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()
{
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 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 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 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 AlignmentParameterTesting2()
{
var run = new RunFactory().CreateRun(@"D:\Data\Orbitrap\Subissue01\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24.RAW");
var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\AlignmentInfo\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24_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 sb = new StringBuilder();
sb.Append("mtid\tscanLC\ttheorMZ\tobsMZ\talignedMZ\tppmErrorBefore\tppmErrorAfter\n");
parameters.MassCalibrationWindow = 20;
parameters.MassCalibrationNumMassDeltaBins = 100;
// int[] massCalXSliceValues = { 3, 6, 9, 12, 15 };
int[] massCalXSliceValues = { 15 };
foreach (var xsliceVal in massCalXSliceValues)
{
var ppmErrorsBefore = new List<double>();
var ppmErrorsAfter = new List<double>();
parameters.MassCalibrationNumXSlices = (short)xsliceVal;
aligner.AlignerParameters = parameters;
aligner.Execute(run);
foreach (var result in repo.Results)
{
var mt = mtc.TargetList.Where(p => p.ID == result.TargetID).Where(p => p.ChargeState == result.ChargeState).First();
var theorMZ = mt.MZ;
var obsMZ = result.MonoMZ;
double scan = result.ScanLC;
var alignedMZ = run.GetAlignedMZ(obsMZ, scan);
var ppmErrorBefore = (theorMZ - obsMZ) / theorMZ * 1e6;
var ppmErrorAfter = (theorMZ - alignedMZ) / theorMZ * 1e6;
sb.Append(result.TargetID + "\t" + result.ScanLC + "\t" + theorMZ.ToString("0.00000") + "\t" + obsMZ.ToString("0.00000") + "\t" + alignedMZ.ToString("0.00000") + "\t" + ppmErrorBefore.ToString("0.0") + "\t" + ppmErrorAfter.ToString("0.0"));
sb.Append(Environment.NewLine);
ppmErrorsAfter.Add(ppmErrorAfter);
ppmErrorsBefore.Add(ppmErrorBefore);
}
Console.WriteLine(sb.ToString());
Console.WriteLine();
Console.WriteLine();
Console.WriteLine("Average ppm error before alignment = " + ppmErrorsBefore.Average().ToString("0.00"));
Console.WriteLine("Average ppm error after alignment = " + ppmErrorsAfter.Average().ToString("0.00"));
Console.WriteLine();
Console.WriteLine();
Console.WriteLine(xsliceVal + "\t" + ppmErrorsBefore.Average().ToString("0.00") + "\t" + ppmErrorsAfter.Average().ToString("0.00"));
}
}
public void Issue0725_AlignmentProblemsTest1()
{
var run = new RunFactory().CreateRun(@"D:\Data\Orbitrap\Issue0725_badAlignment\QC_Shew_10_03-2_100min_06May10_Tiger_10-04-08.RAW");
var alignmentFeaturesFile = run.Filename.Replace(".RAW", "_alignedFeatures.txt");
var importer = new UnlabelledTargetedResultFromTextImporter(alignmentFeaturesFile);
var repo = importer.Import();
var massTagFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\MassTags\QCShew_Formic_MassTags_for_alignment.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 sb = new StringBuilder();
sb.Append("mtid\tscanLC\ttheorMZ\tobsMZ\talignedMZ\tppmErrorBefore\tppmErrorAfter\n");
parameters.MassCalibrationWindow = 50;
parameters.MassCalibrationNumMassDeltaBins = 100;
int[] massCalXSliceValues = { 3, 6, 9, 10, 12, 15,18,20 };
//int[] massCalXSliceValues = { 6 };
foreach (var xsliceVal in massCalXSliceValues)
{
var ppmErrorsBefore = new List<double>();
var ppmErrorsAfter = new List<double>();
parameters.MassCalibrationNumXSlices = (short)xsliceVal;
aligner.AlignerParameters = parameters;
aligner.Execute(run);
foreach (var result in repo.Results)
{
var mt = mtc.TargetList.Where(p => p.ID == result.TargetID).Where(p => p.ChargeState == result.ChargeState).First();
var theorMZ = mt.MZ;
var obsMZ = result.MonoMZ;
double scan = result.ScanLC;
var alignedMZ = run.GetAlignedMZ(obsMZ, scan);
var ppmErrorBefore = (theorMZ - obsMZ) / theorMZ * 1e6;
var ppmErrorAfter = (theorMZ - alignedMZ) / theorMZ * 1e6;
double theorNET = mt.NormalizedElutionTime;
double obsNET = result.NET;
var alignedNET = run.NetAlignmentInfo.GetNETValueForScan((int) scan);
sb.Append(result.TargetID + "\t" + result.ScanLC + "\t" + theorMZ.ToString("0.00000") + "\t" + obsMZ.ToString("0.00000") + "\t" + alignedMZ.ToString("0.00000") + "\t" + ppmErrorBefore.ToString("0.0") + "\t" + ppmErrorAfter.ToString("0.0") + "\t" + theorNET.ToString("0.0000") + "\t" + obsNET.ToString("0.0000") + "\t" + alignedNET.ToString("0.0000"));
//sb.Append(result.MassTagID + "\t" + result.ScanLC + "\t" + theo
sb.Append(Environment.NewLine);
ppmErrorsAfter.Add(ppmErrorAfter);
ppmErrorsBefore.Add(ppmErrorBefore);
}
// Console.WriteLine(sb.ToString());
//Console.WriteLine();
//Console.WriteLine();
//Console.WriteLine("Average ppm error before alignment = " + filterWithGrubbsApplied(ppmErrorsBefore).Average().ToString("0.00"));
//Console.WriteLine("Average ppm error after alignment = " + filterWithGrubbsApplied(ppmErrorsAfter).Average().ToString("0.00"));
//Console.WriteLine();
//Console.WriteLine();
Console.WriteLine(xsliceVal + "\t" + filterWithGrubbsApplied(ppmErrorsBefore).Average().ToString("0.00") + "\t" + filterWithGrubbsApplied(ppmErrorsAfter).Average().ToString("0.00"));
}
}
public void AlignmentParameterTesting1()
{
var run = new RunFactory().CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var alignmentFeaturesFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\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 sb = new StringBuilder();
sb.Append("theorMZ\tobsMZ\talignedMZ\tppmErrorBefore\tppmErrorAfter\n");
parameters.MassCalibrationWindow = 50;
parameters.MassCalibrationNumMassDeltaBins = 100;
int[]massCalXSliceValues = {3,6,9,12,15,20,30,50};
foreach (var xsliceVal in massCalXSliceValues)
{
var ppmErrorsBefore = new List<double>();
var ppmErrorsAfter = new List<double>();
parameters.MassCalibrationNumXSlices =(short)xsliceVal;
aligner.AlignerParameters = parameters;
aligner.Execute(run);
foreach (var result in repo.Results)
{
var mt = mtc.TargetList.Where(p => p.ID == result.TargetID).Where(p => p.ChargeState == result.ChargeState).First();
var theorMZ = mt.MZ;
var obsMZ = result.MonoMZ;
double scan = result.ScanLC;
var alignedMZ = run.GetAlignedMZ(obsMZ, scan);
var ppmErrorBefore = (theorMZ - obsMZ) / theorMZ * 1e6;
var ppmErrorAfter = (theorMZ - alignedMZ) / theorMZ * 1e6;
sb.Append(result.TargetID + "\t" + result.ScanLC + "\t" + theorMZ.ToString("0.00000") + "\t" + obsMZ.ToString("0.00000") + "\t" + alignedMZ.ToString("0.00000") + "\t" + ppmErrorBefore.ToString("0.0") + "\t" + ppmErrorAfter.ToString("0.0"));
sb.Append(Environment.NewLine);
ppmErrorsAfter.Add(ppmErrorAfter);
ppmErrorsBefore.Add(ppmErrorBefore);
}
Console.WriteLine(xsliceVal + "\t" + ppmErrorsBefore.Average().ToString("0.00") + "\t"+ ppmErrorsAfter.Average().ToString("0.00"));
//Console.WriteLine(sb.ToString());
//Console.WriteLine();
//Console.WriteLine();
//Console.WriteLine("Average ppm error before alignment = " + ppmErrorsBefore.Average().ToString("0.00"));
//Console.WriteLine("Average ppm error after alignment = " + ppmErrorsAfter.Average().ToString("0.00"));
}
}
