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 tester()
{
Run run = new XCaliburRun(xcaliburTestfile);
MassTagCollection massTagColl = new MassTagCollection();
MassTagIDGenericImporter mtidImporter = new MassTagIDGenericImporter(smartMethionineMatches, '\t');
mtidImporter.Import(massTagColl);
Console.WriteLine("SMART matches = " + massTagColl.MassTagIDList.Count());
MassTagCollection matchedMassTag = new MassTagCollection();
MassTagIDGenericImporter matchImporter = new MassTagIDGenericImporter(targetedMethionineMatches, '\t');
matchImporter.Import(matchedMassTag);
Console.WriteLine("Targeted matches = " + matchedMassTag.MassTagIDList.Distinct().Count());
//List<long> common_massTags = massTagColl.MassTagIDList.Intersect(matchedMassTag.MassTagIDList).ToList();
List <long> common_massTags = matchedMassTag.MassTagIDList.Intersect(massTagColl.MassTagIDList).ToList();
List <long> targetedUniqueTags = matchedMassTag.MassTagIDList.Except(massTagColl.MassTagIDList).ToList();
List <long> smartUniqueTags = massTagColl.MassTagIDList.Except(matchedMassTag.MassTagIDList).ToList();
string listOfMTsForSMARTUnique = getStringListOfMassTags(smartUniqueTags);
Console.WriteLine("Common matches = " + common_massTags.Count);
Console.WriteLine("Unique to targeted = " + targetedUniqueTags.Count);
Console.WriteLine("Unique to SMART = " + smartUniqueTags.Count);
Console.WriteLine();
Console.WriteLine(listOfMTsForSMARTUnique);
}
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 analyzeMassTags(Run run, List <long> massTagIDList, List <Task> taskList)
{
MassTagCollection massTagColl = new MassTagCollection();
run.ResultCollection.MassTagResultType = DeconTools.Backend.Globals.MassTagResultType.N14N15_MASSTAG_RESULT;
massTagColl.MassTagIDList = massTagIDList;
MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_R_sphaeroides241_P513", "Albert");
importer.chargeStateFilterThreshold = 0.05;
importer.Import(massTagColl);
List <long> timingResults = new List <long>();
foreach (MassTag mt in massTagColl.MassTagList)
{
run.CurrentMassTag = mt;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NETVal.ToString("0.000") + "; Sequence = " + mt.PeptideSequence + "\n");
Stopwatch sw = new Stopwatch();
sw.Start();
try
{
foreach (var task in taskList)
{
task.Execute(run.ResultCollection);
}
MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
Console.WriteLine("------------------------------ end --------------------------");
}
catch (Exception ex)
{
Console.WriteLine("Task failed. Message: " + ex.Message + ex.StackTrace);
}
sw.Stop();
timingResults.Add(sw.ElapsedMilliseconds);
}
foreach (long tr in timingResults)
{
Console.WriteLine(tr);
}
Console.WriteLine("-------- Analysis time for all MTs = " + timingResults.Sum());
Console.WriteLine("-------- Average time for each MT = " + timingResults.Average());
Console.WriteLine();
}
public void SetMassTags(string massTagFilename)
{
MassTagFromTextFileImporter importer = new MassTagFromTextFileImporter(massTagFilename);
MassTagCollection mtc = importer.Import();
MassTagList = mtc.MassTagList;
}
public void test1()
{
MassTagCollection massTagColl = new MassTagCollection();
MassTagIDGenericImporter mtidImporter = new MassTagIDGenericImporter(mt_sourceFile1, ',');
mtidImporter.Import(massTagColl);
Assert.AreEqual(8353, massTagColl.MassTagIDList.Count);
}
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());
}
public void exporterTest1()
{
string testFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
string peaksTestFile = FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
string massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\qcshew_standard_file_NETVals0.3-0.33.txt";
string exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "UnlabelledTargetedResultsExporterOutput1.txt");
if (File.Exists(exportedResultFile))
{
File.Delete(exportedResultFile);
}
Run run = RunUtilities.CreateAndAlignRun(testFile, peaksTestFile);
MassTagCollection mtc = new MassTagCollection();
MassTagFromTextFileImporter mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
List <MassTag> selectedMassTags = mtc.MassTagList.OrderBy(p => p.ID).Take(10).ToList();
DeconToolsTargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
BasicTargetedWorkflow workflow = new BasicTargetedWorkflow(run, parameters);
foreach (var mt in selectedMassTags)
{
run.CurrentMassTag = mt;
workflow.Execute();
}
TargetedResultRepository repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
UnlabelledTargetedResultToTextExporter exporter = new UnlabelledTargetedResultToTextExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}
public void import100MassTagIDs_andLookUpInDMSTest1()
{
this.massTagColl = new MassTagCollection();
MassTagIDGenericImporter mtidImporter = new MassTagIDGenericImporter(mt_sourceFile1, ',');
mtidImporter.Import(massTagColl);
Assert.AreEqual(100, massTagColl.MassTagIDList.Count);
Assert.AreEqual(85, massTagColl.MassTagIDList.Distinct().Count());
MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_Shewanella_ProdTest_P352", "porky");
importer.Import(massTagColl);
massTagColl.Display();
Assert.AreEqual(114, massTagColl.MassTagList.Count);
}
public void get14864MassTagsTest() // this takes about 1 minute on Gord's machine
{
MassTagCollection massTagColl = new MassTagCollection();
MassTagIDGenericImporter mtidImporter = new MassTagIDGenericImporter(mt_sourceFile2, ',');
mtidImporter.Import(massTagColl);
Assert.AreEqual(21047, massTagColl.MassTagIDList.Count);
Assert.AreEqual(14864, massTagColl.MassTagIDList.Distinct().Count());
massTagColl.MassTagIDList = massTagColl.MassTagIDList.Distinct().ToList();
MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_Shewanella_ProdTest_P352", "porky");
importer.SetMassTagsToRetrieve(massTagColl.MassTagIDList);
importer.Import(massTagColl);
massTagColl.Display();
Assert.AreEqual(14864, massTagColl.MassTagList.Count);
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
MassTagCollection massTagColl = new MassTagCollection();
MassTagIDGenericImporter mtidImporter = new MassTagIDGenericImporter(cysteineMassTagSourceFile1, '\t');
mtidImporter.Import(massTagColl);
MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_Shewanella_ProdTest_P352", "porky");
importer.Import(massTagColl);
Assert.AreEqual(737, massTagColl.MassTagIDList.Count);
Assert.AreEqual(826, massTagColl.MassTagList.Count);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5);
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 0.75, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(6);
Task exporter = new BasicMTResultSQLiteExporter(cysteineAnalysisOutput1);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
int successCounter = 0;
List <long> timingResults = new List <long>();
foreach (MassTag mt in massTagColl.MassTagList)
{
run.CurrentMassTag = mt;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NETVal.ToString("0.000") + "; Sequence = " + mt.PeptideSequence + "\n");
Stopwatch sw = new Stopwatch();
sw.Start();
try
{
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
Console.WriteLine("------------------------------ end --------------------------");
}
catch (Exception ex)
{
Console.WriteLine("Task failed. Message: " + ex.Message + ex.StackTrace);
}
sw.Stop();
timingResults.Add(sw.ElapsedMilliseconds);
if (mt == massTagColl.MassTagList.Last())
{
exporter.Execute(run.ResultCollection);
}
}
exporter.Cleanup();
//List<IMassTagResult> successfulResults = run.ResultCollection.GetSuccessfulMassTagResults();
foreach (long tr in timingResults)
{
Console.WriteLine(tr);
}
Console.WriteLine("-------- Analysis time for all MTs = " + timingResults.Sum());
Console.WriteLine("-------- Average time for each MT = " + timingResults.Average());
Console.WriteLine();
}
public void run_fullAnalysisTest1()
{
Run run = new BrukerRun(rsph_AOnly_28_run1File);
MassTagCollection massTagColl = new MassTagCollection();
run.ResultCollection.MassTagResultType = DeconTools.Backend.Globals.MassTagResultType.N14N15_MASSTAG_RESULT;
massTagColl.MassTagIDList = fourTestMTs;
MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_R_sphaeroides241_P513", "Albert");
importer.chargeStateFilterThreshold = 0.05;
importer.Import(massTagColl);
Assert.AreEqual(7, massTagColl.MassTagList.Count);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(rsph_Aonly_28_run1_scans500_1000_peaks);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5);
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 3, false, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
N14N15TFFTask finder = new N14N15TFFTask(0.01);
N14N15QuantifierTask quant = new N14N15QuantifierTask(1);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
List <long> timingResults = new List <long>();
foreach (MassTag mt in massTagColl.MassTagList)
{
run.CurrentMassTag = mt;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------");
Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NETVal.ToString("0.000") + "; Sequence = " + mt.PeptideSequence + "\n");
Stopwatch sw = new Stopwatch();
sw.Start();
try
{
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
chromPeakSel.Execute(run.ResultCollection);
msgen.Execute(run.ResultCollection);
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
finder.Execute(run.ResultCollection);
quant.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[mt];
massTagResult.DisplayToConsole();
Console.WriteLine("------------------------------ end --------------------------");
}
catch (Exception ex)
{
Console.WriteLine("Task failed. Message: " + ex.Message + ex.StackTrace);
}
sw.Stop();
timingResults.Add(sw.ElapsedMilliseconds);
}
foreach (long tr in timingResults)
{
Console.WriteLine(tr);
}
Console.WriteLine("-------- Analysis time for all MTs = " + timingResults.Sum());
Console.WriteLine("-------- Average time for each MT = " + timingResults.Average());
Console.WriteLine();
}
