_Griffin_10-01-28_LCMSFeatures.txt";
// load LCMSFeatures as targets
var importer =
new LcmsTargetFromFeaturesFileImporter(lcmsfeaturesFile);
var lcmsTargetCollection = importer.Import();
// load MassTags
var massTagFile1 =
@"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2012\C12C13YellowStone\2011_02_20_SIPPER_workflow_standards\Yellow_C13_070_23Mar10_Griffin_10-01-28_MassTags.txt";
var massTagImporter = new MassTagFromTextFileImporter(massTagFile1);
var massTagCollection = massTagImporter.Import();
var masstagIDlist = (from n in massTagCollection.TargetList select n.ID).ToList();
// Update LCMSFeatures using MassTag info
foreach (LcmsFeatureTarget target in lcmsTargetCollection.TargetList)
{
if (masstagIDlist.Contains(target.ID))
{
var mt = massTagCollection.TargetList.Where(p => p.ID == target.FeatureToMassTagID).First();
target.Code = mt.Code;
target.EmpiricalFormula = mt.EmpiricalFormula;
}
else
{
}
}
int[] testMassTags = { 344540889, 344540889, 344972415, 354881152, 355157363, 355162540, 355315129 };
var filteredLcmsFeatureTargets = (from n in lcmsTargetCollection.TargetList
where testMassTags.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
select n).ToList();
foreach (LcmsFeatureTarget filteredLcmsFeatureTarget in filteredLcmsFeatureTargets)
{
Console.WriteLine(filteredLcmsFeatureTarget);
}
}
public void test2()
{
MassTagCollection mtc = new MassTagCollection();
MassTagFromTextFileImporter massTagImporter = new MassTagFromTextFileImporter(massTagTestFile2);
massTagImporter.Import(mtc);
Assert.AreEqual(3, mtc.MassTagList.Count);
//Assert.AreEqual("SAMPLER", mtc.MassTagList[0].PeptideSequence);
//Assert.AreEqual(2, mtc.MassTagList[0].ChargeState);
//Assert.AreEqual(0.34m, (decimal)mtc.MassTagList[0].NETVal);
//Assert.AreEqual("C33H58N10O11S1", mtc.MassTagList[0].Peptide.GetEmpiricalFormula());
}
protected TargetCollection GetMassTagTargets(string massTagFileName, List <int> targetIDsToFilterOn)
{
if (String.IsNullOrEmpty(massTagFileName) || !File.Exists(massTagFileName))
{
return(new TargetCollection());
}
if (massTagFileName.ToLower().Contains("_msgfplus.tsv"))
{
var iqTargetImporter = new BasicIqTargetImporter(massTagFileName);
var iqTargets = iqTargetImporter.Import();
var targetUtilities = new IqTargetUtilities();
var targetCollection = new TargetCollection
{
TargetList = new List <TargetBase>()
};
foreach (var iqTarget in iqTargets)
{
if (iqTarget.QualityScore > MsgfFdrScoreCutoff)
{
continue;
}
targetUtilities.UpdateTargetMissingInfo(iqTarget);
TargetBase oldStyleTarget = new PeptideTarget();
oldStyleTarget.ChargeState = (short)iqTarget.ChargeState;
oldStyleTarget.Code = iqTarget.Code;
oldStyleTarget.EmpiricalFormula = iqTarget.EmpiricalFormula;
oldStyleTarget.ID = iqTarget.ID;
oldStyleTarget.MZ = iqTarget.MZTheor;
oldStyleTarget.MonoIsotopicMass = iqTarget.MonoMassTheor;
oldStyleTarget.ScanLCTarget = iqTarget.ScanLC;
oldStyleTarget.NormalizedElutionTime = (float)iqTarget.ElutionTimeTheor;
oldStyleTarget.ElutionTimeUnit = DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum;
targetCollection.TargetList.Add(oldStyleTarget);
}
return(targetCollection);
}
var importer = new MassTagFromTextFileImporter(massTagFileName);
return(importer.Import(targetIDsToFilterOn));
}
public void ImportTargetsContainingEmpiricalFormulaAndScanNumber()
{
var testfile = @"..\\..\\..\\TestFiles\\FileIOTests\\BSAmassTags_EmpiricalFormula_and_scans.txt";
var mtc = new TargetCollection();
var massTagImporter = new MassTagFromTextFileImporter(testfile);
mtc = massTagImporter.Import();
Assert.AreNotEqual(null, mtc.TargetList);
foreach (PeptideTarget peptideTarget in mtc.TargetList)
{
Console.WriteLine(peptideTarget);
}
}
public void IqWorkflowTest1()
{
//see https://jira.pnnl.gov/jira/browse/OMCS-709
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
var oldStyleTarget = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
parameters.ChromSmootherNumPointsInSmooth = 9;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromPeakDetectorSigNoise = 1;
IqWorkflow iqWorkflow = new BasicIqWorkflow(run, parameters);
IqTarget target = new IqChargeStateTarget(iqWorkflow);
target.ID = oldStyleTarget.ID;
target.MZTheor = oldStyleTarget.MZ;
target.ElutionTimeTheor = oldStyleTarget.NormalizedElutionTime;
target.MonoMassTheor = oldStyleTarget.MonoIsotopicMass;
target.EmpiricalFormula = oldStyleTarget.EmpiricalFormula;
target.ChargeState = oldStyleTarget.ChargeState;
Console.WriteLine(target.EmpiricalFormula + "\t" + target.ChargeState);
target.DoWorkflow();
var result = target.GetResult();
Assert.IsNotNull(result, "result is null");
var reportString = result.ToStringWithDetailedReport();
Console.WriteLine(reportString);
}
public void ImportTargetsContainingOnlyEmpiricalFormula()
{
var testfile = @"..\\..\\..\\TestFiles\\FileIOTests\\QCShew_Bin10_Top10_empiricalFormula_NET_only.txt";
var mtc = new TargetCollection();
var massTagImporter = new MassTagFromTextFileImporter(testfile);
mtc = massTagImporter.Import();
Assert.AreNotEqual(null, mtc.TargetList);
foreach (PeptideTarget peptideTarget in mtc.TargetList)
{
Console.WriteLine(peptideTarget);
}
}
public void ensureAlignment_was_executed()
{
var run = new RunFactory().CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_READONLY_alignedFeatures.txt";
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\QCShew_Formic_MassTags_Bin10_all.txt";
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var parameters = new NETAndMassAlignerParameters();
var aligner = new NETAndMassAligner();
aligner.SetFeaturesToBeAligned(repo.Results);
aligner.SetReferenceMassTags(mtc.TargetList);
var scan = 7835;
var theorMZ = 780.08485; //massTagID = 24701 (+3)
var obsMZ = 780.0824;
var netBeforeAlignment = run.NetAlignmentInfo.GetNETValueForScan(scan);
var mzBeforeAlignment = run.GetAlignedMZ(obsMZ);
aligner.Execute(run);
var netAfterAlignment = run.NetAlignmentInfo.GetNETValueForScan(scan);
var mzAfterAlignment = run.GetAlignedMZ(obsMZ);
Console.WriteLine("NET before alignment = " + netBeforeAlignment);
Console.WriteLine("NET after alignment = " + netAfterAlignment);
Console.WriteLine("Theor MZ = " + theorMZ);
Console.WriteLine("MZ before alignment = " + mzBeforeAlignment);
Console.WriteLine("MZ after alignment = " + mzAfterAlignment);
Console.WriteLine("PPMDiff before alignment = " + (theorMZ - mzBeforeAlignment) / theorMZ * 1e6);
Console.WriteLine("PPMDiff after alignment = " + (theorMZ - mzAfterAlignment) / theorMZ * 1e6);
}
public void Test1()
{
var rawdataFile = @"D:\Data\Orbitrap\QC_Shew_09_05-pt5-6_4Jan10_Doc_09-11-08.RAW";
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var parameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\UnlabelledTargeted_WorkflowParameters_noSum.xml";
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
var mtc = new TargetCollection();
mtc = mtimporter.Import();
var run = new RunFactory().CreateRun(rawdataFile);
//RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
var expectedPeaksFilename = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(expectedPeaksFilename, null);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var testMassTagID = 3513677;
var massTagChargeState = 2;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == massTagChargeState select n).First();
var parameters = WorkflowParameters.CreateParameters(parameterFile);
var workflow = TargetedWorkflow.CreateWorkflow(parameters);
workflow.Run = run;
workflow.Execute();
workflow.Result.DisplayToConsole();
RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
workflow.Execute();
workflow.Result.DisplayToConsole();
}
public void findSingleMassTag_checkAlignmentData_test1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 24800;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.AreEqual(false, result.FailedResult);
result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
Assert.AreEqual(718.41m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2));
Assert.AreEqual(5947m, (decimal)Math.Round(result.ChromPeakSelected.XValue));
Assert.AreEqual(5.91, (decimal)(Math.Round(result.GetMassErrorAfterAlignmentInPPM(), 2)));
Assert.AreEqual(0.0001585m, (decimal)(Math.Round(result.GetNETAlignmentError(), 7)));
RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
//these might change due to unit tests elsewhere. Need a better way of doing this
//Assert.AreEqual(1.99290383722318m, (decimal)result.GetMassErrorAfterAlignmentInPPM());
//Assert.AreEqual(0.00076708197593689m, (decimal)result.GetNETAlignmentError());
}
public void exporterTest1()
{
var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";
var exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "UnlabelledTargetedResultsExporterOutput1.txt");
if (File.Exists(exportedResultFile))
{
File.Delete(exportedResultFile);
}
var run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var selectedMassTags = mtc.TargetList.OrderBy(p => p.ID).Take(10).ToList();
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var workflow = new BasicTargetedWorkflow(run, parameters);
foreach (var mt in selectedMassTags)
{
run.CurrentMassTag = mt;
workflow.Execute();
}
var repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
var exporter = new UnlabelledTargetedResultToTextExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}
public void findSingleModifiedMassTagTest1()
{
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile);
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var testMassTagID = 189685150;
run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First();
Assert.AreEqual(true, run.CurrentMassTag.ContainsMods);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromatogramCorrelationIsPerformed = true;
var workflow = new BasicTargetedWorkflow(run, parameters);
workflow.Execute();
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult;
Assert.AreEqual(false, result.FailedResult);
result.DisplayToConsole();
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.AreEqual(2, result.IsotopicProfile.ChargeState);
Assert.AreEqual(959.48m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2));
//Assert.AreEqual(6070, (decimal)Math.Round(result.ChromPeakSelected.XValue));
foreach (var dataItem in result.ChromCorrelationData.CorrelationDataItems)
{
Console.WriteLine(dataItem);
}
}
public void ImportPeptidesWithModsTest1()
{
var mtc = new TargetCollection();
var massTagImporter = new MassTagFromTextFileImporter(massTagsWithModsFile1);
mtc = massTagImporter.Import();
Assert.AreNotEqual(null, mtc.TargetList);
Assert.AreEqual(1868, mtc.TargetList.Count);
var testMassTag = (PeptideTarget)mtc.TargetList[1021];
Assert.AreEqual(testMassTag.EmpiricalFormula, "C56H82N10O13");
Assert.AreEqual(1, testMassTag.ModCount);
Assert.AreEqual(testMassTag.ModDescription, "NH3_Loss:1");
//250663994 1102.60623 QFPILLDFK 2 C56H82N10O13 1 NH3_Loss:1
}
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 importFromSQLManagmentStyleTextFile_test1()
{
var mtc = new TargetCollection();
var massTagImporter = new MassTagFromTextFileImporter(massTagTestFile2);
mtc = massTagImporter.Import();
Assert.AreNotEqual(null, mtc.TargetList);
Assert.AreEqual(33, mtc.TargetList.Count);
var testMassTag = mtc.TargetList[0] as PeptideTarget;
Assert.AreEqual("AVTTADQVQQEVER", testMassTag.Code);
Assert.AreEqual(2, testMassTag.ChargeState);
Assert.AreEqual(0.2365603m, (decimal)testMassTag.NormalizedElutionTime);
Assert.AreEqual("C64H108N20O26", testMassTag.EmpiricalFormula);
Assert.AreEqual(137, testMassTag.RefID);
Assert.AreEqual(1572.774283m, (decimal)testMassTag.MonoIsotopicMass);
Assert.AreEqual(787.39441799m, (decimal)testMassTag.MZ);
Assert.AreEqual(6, testMassTag.ObsCount);
Assert.AreEqual(354885422, testMassTag.ID);
}
public void ImportPeptidesContainingOnlySequenceInfo()
{
var testfile = @"..\\..\\..\\TestFiles\\FileIOTests\\BSAmassTags_MinimalInfo1.txt";
var mtc = new TargetCollection();
var massTagImporter = new MassTagFromTextFileImporter(testfile);
mtc = massTagImporter.Import();
Assert.AreNotEqual(null, mtc.TargetList);
foreach (PeptideTarget peptideTarget in mtc.TargetList)
{
Console.WriteLine(peptideTarget);
}
Assert.AreEqual(111, mtc.TargetList.Count);
var testMassTag = (PeptideTarget)mtc.TargetList[0];
Assert.AreEqual("LFTFHADICTLPDTEK", testMassTag.Code);
Assert.AreEqual("C84H127N19O26S", testMassTag.EmpiricalFormula);
Assert.IsTrue(testMassTag.MonoIsotopicMass > 0);
}
