public void WriteMzmlTest()
{
var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
ChemicalFormulaModification carbamidomethylationOfCMod = new ChemicalFormulaModification("H3C2NO", "carbamidomethylation of C", ModificationSites.C);
peptide.AddModification(carbamidomethylationOfCMod);
DefaultMzSpectrum MS1 = createSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
DefaultMzSpectrum MS2 = createMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
MsDataScan <IMzSpectrum <MzPeak> >[] Scans = new MsDataScan <IMzSpectrum <MzPeak> > [2];
Scans[0] = new MsDataScan <IMzSpectrum <MzPeak> >(1, MS1.newSpectrumApplyFunctionToX(b => b + 0.000001 * b + 0.000001), "spectrum 1", 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "FTMS first spectrum", MZAnalyzerType.Unknown, 1, MS1.SumOfAllY);
Scans[1] = new MsDataScan <IMzSpectrum <MzPeak> >(2, MS2.newSpectrumApplyFunctionToX(b => b + 0.00001 * b + 0.00001), "spectrum 2", 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "FTMS second spectrum", MZAnalyzerType.Unknown, 1, MS2.SumOfAllY, "spectrum 1", 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 0.141146966879759, 1134.26091302033);
var myMsDataFile = new FakeMsDataFile(@"myFakeFile.mzML", Scans);
MzmlMethods.CreateAndWriteMyIndexedMZmlwithCalibratedSpectra(myMsDataFile, Path.Combine(Path.GetDirectoryName(myMsDataFile.FilePath), Path.GetFileNameWithoutExtension(myMsDataFile.FilePath)) + ".mzML");
Mzml okay = new Mzml(@"myFakeFile.mzML");
okay.Open();
okay.GetScan(2);
Assert.AreEqual(1, okay.GetSpectrumNumber(1));
Assert.AreEqual(2, okay.GetSpectrumNumber(2));
}
public MsDataFile LoadFile(string origDataFile, int?topNpeaks, double?minRatio, bool trimMs1Peaks, bool trimMsMsPeaks, CommonParameters commonParameters)
{
FilteringParams filter = new FilteringParams(topNpeaks, minRatio, 1, trimMs1Peaks, trimMsMsPeaks);
if (MyMsDataFiles.TryGetValue(origDataFile, out MsDataFile value) && value != null)
{
return(value);
}
// By now know that need to load this file!!!
lock (FileLoadingLock) // Lock because reading is sequential
{
if (Path.GetExtension(origDataFile).Equals(".mzML", StringComparison.OrdinalIgnoreCase))
{
MyMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter, commonParameters.MaxThreadsToUsePerFile);
}
else if (Path.GetExtension(origDataFile).Equals(".mgf", StringComparison.OrdinalIgnoreCase))
{
MyMsDataFiles[origDataFile] = Mgf.LoadAllStaticData(origDataFile, filter);
}
else
{
#if NETFRAMEWORK
MyMsDataFiles[origDataFile] = ThermoStaticData.LoadAllStaticData(origDataFile, filter);
#else
Warn("No capability for reading " + origDataFile);
#endif
}
return(MyMsDataFiles[origDataFile]);
}
}
public static void TestClassicSearchEngineTopDown()
{
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(protease: "top-down"),
scoreCutoff: 1,
assumeOrphanPeaksAreZ1Fragments: false);
MetaMorpheusTask.DetermineAnalyteType(CommonParameters);
// test output file name (should be proteoform and not peptide)
Assert.That(GlobalVariables.AnalyteType == "Proteoform");
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein>
{
new Protein("MPKVYSYQEVAEHNGPENFWIIIDDKVYDVSQFKDEHPGGDEIIMDLGGQDATESFVDIGHSDEALRLLKGLYIGDVDKTSERVSVEKVSTSENQSKGSGTLVVILAILMLGVAYYLLNE", "P40312")
};
var myMsDataFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TopDownTestData\slicedTDYeast.mzML"));
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>()).Run();
var psm = allPsmsArray.Where(p => p != null).FirstOrDefault();
Assert.That(psm.MatchedFragmentIons.Count == 47);
}
public static void testingTMTonBigScan()
{
Dictionary <string, MsDataFile> MyMsDataFiles = new Dictionary <string, MsDataFile>();
var origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\tmt18test.mzML");
FilteringParams filter = new FilteringParams();
MyMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter, 1);
var scans2 = MyMsDataFiles[origDataFile].GetAllScansList();
var trimmedScans = scans2.Where(m => m.MsnOrder == 3).ToList();
Protein p = new Protein("LAALNPESNTAGLDIFAK", "accession");
List <Modification> fixedModifications = new List <Modification>();
fixedModifications.AddRange(GlobalVariables.AllModsKnown);
List <Modification> tmt18Mods = fixedModifications.Where(m => m.ModificationType == "Multiplex Label" && m.IdWithMotif.Contains("TMT18")).ToList();
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
var aPeptideWithSetModifications = p.Digest(digestionParams, tmt18Mods, new List <Modification>()).First();
var theseTheoreticalFragments = new List <Product>();
aPeptideWithSetModifications.Fragment(DissociationType.HCD, FragmentationTerminus.Both, theseTheoreticalFragments);
theseTheoreticalFragments = theseTheoreticalFragments.Where(n => n.ProductType == ProductType.D).ToList();
double ppmTolerance = 20;
int roundTo = 5;
List <double> diagnosticIons = new List <double>();
for (int k = 0; k < theseTheoreticalFragments.Count(); k++)
{
diagnosticIons.Add(Math.Round(theseTheoreticalFragments[k].NeutralMass, roundTo));
}
int i = 460;
do
{
if (i == trimmedScans.Count())
{
break;
}
var massList = trimmedScans[i].MassSpectrum.XArray.ToList();
for (int j = 0; j < massList.Count(); j++)
{
massList[j] = Math.Round(massList[j], roundTo);
}
for (int l = 0; l < massList.Count(); l++)
{
for (int m = 0; m < diagnosticIons.Count(); m++)
{
double toleranceValue = ppmTolerance / Math.Pow(10, 6) * massList[l];
if ((massList[l] < diagnosticIons[m] + toleranceValue) & (massList[l] > diagnosticIons[m] - toleranceValue))
{
diagnosticIons.Remove(diagnosticIons[m]);
}
}
}
i++;
} while (diagnosticIons.Count() > 0);
Assert.AreEqual(0, diagnosticIons.Count());
}
public void LoadMzmlTest()
{
Assert.Throws <AggregateException>(() =>
{
Mzml.LoadAllStaticData(@"tiny.pwiz.1.1.mzML");
}, "Reading profile mode mzmls not supported");
}
internal IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > LoadFile(string origDataFile, int?topNpeaks, double?minRatio, bool trimMs1Peaks, bool trimMsMsPeaks)
{
FilteringParams filter = new FilteringParams(topNpeaks, minRatio, null, trimMs1Peaks, trimMsMsPeaks);
if (myMsDataFiles.TryGetValue(origDataFile, out IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > value) && value != null)
{
return(value);
}
// By now know that need to load this file!!!
lock (fileLoadingLock) // Lock because reading is sequential
if (Path.GetExtension(origDataFile).Equals(".mzML", StringComparison.OrdinalIgnoreCase))
{
myMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter);
}
else
{
#if NETFRAMEWORK
myMsDataFiles[origDataFile] = ThermoStaticData.LoadAllStaticData(origDataFile, filter);
#else
Warn("No capability for reading " + origDataFile);
#endif
}
return(myMsDataFiles[origDataFile]);
}
public static void ProcessXcorrInB6MzSpectrum()
{
Dictionary <string, MsDataFile> MyMsDataFiles = new Dictionary <string, MsDataFile>();
string origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DatabaseTests\sliced_b6.mzML");
FilteringParams filter = new FilteringParams(200, 0.01, null, 1, false, false, false);
string expectedResultFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DatabaseTests\Working_86.tsv");
List <string> expectedResults = File.ReadAllLines(expectedResultFile, Encoding.UTF8).ToList();
MyMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter, 1);
var scans = MyMsDataFiles[origDataFile].GetAllScansList();
List <double> xArrayProcessed = new List <double>();
foreach (MsDataScan scan in scans.Where(s => s.MsnOrder > 1))
{
if (scan.OneBasedScanNumber == 86)
{
scan.MassSpectrum.XCorrPrePreprocessing(0, 1969, scan.IsolationMz.Value);
xArrayProcessed = scan.MassSpectrum.XArray.ToList();
}
}
for (int i = 0; i < expectedResults.Count; i++)
{
Assert.That(double.Parse(expectedResults[i]), Is.EqualTo(xArrayProcessed[i]).Within(0.001));
}
}
public static void TestModernSearchEngineTopDown()
{
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(protease: "top-down"),
scoreCutoff: 1,
assumeOrphanPeaksAreZ1Fragments: false);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein>
{
new Protein("MPKVYSYQEVAEHNGPENFWIIIDDKVYDVSQFKDEHPGGDEIIMDLGGQDATESFVDIGHSDEALRLLKGLYIGDVDKTSERVSVEKVSTSENQSKGSGTLVVILAILMLGVAYYLLNE", "P40312")
};
var myMsDataFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TopDownTestData\slicedTDYeast.mzML"));
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, 1, DecoyType.Reverse, CommonParameters, 30000, false, new List <FileInfo>(), new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
new ModernSearchEngine(allPsmsArray, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, CommonParameters, searchMode, 0, new List <string>()).Run();
var psm = allPsmsArray.Where(p => p != null).FirstOrDefault();
Assert.That(psm.MatchedFragmentIons.Count > 50);
}
public static void DifferentAnalyzersTest()
{
IMzmlScan[] scans = new IMzmlScan[2];
double[] intensities1 = new double[] { 1 };
double[] mz1 = new double[] { 50 };
MzmlMzSpectrum massSpec1 = new MzmlMzSpectrum(mz1, intensities1, false);
scans[0] = new MzmlScan(1, massSpec1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "1");
double[] intensities2 = new double[] { 1 };
double[] mz2 = new double[] { 30 };
MzmlMzSpectrum massSpec2 = new MzmlMzSpectrum(mz2, intensities2, false);
scans[1] = new MzmlScanWithPrecursor(2, massSpec2, 2, true, Polarity.Positive, 2, new MzRange(1, 100), "f", MZAnalyzerType.IonTrap3D, massSpec2.SumOfAllY,
50, null, null, 50, 1, DissociationType.CID, 1, null, null, "2");
FakeMsDataFile f = new FakeMsDataFile(scans);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(f, Path.Combine(TestContext.CurrentContext.TestDirectory, "asdfefsf.mzML"), false);
Mzml ok = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "asdfefsf.mzML"));
Assert.AreEqual(MZAnalyzerType.Orbitrap, ok.First().MzAnalyzer);
Assert.AreEqual(MZAnalyzerType.IonTrap3D, ok.Last().MzAnalyzer);
}
public MsDataFile LoadFile(string origDataFile, CommonParameters commonParameters)
{
FilteringParams filter = new FilteringParams(commonParameters.NumberOfPeaksToKeepPerWindow, commonParameters.MinimumAllowedIntensityRatioToBasePeak, commonParameters.WindowWidthThomsons, commonParameters.NumberOfWindows, commonParameters.NormalizePeaksAccrossAllWindows, commonParameters.TrimMs1Peaks, commonParameters.TrimMsMsPeaks);
if (commonParameters.DissociationType == DissociationType.LowCID || commonParameters.MS2ChildScanDissociationType == DissociationType.LowCID || commonParameters.MS3ChildScanDissociationType == DissociationType.LowCID)
{
filter = null;
}
if (MyMsDataFiles.TryGetValue(origDataFile, out MsDataFile value) && value != null)
{
return(value);
}
// By now know that need to load this file!!!
lock (FileLoadingLock) // Lock because reading is sequential
{
if (Path.GetExtension(origDataFile).Equals(".mzML", StringComparison.OrdinalIgnoreCase))
{
MyMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter, commonParameters.MaxThreadsToUsePerFile);
}
else if (Path.GetExtension(origDataFile).Equals(".mgf", StringComparison.OrdinalIgnoreCase))
{
MyMsDataFiles[origDataFile] = Mgf.LoadAllStaticData(origDataFile, filter);
}
else
{
MyMsDataFiles[origDataFile] = ThermoRawFileReaderData.LoadAllStaticData(origDataFile, filter, commonParameters.MaxThreadsToUsePerFile);
}
return(MyMsDataFiles[origDataFile]);
}
}
public bool Run_TdMzCal(InputFile raw_file, List <TopDownHit> topdown_hits)
{
all_topdown_hits = topdown_hits.Where(h => h.score > 0).ToList();
//need to reset m/z in case same td hits used for multiple calibration raw files...
Parallel.ForEach(all_topdown_hits, h => h.mz = h.reported_mass.ToMz(h.charge));
high_scoring_topdown_hits = all_topdown_hits.Where(h => h.score >= 40).ToList();
this.raw_file = raw_file;
if (high_scoring_topdown_hits.Count < 5)
{
return(false);
}
myMsDataFile = Path.GetExtension(raw_file.complete_path) == ".raw" ?
ThermoStaticData.LoadAllStaticData(raw_file.complete_path) :
null;
if (myMsDataFile == null)
{
myMsDataFile = Mzml.LoadAllStaticData(raw_file.complete_path);
}
if (myMsDataFile == null)
{
return(false);
}
DataPointAquisitionResults dataPointAcquisitionResult = GetDataPoints();
if (dataPointAcquisitionResult.Ms1List.Count < 10)
{
return(false);
}
var myMs1DataPoints = new List <(double[] xValues, double yValue)>();
for (int i = 0; i < dataPointAcquisitionResult.Ms1List.Count; i++)
{
//x values
var explanatoryVariables = new double[4];
explanatoryVariables[0] = dataPointAcquisitionResult.Ms1List[i].mz;
explanatoryVariables[1] = dataPointAcquisitionResult.Ms1List[i].retentionTime;
explanatoryVariables[2] = dataPointAcquisitionResult.Ms1List[i].logTotalIonCurrent;
explanatoryVariables[3] = dataPointAcquisitionResult.Ms1List[i].logInjectionTime;
//yvalue
double mzError = dataPointAcquisitionResult.Ms1List[i].massError;
myMs1DataPoints.Add((explanatoryVariables, mzError));
}
var ms1Model = GetRandomForestModel(myMs1DataPoints);
CalibrateHitsAndComponents(ms1Model);
if (Sweet.lollipop.calibrate_raw_files)
{
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, raw_file.directory + "\\" + raw_file.filename + "_calibrated.mzML", false);
}
return(true);
}
public void LoadMzmlTest()
{
Mzml a = new Mzml(@"tiny.pwiz.1.1.mzML");
a.Open();
Assert.AreEqual(true, a.IsIndexedMzML);
var ya = a.GetScan(1).MassSpectrum;
}
public static void TestLookingForAcceptableIsotopicEnvelopes()
{
CommonParameters CommonParameters = new CommonParameters();
MetaMorpheusTask.DetermineAnalyteType(CommonParameters);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein>
{
new Protein("AAAHSSLK", ""), new Protein("RQPAQPR", ""), new Protein("EKAEAEAEK", "")
};
var myMsDataFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML"));
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
var ms2ScanTest = listOfSortedms2Scans[0];
//test when all the masses are not in the given range
//test1 when all the masses are too small
var test1 = ms2ScanTest.GetClosestExperimentalIsotopicEnvelopeList(50, 95);
Assert.AreEqual(test1, null);
//test2 when all the masses are too big
var test2 = ms2ScanTest.GetClosestExperimentalIsotopicEnvelopeList(582, 682);
Assert.AreEqual(test2, null);
//test3 when the mass which is bigger than given min mass is bigger than the mass which is smaller than the given max mass
//for example: the mass array is [1,2,3,4,5], the given min mass is 2.2, the given max mass is 2.8
var test3 = ms2ScanTest.GetClosestExperimentalIsotopicEnvelopeList(110, 111);
Assert.AreEqual(test3, null);
//test normal conditions:look for IsotopicEnvelopes which are in the range of acceptable mass
var test4 = ms2ScanTest.GetClosestExperimentalIsotopicEnvelopeList(120, 130);
IsotopicEnvelope[] expected4 = ms2ScanTest.ExperimentalFragments.Skip(15).Take(9).ToArray();
Assert.That(ms2ScanTest.ExperimentalFragments[15].MonoisotopicMass > 120 && ms2ScanTest.ExperimentalFragments[14].MonoisotopicMass < 120);
Assert.That(ms2ScanTest.ExperimentalFragments[23].MonoisotopicMass < 130 && ms2ScanTest.ExperimentalFragments[24].MonoisotopicMass > 130);
Assert.AreEqual(test4, expected4);
var test5 = ms2ScanTest.GetClosestExperimentalIsotopicEnvelopeList(400, 500);
IsotopicEnvelope[] expected5 = ms2ScanTest.ExperimentalFragments.Skip(150).Take(7).ToArray();
Assert.That(ms2ScanTest.ExperimentalFragments[150].MonoisotopicMass > 400 && ms2ScanTest.ExperimentalFragments[149].MonoisotopicMass < 400);
Assert.That(ms2ScanTest.ExperimentalFragments[156].MonoisotopicMass < 500 && ms2ScanTest.ExperimentalFragments[157].MonoisotopicMass > 500);
Assert.AreEqual(test5, expected5);
}
public static void Test_ChargeDeconv()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/2076.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
Stopwatch stopwatch0 = new Stopwatch();
stopwatch0.Start();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
stopwatch0.Stop();
Stopwatch stopwatch_iso = new Stopwatch();
stopwatch_iso.Start();
var iso = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, deconvolutionParameter);
stopwatch_iso.Stop();
Stopwatch stopwatch1 = new Stopwatch();
stopwatch1.Start();
var x = ChargeDecon.FindChargesForScan(spectrum, deconvolutionParameter);
stopwatch1.Stop();
//Stopwatch stopwatch2 = new Stopwatch();
//stopwatch2.Start();
var stopwatch2 = Stopwatch.StartNew();
var x2 = ChargeDecon.QuickFindChargesForScan(spectrum, deconvolutionParameter);
stopwatch2.Stop();
// Stopwatch stopwatch3 = new Stopwatch();
// stopwatch3.Start();
// int indUp = spectrum.ExtractIndicesByY().First();
// double mass_up = spectrum.XArray[indUp];
// var highest = ChargeDecon.FindChargesForPeak(spectrum, indUp, new DeconvolutionParameter());
// stopwatch3.Stop();
// var Parameters = Program.AddParametersFromFile("");
// List<double> masses = highest.Select(p => p.Value.Mz).ToList();
// string dynamicTargets;
// string dynamicMaxITs;
// Stopwatch stopwatch4 = new Stopwatch();
// stopwatch4.Start();
// var test = BoxCarScan.BuildDynamicBoxString(Parameters, masses, out dynamicTargets, out dynamicMaxITs);
// stopwatch4.Stop();
// Assert.That(test == "[(400.0,522.8),(524.8,542.2),(544.2,563.1),(565.1,585.6),(587.6,610.0),(612.0,636.5),(638.5,665.4),(667.4,697.1),(699.1,732.0),(734.0,770.5),(772.5,813.3),(815.3,861.1),(863.1,915.0),(917.0,976.0),(978.0,1045.7),(1047.7,1126.1),(1128.1,1200.0)]");
}
public static void TestSummedMsDataFile()
{
ThermoStaticData rawFile = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
// 3 scans
SummedMsDataFile summed3 = new SummedMsDataFile(rawFile, 3, 10);
Assert.AreEqual(rawFile.NumSpectra - 2, summed3.NumSpectra);
var resultingTic = summed3.GetOneBasedScan(1).TotalIonCurrent;
var mySummedTic = rawFile.GetOneBasedScan(1).MassSpectrum.SumOfAllY + rawFile.GetOneBasedScan(2).MassSpectrum.SumOfAllY + rawFile.GetOneBasedScan(3).MassSpectrum.SumOfAllY;
var instrumentSummedTic = rawFile.GetOneBasedScan(1).TotalIonCurrent + rawFile.GetOneBasedScan(2).TotalIonCurrent + rawFile.GetOneBasedScan(3).TotalIonCurrent;
// Tics are approximately what they should be
Assert.IsTrue(Math.Abs(resultingTic - mySummedTic) / mySummedTic < 1e-4);
Assert.IsTrue(Math.Abs(resultingTic - instrumentSummedTic) / instrumentSummedTic < 1e-1);
// Equal to representative
Assert.AreEqual(summed3.GetOneBasedScan(1).RetentionTime, rawFile.GetOneBasedScan(2).RetentionTime);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size <= rawFile.GetOneBasedScan(1).MassSpectrum.Size + rawFile.GetOneBasedScan(2).MassSpectrum.Size + rawFile.GetOneBasedScan(3).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(1).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(2).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(3).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY == rawFile.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY + rawFile.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY + rawFile.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY);
// Interval of 893-899 mz
Assert.AreEqual(2, rawFile.GetOneBasedScan(1).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(2, rawFile.GetOneBasedScan(2).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(1, rawFile.GetOneBasedScan(3).MassSpectrum.NumPeaksWithinRange(893, 899));
// One peak persists across the three scans! So instead of 5 see three peaks in summed
Assert.AreEqual(3, summed3.GetOneBasedScan(1).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(summed3.GetOneBasedScan(1).MassSpectrum.FirstX, Math.Min(Math.Min(rawFile.GetOneBasedScan(1).MassSpectrum.FirstX.Value, rawFile.GetOneBasedScan(2).MassSpectrum.FirstX.Value), rawFile.GetOneBasedScan(3).MassSpectrum.FirstX.Value));
Assert.AreEqual(summed3.GetOneBasedScan(1).MassSpectrum.LastX, Math.Max(Math.Max(rawFile.GetOneBasedScan(1).MassSpectrum.LastX.Value, rawFile.GetOneBasedScan(2).MassSpectrum.LastX.Value), rawFile.GetOneBasedScan(3).MassSpectrum.LastX.Value));
// 5 scans
SummedMsDataFile summed5 = new SummedMsDataFile(rawFile, 5, 10);
Assert.AreEqual(rawFile.NumSpectra - 4, summed5.NumSpectra);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(summed5, "testSummed.mzML", false);
var ok = Mzml.LoadAllStaticData("testSummed.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(ok, "testSummed2.mzML", false);
Mzml.LoadAllStaticData("testSummed2.mzML");
}
public static void WriteIndexedMzmlFromThermoTest()
{
var smallThermo = ThermoStaticData.LoadAllStaticData(@"small.raw");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(smallThermo, Path.Combine(TestContext.CurrentContext.TestDirectory, "Hi.mzML"), true);
var smallMzml = Mzml.LoadAllStaticData(@"Hi.mzML");
Assert.AreEqual(smallMzml.NumSpectra, 48);
Assert.AreEqual(smallMzml.GetOneBasedScan(8).OneBasedScanNumber, 8);
Assert.AreEqual(smallThermo.GetOneBasedScan(5).RetentionTime, smallMzml.GetOneBasedScan(5).RetentionTime);
}
public static void TestXicExtraction()
{
string dataFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "SmallCalibratibleYeast.mzml");
var data = Mzml.LoadAllStaticData(dataFilePath);
var peptide = new PeptideWithSetModifications("KAPAGGAADAAAK", new Dictionary <string, Modification>());
var xic = data.ExtractIonChromatogram(peptide.MonoisotopicMass, 2, new PpmTolerance(10), 24.806);
Assert.That(xic.Data.Count(p => p.Y > 0) == 4);
}
public static void Test_RealDataDeconv()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/20170802_QEp1_FlMe_SA_BOX0_SILAC_BoxCar_SLICED.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
var test = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
var ms1scans = scans.Where(p => p.MsnOrder == 1).ToList();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
}
public static void Test_FragmentMesh()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/2076.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
var CEs = ChargeDecon.FindChargesForScan(spectrum, deconvolutionParameter);
var mesh = CEs.First().mzs_box;
Assert.That(mesh.Count() == 3);
}
public static void BU_dynamicBoxCarRange()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/20170802_QEp1_FlMe_SA_BOX0_SILAC_BoxCar_SLICED.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
Parameters parameters = Program.AddParametersFromFile("");
var isos = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, parameters.DeconvolutionParameter);
List <List <Tuple <double, double, double> > > Boxes = new List <List <Tuple <double, double, double> > >();
BoxCarScan.GenerateDynamicBoxes_BU(isos, parameters, Boxes);
Assert.That(Boxes.Count == 2);
}
/// <summary>
/// Tests peak filtering for ThermoRawFileReader
/// </summary>
public static void TestPeakFilteringRawFileReader(string infile)
{
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
var filterParams = new FilteringParams(200, 0.01, 0, 1, false, true, true);
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", infile);
var a = ThermoRawFileReader.LoadAllStaticData(path, filterParams, maxThreads: 1);
var rawScans = a.GetAllScansList();
foreach (var scan in rawScans)
{
Assert.That(scan.MassSpectrum.XArray.Length <= 200);
}
string outfile1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", Path.GetFileNameWithoutExtension(infile) + ".mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, outfile1, false);
var mzml = Mzml.LoadAllStaticData(outfile1, filterParams, maxThreads: 1);
var mzmlScans = mzml.GetAllScansList();
for (int i = 0; i < mzmlScans.Count; i++)
{
var mzmlScan = mzmlScans[i];
var rawScan = rawScans[i];
for (int j = 0; j < mzmlScan.MassSpectrum.XArray.Length; j++)
{
double roundedMzmlMz = Math.Round(mzmlScan.MassSpectrum.XArray[j], 2);
double roundedRawMz = Math.Round(rawScan.MassSpectrum.XArray[j], 2);
Assert.AreEqual(roundedMzmlMz, roundedRawMz);
double roundedMzmlIntensity = Math.Round(mzmlScan.MassSpectrum.XArray[j], 0);
double roundedRawIntensity = Math.Round(rawScan.MassSpectrum.XArray[j], 0);
Assert.AreEqual(roundedMzmlIntensity, roundedRawIntensity);
}
}
Console.WriteLine($"Analysis time for TestPeakFilteringRawFileReader: {stopwatch.Elapsed.Hours}h " +
$"{stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
}
public static void WriteEmptyScan()
{
double[] intensities1 = new double[] { };
double[] mz1 = new double[] { };
MzmlMzSpectrum massSpec1 = new MzmlMzSpectrum(mz1, intensities1, false);
IMzmlScan[] scans = new IMzmlScan[] {
new MzmlScan(1, massSpec1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "1")
};
FakeMsDataFile f = new FakeMsDataFile(scans);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(f, Path.Combine(TestContext.CurrentContext.TestDirectory, "mzmlWithEmptyScan.mzML"), false);
Mzml ok = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "mzmlWithEmptyScan.mzML"));
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(ok, Path.Combine(TestContext.CurrentContext.TestDirectory, "mzmlWithEmptyScan2.mzML"), false);
}
public static void LoadCompressedMzml()
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"small.RAW");
Mzml b = Mzml.LoadAllStaticData(@"smallCentroid.mzML");
Assert.AreEqual(a.NumSpectra, b.NumSpectra);
Assert.AreEqual(a.GetOneBasedScan(1).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(1).MassSpectrum.XofPeakWithHighestY.Value, 1e-8);
Assert.IsTrue(Math.Abs((a.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8);
Assert.AreEqual(a.GetOneBasedScan(2).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(2).MassSpectrum.XofPeakWithHighestY, 1e-8);
Assert.IsTrue(Math.Abs((a.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8);
Assert.AreEqual(a.GetOneBasedScan(3).MassSpectrum.XofPeakWithHighestY.Value, b.GetOneBasedScan(3).MassSpectrum.XofPeakWithHighestY.Value, 1e-8);
Assert.IsTrue(Math.Abs((a.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY.Value - b.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY.Value) / b.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY.Value) < 1e-8);
}
public void LoadMzmlAnotherTest()
{
Mzml a = Mzml.LoadAllStaticData(@"small.pwiz.1.1.mzML");
Assert.AreEqual(19914, a.First().MassSpectrum.Size);
//a = new Mzml(@"small.pwiz.1.1.mzML", 400);
//a.Open();
//Assert.AreEqual(400, a.First().MassSpectrum.Size);
//var cool = a.GetOneBasedScan(6) as MzmlScanWithPrecursor;
//Assert.AreEqual(1, cool.IsolationWidth);
//a.Close();
}
public void WriteMzmlTest()
{
var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
OldSchoolChemicalFormulaModification carbamidomethylationOfCMod = new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H3C2NO"), "carbamidomethylation of C", ModificationSites.C);
peptide.AddModification(carbamidomethylationOfCMod);
MzmlMzSpectrum MS1 = CreateSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
MzmlMzSpectrum MS2 = CreateMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
IMzmlScan[] Scans = new IMzmlScan[2];
Scans[0] = new MzmlScan(1, MS1, 1, true, Polarity.Positive, 1.0, new MzRange(300, 2000), " first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, 1, "scan=1");
Scans[1] = new MzmlScanWithPrecursor(2, MS2, 2, true, Polarity.Positive, 2.0, new MzRange(100, 1500), " second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 1134.26091302033, 1, "scan=2");
var myMsDataFile = new FakeMsDataFile(Scans);
var oldFirstValue = myMsDataFile.GetOneBasedScan(1).MassSpectrum.FirstX;
var secondScan = myMsDataFile.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>;
Assert.AreEqual(1, secondScan.IsolationRange.Maximum - secondScan.IsolationRange.Minimum);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, "argh.mzML", false);
Mzml okay = Mzml.LoadAllStaticData(@"argh.mzML");
okay.GetOneBasedScan(2);
Assert.AreEqual(1, okay.GetClosestOneBasedSpectrumNumber(1));
Assert.AreEqual(2, okay.GetClosestOneBasedSpectrumNumber(2));
var newFirstValue = okay.GetOneBasedScan(1).MassSpectrum.FirstX;
Assert.AreEqual(oldFirstValue.Value, newFirstValue.Value, 1e-9);
var secondScan2 = okay.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>;
Assert.AreEqual(1, secondScan2.IsolationRange.Maximum - secondScan2.IsolationRange.Minimum);
secondScan2.MassSpectrum.ReplaceXbyApplyingFunction((a) => 44);
Assert.AreEqual(44, secondScan2.MassSpectrum.LastX);
}
public static void ProcessXcorrInMzSpectrum()
{
Dictionary <string, MsDataFile> MyMsDataFiles = new Dictionary <string, MsDataFile>();
string origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "BinGenerationTest.mzML");
FilteringParams filter = new FilteringParams(200, 0.01, null, 1, false, false, true);
MyMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter, 1);
var scans = MyMsDataFiles[origDataFile].GetAllScansList();
foreach (MsDataScan scan in scans.Where(s => s.MsnOrder > 1))
{
scan.MassSpectrum.XCorrPrePreprocessing(0, 1968 * 1.0005079, scan.IsolationMz.Value);
}
Assert.AreEqual(6, scans[0].MassSpectrum.XArray.Count());
Assert.AreEqual(20, scans[1].MassSpectrum.XArray.Count());
}
/// <summary>
/// Tests LoadAllStaticData for ThermoRawFileReader
/// </summary>
public static void TestLoadAllStaticDataRawFileReader(string infile, string outfile1, string outfile2)
{
var path = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", infile);
outfile1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", outfile1);
outfile2 = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", outfile2);
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
var a = ThermoRawFileReader.LoadAllStaticData(path, maxThreads: 1);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, outfile1, false);
var aa = Mzml.LoadAllStaticData(outfile1);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(aa, outfile2, true);
Mzml.LoadAllStaticData(outfile2);
Console.WriteLine($"Analysis time for TestLoadAllStaticDataRawFileReader({infile}): {stopwatch.Elapsed.Hours}h {stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
}
public void LoadMzmlTest()
{
Mzml a = Mzml.LoadAllStaticData(@"tiny.pwiz.1.1.mzML");
var ya = a.GetOneBasedScan(1).MassSpectrum;
Assert.AreEqual(15, ya.Size);
var ya2 = a.GetOneBasedScan(2).MassSpectrum;
Assert.AreEqual(10, ya2.Size);
var ya3 = a.GetOneBasedScan(3).MassSpectrum;
Assert.AreEqual(0, ya3.Size);
var ya4 = a.GetOneBasedScan(4).MassSpectrum;
Assert.AreEqual(15, ya4.Size);
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > ok = a;
Assert.AreEqual(1, ok.GetClosestOneBasedSpectrumNumber(5));
}
public static void AnotherMzMLtest()
{
IMzmlScan[] scans = new IMzmlScan[4];
double[] intensities1 = new double[] { 1 };
double[] mz1 = new double[] { 50 };
MzmlMzSpectrum massSpec1 = new MzmlMzSpectrum(mz1, intensities1, false);
scans[0] = new MzmlScan(1, massSpec1, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "1");
double[] intensities2 = new double[] { 1 };
double[] mz2 = new double[] { 30 };
MzmlMzSpectrum massSpec2 = new MzmlMzSpectrum(mz2, intensities2, false);
scans[1] = new MzmlScanWithPrecursor(2, massSpec2, 2, true, Polarity.Positive, 2, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec2.SumOfAllY,
50, null, null, 50, 1, DissociationType.CID, 1, null, null, "2");
double[] intensities3 = new double[] { 1 };
double[] mz3 = new double[] { 50 };
MzmlMzSpectrum massSpec3 = new MzmlMzSpectrum(mz3, intensities3, false);
scans[2] = new MzmlScan(3, massSpec3, 1, true, Polarity.Positive, 1, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec1.SumOfAllY, null, "3");
double[] intensities4 = new double[] { 1 };
double[] mz4 = new double[] { 30 };
MzmlMzSpectrum massSpec4 = new MzmlMzSpectrum(mz4, intensities4, false);
scans[3] = new MzmlScanWithPrecursor(4, massSpec4, 2, true, Polarity.Positive, 2, new MzRange(1, 100), "f", MZAnalyzerType.Orbitrap, massSpec2.SumOfAllY,
50, null, null, 50, 1, DissociationType.CID, 3, null, null, "4");
FakeMsDataFile f = new FakeMsDataFile(scans);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(f, Path.Combine(TestContext.CurrentContext.TestDirectory, "what.mzML"), false);
Mzml ok = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "what.mzML"));
var scanWithPrecursor = ok.Last(b => b is IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
Assert.AreEqual(3, scanWithPrecursor.OneBasedPrecursorScanNumber);
}
public void LoadMzmlFromConvertedMGFTest()
{
Mzml a = Mzml.LoadAllStaticData(@"tester.mzML");
var ya = a.GetOneBasedScan(1).MassSpectrum;
Assert.AreEqual(192, ya.Size);
var ya2 = a.GetOneBasedScan(3).MassSpectrum;
Assert.AreEqual(165, ya2.Size);
var ya3 = a.GetOneBasedScan(5).MassSpectrum;
Assert.AreEqual(551, ya3.Size);
var ya4 = a.GetOneBasedScan(975).MassSpectrum;
Assert.AreEqual(190, ya4.Size);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, "CreateFileFromConvertedMGF.mzML", false);
Mzml b = Mzml.LoadAllStaticData(@"CreateFileFromConvertedMGF.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(b, "CreateFileFromConvertedMGF2.mzML", false);
}
