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);
}
/// <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 = ThermoRawFileReaderData.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 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 void LoadThermoTest()
{
ThermoRawFile a = new ThermoRawFile(@"Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20.RAW");
a.Open();
a.Open();
Assert.AreEqual(1, a.FirstSpectrumNumber);
Assert.AreEqual(3316, a.LastSpectrumNumber);
Assert.AreEqual(3316, a.LastSpectrumNumber);
var scan = a.GetScan(53);
Assert.AreEqual(1.2623333333333333, scan.RetentionTime);
Assert.AreEqual(1, scan.MsnOrder);
Assert.AreEqual("controllerType=0 controllerNumber=1 scan=53", scan.id);
Assert.AreEqual("+ c ESI Full ms [400.00-2000.00]", scan.ScanFilter);
var spectrum = a.GetScan(53).MassSpectrum;
var peak = spectrum.PeakWithHighestY;
Assert.AreEqual(75501, peak.Intensity);
Assert.AreEqual(1, spectrum.newSpectrumFilterByY(7.5e4).Count);
Assert.AreEqual(2, spectrum.newSpectrumExtract(new DoubleRange(923, 928)).Count);
Assert.AreEqual(double.NaN, spectrum.GetSignalToNoise(1));
Assert.AreEqual("1.3", a.GetSofwareVersion());
double ya;
a.GetScan(948).TryGetSelectedIonGuessIntensity(out ya);
Assert.AreEqual(4125760, ya);
Assert.AreEqual("LCQ", a.GetInstrumentName());
Assert.AreEqual("LCQ", a.GetInstrumentModel());
Assert.AreEqual(0, a.GetMSXPrecursors(1289).Count);
Assert.AreEqual(1, a.GetMSXPrecursors(1290).Count);
Assert.AreEqual(1194.53, a.GetMSXPrecursors(1290).First());
MzmlMethods.CreateAndWriteMyIndexedMZmlwithCalibratedSpectra(a, Path.Combine(Path.GetDirectoryName(a.FilePath), Path.GetFileNameWithoutExtension(a.FilePath)) + ".mzML");
}
/// <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 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);
}
public static void LoadThermoTest2()
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
Assert.AreEqual(360, a.NumSpectra);
Assert.GreaterOrEqual(1000, a.GetOneBasedScan(1).MassSpectrum.Extract(0, 500).Last().Mz);
Assert.AreEqual(2, a.GetOneBasedScan(1).MassSpectrum.FilterByY(5e6, double.MaxValue).Count());
var ye = a.GetOneBasedScan(1).MassSpectrum.CopyTo2DArray();
Assert.AreEqual(77561752, a.GetOneBasedScan(1).TotalIonCurrent);
Assert.AreEqual(144, a.GetClosestOneBasedSpectrumNumber(2));
MzSpectrum newSpectrum = new MzSpectrum(a.GetOneBasedScan(51).MassSpectrum.XArray, a.GetOneBasedScan(51).MassSpectrum.YArray, true);
Assert.AreEqual(1120, a.GetOneBasedScan(1).MassSpectrum.Size);
var newDeconvolution = a.GetOneBasedScan(1).MassSpectrum.Deconvolute(new MzRange(double.MinValue, double.MaxValue), 1, 10, 1, 4).ToList();
Assert.IsTrue(newDeconvolution.Any(b => Math.Abs(b.peaks.First().mz.ToMass(b.charge) - 523.257) < 0.001));
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, Path.Combine(TestContext.CurrentContext.TestDirectory, "convertedThermo.mzML"), false);
var sdafaf = a.Deconvolute(null, null, 1, 30, 10, 3, 10, b => true).OrderByDescending(b => b.NumPeaks).First();
Assert.IsTrue(Math.Abs(262.64 - sdafaf.Mass.ToMz(2)) <= 0.01);
using (ThermoDynamicData dynamicThermo = ThermoDynamicData.InitiateDynamicConnection(@"05-13-16_cali_MS_60K-res_MS.raw"))
{
Assert.AreEqual(136, dynamicThermo.GetClosestOneBasedSpectrumNumber(1.89));
dynamicThermo.ClearCachedScans();
}
Mzml readCovertedMzmlFile = Mzml.LoadAllStaticData(Path.Combine(TestContext.CurrentContext.TestDirectory, "convertedThermo.mzML"));
Assert.AreEqual(a.GetAllScansList().First().Polarity, readCovertedMzmlFile.GetAllScansList().First().Polarity);
}
public static void ReadWriteReadEtc()
{
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"testFileWMS2.raw");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, "a.mzML", false);
var aa = Mzml.LoadAllStaticData("a.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(aa, "aa.mzML", true);
Mzml.LoadAllStaticData("aa.mzML");
}
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"small.raw");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, "a.mzML", false);
var aa = Mzml.LoadAllStaticData("a.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(aa, "aa.mzML", true);
Mzml.LoadAllStaticData("aa.mzML");
}
{
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(a, "a.mzML", false);
var aa = Mzml.LoadAllStaticData("a.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(aa, "aa.mzML", true);
Mzml.LoadAllStaticData("aa.mzML");
}
}
public static void TestIndividualFileOutput()
{
string subFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"IndividualOutputTest");
Directory.CreateDirectory(subFolder);
string outputFolder = Path.Combine(subFolder, "Results");
SearchTask allowFilesTask = new SearchTask();
allowFilesTask.SearchParameters.WriteIndividualFiles = true;
allowFilesTask.SearchParameters.CompressIndividualFiles = false;
SearchTask compressFilesTask = new SearchTask();
compressFilesTask.SearchParameters.WriteIndividualFiles = true;
compressFilesTask.SearchParameters.CompressIndividualFiles = true;
SearchTask noFilesTask = new SearchTask();
noFilesTask.SearchParameters.WriteIndividualFiles = false;
PeptideWithSetModifications pwsm = new PeptideWithSetModifications("AAFNSGK", null);
List <(string, MetaMorpheusTask)> tasks = new List <(string, MetaMorpheusTask)> {
("allowFiles", allowFilesTask), ("compressFiles", compressFilesTask), ("noFiles", noFilesTask)
};
DbForTask db = new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "gapdh.fasta"), false);
TestDataFile datafile = new TestDataFile(pwsm);
string pathOne = Path.Combine(subFolder, "fileOne.mzml");
string pathTwo = Path.Combine(subFolder, "fileTwo.mzml");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(datafile, pathOne, false);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(datafile, pathTwo, false);
new EverythingRunnerEngine(tasks, new List <string> {
pathOne, pathTwo
}, new List <DbForTask> {
db
}, outputFolder).Run();
//check that the first task wrote everything fine
HashSet <string> expectedFiles = new HashSet <string>
{
".mzID",
"_Peptides.psmtsv",
"_ProteinGroups.tsv",
"_PSMs.psmtsv",
"_PSMsFormattedForPercolator.tab",
"_QuantifiedPeaks.tsv"
};
HashSet <string> writtenFiles = new HashSet <string>(Directory.GetFiles(Path.Combine(outputFolder, "allowFiles", "Individual File Results")).Select(v => Path.GetFileName(v).Substring(7)));
//check they're the same
Assert.IsTrue(expectedFiles.Except(writtenFiles).Count() == 0);
//check the second one is compressed and contains all the information
writtenFiles = new HashSet <string>(Directory.GetFiles(Path.Combine(outputFolder, "compressFiles")).Select(v => Path.GetFileName(v)));
//check the zip exists
Assert.IsTrue(writtenFiles.Contains("Individual File Results.zip"));
//check the original folder does not exist
string[] subfolders = Directory.GetDirectories(Path.Combine(outputFolder, "compressFiles"));
Assert.IsTrue(subfolders.Length == 0);
ZipFile.ExtractToDirectory(Path.Combine(outputFolder, "compressFiles", "Individual File Results.zip"), Path.Combine(outputFolder, "compressFiles", "Individual File Results"));
//read the extracted files
writtenFiles = new HashSet <string>(Directory.GetFiles(Path.Combine(outputFolder, "compressFiles", "Individual File Results")).Select(v => Path.GetFileName(v).Substring(7)));
//check they're the same
Assert.IsTrue(expectedFiles.Except(writtenFiles).Count() == 0);
//check the last one to make sure nothing was written except for the mzID files
writtenFiles = new HashSet <string>(Directory.GetFiles(Path.Combine(outputFolder, "noFiles", "Individual File Results")).Select(v => Path.GetFileName(v).Substring(7)));
Assert.IsTrue(writtenFiles.Count == 1);
Assert.IsTrue(writtenFiles.Contains(".mzID"));
Directory.Delete(outputFolder, true);
//Do a check that we don't crash if there's only one file but somebody tries to zip the individual file results
SearchTask weirdTask = new SearchTask();
weirdTask.SearchParameters.CompressIndividualFiles = true;
weirdTask.SearchParameters.WriteMzId = false;
new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("weird", weirdTask)
}, new List <string> {
public bool Run_TdMzCal(InputFile raw_file, List <SpectrumMatch> 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);
}
if (Sweet.lollipop.mass_calibration)
{
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);
}
}
if (Sweet.lollipop.retention_time_calibration)
{
var myMs1DataPoints = new List <(double[] xValues, double yValue)>();
List <SpectrumMatch> firstElutingTopDownHit = new List <SpectrumMatch>();
List <string> PFRs = high_scoring_topdown_hits.Select(h => h.pfr_accession).Distinct().ToList();
foreach (var PFR in PFRs)
{
var firstHitWithPFR = high_scoring_topdown_hits
.Where(h => h.pfr_accession == PFR).OrderBy(h => h.ms2_retention_time).First();
firstElutingTopDownHit.Add(firstHitWithPFR);
}
for (int i = 0; i < dataPointAcquisitionResult.Ms1List.Count; i++)
{
if (firstElutingTopDownHit.Contains(dataPointAcquisitionResult.Ms1List[i].identification))
{
//x values
var explanatoryVariables = new double[1];
explanatoryVariables[0] = dataPointAcquisitionResult.Ms1List[i].retentionTime;
//yvalue
double RTError = dataPointAcquisitionResult.Ms1List[i].RTError;
myMs1DataPoints.Add((explanatoryVariables, RTError));
}
}
if (myMs1DataPoints.Count < 10)
{
return(false);
}
var ms1Model = GetRandomForestModel(myMs1DataPoints);
foreach (Component c in Sweet.lollipop.calibration_components.Where(h => h.input_file.lt_condition == raw_file.lt_condition && h.input_file.biological_replicate == raw_file.biological_replicate && h.input_file.fraction == raw_file.fraction && h.input_file.technical_replicate == raw_file.technical_replicate))
{
c.rt_apex = c.rt_apex - ms1Model.Predict(new double[] { c.rt_apex });
}
}
return(true);
}
protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList)
{
LoadModifications(taskId, out var variableModifications, out var fixedModifications, out var localizeableModificationTypes);
// load proteins
List <Protein> proteinList = LoadProteins(taskId, dbFilenameList, true, DecoyType.Reverse, localizeableModificationTypes, CommonParameters);
// write prose settings
ProseCreatedWhileRunning.Append("The following calibration settings were used: ");
ProseCreatedWhileRunning.Append("protease = " + CommonParameters.DigestionParams.Protease + "; ");
ProseCreatedWhileRunning.Append("maximum missed cleavages = " + CommonParameters.DigestionParams.MaxMissedCleavages + "; ");
ProseCreatedWhileRunning.Append("minimum peptide length = " + CommonParameters.DigestionParams.MinPeptideLength + "; ");
ProseCreatedWhileRunning.Append(CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ?
"maximum peptide length = unspecified; " :
"maximum peptide length = " + CommonParameters.DigestionParams.MaxPeptideLength + "; ");
ProseCreatedWhileRunning.Append("initiator methionine behavior = " + CommonParameters.DigestionParams.InitiatorMethionineBehavior + "; ");
ProseCreatedWhileRunning.Append("fixed modifications = " + string.Join(", ", fixedModifications.Select(m => m.IdWithMotif)) + "; ");
ProseCreatedWhileRunning.Append("variable modifications = " + string.Join(", ", variableModifications.Select(m => m.IdWithMotif)) + "; ");
ProseCreatedWhileRunning.Append("max mods per peptide = " + CommonParameters.DigestionParams.MaxModsForPeptide + "; ");
ProseCreatedWhileRunning.Append("max modification isoforms = " + CommonParameters.DigestionParams.MaxModificationIsoforms + "; ");
ProseCreatedWhileRunning.Append("precursor mass tolerance = " + CommonParameters.PrecursorMassTolerance + "; ");
ProseCreatedWhileRunning.Append("product mass tolerance = " + CommonParameters.ProductMassTolerance + ". ");
ProseCreatedWhileRunning.Append("The combined search database contained " + proteinList.Count(p => !p.IsDecoy) + " non-decoy protein entries including " + proteinList.Count(p => p.IsContaminant) + " contaminant sequences. ");
// start the calibration task
Status("Calibrating...", new List <string> {
taskId
});
MyTaskResults = new MyTaskResults(this)
{
NewSpectra = new List <string>(),
NewFileSpecificTomls = new List <string>()
};
var myFileManager = new MyFileManager(true);
List <string> spectraFilesAfterCalibration = new List <string>();
for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++)
{
if (GlobalVariables.StopLoops)
{
break;
}
bool couldNotFindEnoughDatapoints = false;
// get filename stuff
var originalUncalibratedFilePath = currentRawFileList[spectraFileIndex];
var originalUncalibratedFilenameWithoutExtension = Path.GetFileNameWithoutExtension(originalUncalibratedFilePath);
string calibratedFilePath = Path.Combine(OutputFolder, originalUncalibratedFilenameWithoutExtension + CalibSuffix + ".mzML");
// mark the file as in-progress
StartingDataFile(originalUncalibratedFilePath, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilePath
});
CommonParameters combinedParams = SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[spectraFileIndex]);
// load the file
Status("Loading spectra file...", new List <string> {
taskId, "Individual Spectra Files"
});
var myMsDataFile = myFileManager.LoadFile(originalUncalibratedFilePath, CommonParameters);
// get datapoints to fit calibration function to
Status("Acquiring calibration data points...", new List <string> {
taskId, "Individual Spectra Files"
});
DataPointAquisitionResults acquisitionResults = null;
for (int i = 1; i <= 5; i++)
{
acquisitionResults = GetDataAcquisitionResults(myMsDataFile, originalUncalibratedFilePath, variableModifications, fixedModifications, proteinList, taskId, combinedParams, combinedParams.PrecursorMassTolerance, combinedParams.ProductMassTolerance);
// enough data points to calibrate?
if (acquisitionResults.Psms.Count >= NumRequiredPsms && acquisitionResults.Ms1List.Count > NumRequiredMs1Datapoints && acquisitionResults.Ms2List.Count > NumRequiredMs2Datapoints)
{
break;
}
if (i == 1) // failed round 1
{
CommonParameters.PrecursorMassTolerance = new PpmTolerance(20);
CommonParameters.ProductMassTolerance = new PpmTolerance(50);
}
else if (i == 2) // failed round 2
{
CommonParameters.PrecursorMassTolerance = new PpmTolerance(30);
CommonParameters.ProductMassTolerance = new PpmTolerance(100);
}
else if (i == 3) // failed round 3
{
CommonParameters.PrecursorMassTolerance = new PpmTolerance(40);
CommonParameters.ProductMassTolerance = new PpmTolerance(150);
}
else // failed round 4
{
if (acquisitionResults.Psms.Count < NumRequiredPsms)
{
Warn("Calibration failure! Could not find enough high-quality PSMs. Required " + NumRequiredPsms + ", saw " + acquisitionResults.Psms.Count);
}
if (acquisitionResults.Ms1List.Count < NumRequiredMs1Datapoints)
{
Warn("Calibration failure! Could not find enough MS1 datapoints. Required " + NumRequiredMs1Datapoints + ", saw " + acquisitionResults.Ms1List.Count);
}
if (acquisitionResults.Ms2List.Count < NumRequiredMs2Datapoints)
{
Warn("Calibration failure! Could not find enough MS2 datapoints. Required " + NumRequiredMs2Datapoints + ", saw " + acquisitionResults.Ms2List.Count);
}
couldNotFindEnoughDatapoints = true;
FinishedDataFile(originalUncalibratedFilePath, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilePath
});
break;
}
Warn("Could not find enough PSMs to calibrate with; opening up tolerances to " +
Math.Round(CommonParameters.PrecursorMassTolerance.Value, 2) + " ppm precursor and " +
Math.Round(CommonParameters.ProductMassTolerance.Value, 2) + " ppm product");
}
if (couldNotFindEnoughDatapoints)
{
spectraFilesAfterCalibration.Add(Path.GetFileNameWithoutExtension(currentRawFileList[spectraFileIndex]));
ReportProgress(new ProgressEventArgs(100, "Failed to calibrate!", new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
}));
continue;
}
// stats before calibration
int prevPsmCount = acquisitionResults.Psms.Count;
double preCalibrationPrecursorErrorIqr = acquisitionResults.PsmPrecursorIqrPpmError;
double preCalibrationProductErrorIqr = acquisitionResults.PsmProductIqrPpmError;
// generate calibration function and shift data points
Status("Calibrating...", new List <string> {
taskId, "Individual Spectra Files"
});
CalibrationEngine engine = new CalibrationEngine(myMsDataFile, acquisitionResults, CommonParameters, FileSpecificParameters, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
});
engine.Run();
//update file
myMsDataFile = engine.CalibratedDataFile;
// do another search to evaluate calibration results
Status("Post-calibration search...", new List <string> {
taskId, "Individual Spectra Files"
});
acquisitionResults = GetDataAcquisitionResults(myMsDataFile, originalUncalibratedFilePath, variableModifications, fixedModifications, proteinList, taskId, combinedParams, combinedParams.PrecursorMassTolerance, combinedParams.ProductMassTolerance);
//generate calibration function and shift data points AGAIN because it's fast and contributes new data
Status("Calibrating...", new List <string> {
taskId, "Individual Spectra Files"
});
engine = new CalibrationEngine(myMsDataFile, acquisitionResults, CommonParameters, FileSpecificParameters, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
});
engine.Run();
//update file
myMsDataFile = engine.CalibratedDataFile;
// write the calibrated mzML file
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, calibratedFilePath, false);
myFileManager.DoneWithFile(originalUncalibratedFilePath);
// stats after calibration
int postCalibrationPsmCount = acquisitionResults.Psms.Count;
double postCalibrationPrecursorErrorIqr = acquisitionResults.PsmPrecursorIqrPpmError;
double postCalibrationProductErrorIqr = acquisitionResults.PsmProductIqrPpmError;
// did the data improve? (not used for anything yet...)
bool improvement = ImprovGlobal(preCalibrationPrecursorErrorIqr, preCalibrationProductErrorIqr, prevPsmCount, postCalibrationPsmCount, postCalibrationPrecursorErrorIqr, postCalibrationProductErrorIqr);
// write toml settings for the calibrated file
var newTomlFileName = Path.Combine(OutputFolder, originalUncalibratedFilenameWithoutExtension + CalibSuffix + ".toml");
var fileSpecificParams = new FileSpecificParameters();
// carry over file-specific parameters from the uncalibrated file to the calibrated one
if (fileSettingsList[spectraFileIndex] != null)
{
fileSpecificParams = fileSettingsList[spectraFileIndex].Clone();
}
//suggest 4 * interquartile range as the ppm tolerance
fileSpecificParams.PrecursorMassTolerance = new PpmTolerance((4.0 * postCalibrationPrecursorErrorIqr) + Math.Abs(acquisitionResults.PsmPrecursorMedianPpmError));
fileSpecificParams.ProductMassTolerance = new PpmTolerance((4.0 * postCalibrationProductErrorIqr) + Math.Abs(acquisitionResults.PsmProductMedianPpmError));
Toml.WriteFile(fileSpecificParams, newTomlFileName, tomlConfig);
FinishedWritingFile(newTomlFileName, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
});
// finished calibrating this file
spectraFilesAfterCalibration.Add(Path.GetFileNameWithoutExtension(calibratedFilePath));
FinishedWritingFile(calibratedFilePath, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
});
MyTaskResults.NewSpectra.Add(calibratedFilePath);
MyTaskResults.NewFileSpecificTomls.Add(newTomlFileName);
FinishedDataFile(originalUncalibratedFilePath, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilePath
});
ReportProgress(new ProgressEventArgs(100, "Done!", new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
}));
}
// re-write experimental design (if it has been defined) with new calibrated file names
string assumedPathToExperDesign = Directory.GetParent(currentRawFileList.First()).FullName;
assumedPathToExperDesign = Path.Combine(assumedPathToExperDesign, GlobalVariables.ExperimentalDesignFileName);
if (File.Exists(assumedPathToExperDesign))
{
WriteNewExperimentalDesignFile(assumedPathToExperDesign, OutputFolder, spectraFilesAfterCalibration);
}
// finished calibrating all files for the task
ReportProgress(new ProgressEventArgs(100, "Done!", new List <string> {
taskId, "Individual Spectra Files"
}));
return(MyTaskResults);
}
protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList)
{
// load modifications
Status("Loading modifications...", new List <string> {
taskId
});
List <ModificationWithMass> variableModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsVariable.Contains((b.modificationType, b.id))).ToList();
List <ModificationWithMass> fixedModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsFixed.Contains((b.modificationType, b.id))).ToList();
List <string> localizeableModificationTypes = GlobalVariables.AllModTypesKnown.ToList();
// what types of fragment ions to search for
List <ProductType> ionTypes = new List <ProductType>();
if (CommonParameters.BIons)
{
ionTypes.Add(ProductType.BnoB1ions);
}
if (CommonParameters.YIons)
{
ionTypes.Add(ProductType.Y);
}
if (CommonParameters.ZdotIons)
{
ionTypes.Add(ProductType.Zdot);
}
if (CommonParameters.CIons)
{
ionTypes.Add(ProductType.C);
}
// load proteins
List <Protein> proteinList = LoadProteins(taskId, dbFilenameList, true, DecoyType.Reverse, localizeableModificationTypes, CommonParameters);
// write prose settings
ProseCreatedWhileRunning.Append("The following calibration settings were used: ");
ProseCreatedWhileRunning.Append("protease = " + CommonParameters.DigestionParams.Protease + "; ");
ProseCreatedWhileRunning.Append("maximum missed cleavages = " + CommonParameters.DigestionParams.MaxMissedCleavages + "; ");
ProseCreatedWhileRunning.Append("minimum peptide length = " + CommonParameters.DigestionParams.MinPeptideLength + "; ");
ProseCreatedWhileRunning.Append(CommonParameters.DigestionParams.MaxPeptideLength == int.MaxValue ?
"maximum peptide length = unspecified; " :
"maximum peptide length = " + CommonParameters.DigestionParams.MaxPeptideLength + "; ");
ProseCreatedWhileRunning.Append("initiator methionine behavior = " + CommonParameters.DigestionParams.InitiatorMethionineBehavior + "; ");
ProseCreatedWhileRunning.Append("fixed modifications = " + string.Join(", ", fixedModifications.Select(m => m.id)) + "; ");
ProseCreatedWhileRunning.Append("variable modifications = " + string.Join(", ", variableModifications.Select(m => m.id)) + "; ");
ProseCreatedWhileRunning.Append("max mods per peptide = " + CommonParameters.DigestionParams.MaxModsForPeptide + "; ");
ProseCreatedWhileRunning.Append("max modification isoforms = " + CommonParameters.DigestionParams.MaxModificationIsoforms + "; ");
ProseCreatedWhileRunning.Append("precursor mass tolerance = " + CommonParameters.PrecursorMassTolerance + "; ");
ProseCreatedWhileRunning.Append("product mass tolerance = " + CommonParameters.ProductMassTolerance + ". ");
ProseCreatedWhileRunning.Append("The combined search database contained " + proteinList.Count(p => !p.IsDecoy) + " non-decoy protein entries including " + proteinList.Count(p => p.IsContaminant) + " contaminant sequences. ");
// start the calibration task
Status("Calibrating...", new List <string> {
taskId
});
MyTaskResults = new MyTaskResults(this)
{
NewSpectra = new List <string>(),
NewFileSpecificTomls = new List <string>()
};
object lock1 = new object();
var myFileManager = new MyFileManager(true);
for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++)
{
if (GlobalVariables.StopLoops)
{
break;
}
// get filename stuff
var originalUncalibratedFilePath = currentRawFileList[spectraFileIndex];
var originalUncalibratedFilenameWithoutExtension = Path.GetFileNameWithoutExtension(originalUncalibratedFilePath);
string calibratedFilePath = Path.Combine(OutputFolder, originalUncalibratedFilenameWithoutExtension + CalibSuffix + ".mzML");
// mark the file as in-progress
StartingDataFile(originalUncalibratedFilePath, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilePath
});
CommonParameters combinedParams = SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[spectraFileIndex]);
MsDataFile myMsDataFile;
// load the file
Status("Loading spectra file...", new List <string> {
taskId, "Individual Spectra Files"
});
lock (lock1)
{
myMsDataFile = myFileManager.LoadFile(originalUncalibratedFilePath, CommonParameters.TopNpeaks, CommonParameters.MinRatio, CommonParameters.TrimMs1Peaks, CommonParameters.TrimMsMsPeaks, CommonParameters);
}
// get datapoints to fit calibration function to
Status("Acquiring calibration data points...", new List <string> {
taskId, "Individual Spectra Files"
});
DataPointAquisitionResults acquisitionResults = null;
for (int i = 1; i <= 5; i++)
{
acquisitionResults = GetDataAcquisitionResults(myMsDataFile, originalUncalibratedFilePath, variableModifications, fixedModifications, proteinList, taskId, combinedParams, combinedParams.PrecursorMassTolerance, combinedParams.ProductMassTolerance);
// enough data points to calibrate?
if (acquisitionResults.Psms.Count >= NumRequiredPsms && acquisitionResults.Ms1List.Count > NumRequiredMs1Datapoints && acquisitionResults.Ms2List.Count > NumRequiredMs2Datapoints)
{
break;
}
if (i == 1) // failed round 1
{
CommonParameters.PrecursorMassTolerance = new PpmTolerance(20);
CommonParameters.ProductMassTolerance = new PpmTolerance(50);
}
else if (i == 2) // failed round 2
{
CommonParameters.PrecursorMassTolerance = new PpmTolerance(30);
CommonParameters.ProductMassTolerance = new PpmTolerance(100);
}
else if (i == 3) // failed round 3
{
CommonParameters.PrecursorMassTolerance = new PpmTolerance(40);
CommonParameters.ProductMassTolerance = new PpmTolerance(150);
}
else // failed round 4
{
if (acquisitionResults.Psms.Count < NumRequiredPsms)
{
Warn("Calibration failure! Could not find enough high-quality PSMs. Required " + NumRequiredPsms + ", saw " + acquisitionResults.Psms.Count);
}
if (acquisitionResults.Ms1List.Count < NumRequiredMs1Datapoints)
{
Warn("Calibration failure! Could not find enough MS1 datapoints. Required " + NumRequiredMs1Datapoints + ", saw " + acquisitionResults.Ms1List.Count);
}
if (acquisitionResults.Ms2List.Count < NumRequiredMs2Datapoints)
{
Warn("Calibration failure! Could not find enough MS2 datapoints. Required " + NumRequiredMs2Datapoints + ", saw " + acquisitionResults.Ms2List.Count);
}
FinishedDataFile(originalUncalibratedFilePath, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilePath
});
return(MyTaskResults);
}
Warn("Could not find enough PSMs to calibrate with; opening up tolerances to " +
Math.Round(CommonParameters.PrecursorMassTolerance.Value, 2) + " ppm precursor and " +
Math.Round(CommonParameters.ProductMassTolerance.Value, 2) + " ppm product");
}
// stats before calibration
int prevPsmCount = acquisitionResults.Psms.Count;
double preCalibrationPrecursorErrorIqr = acquisitionResults.PsmPrecursorIqrPpmError;
double preCalibrationProductErrorIqr = acquisitionResults.PsmProductIqrPpmError;
// generate calibration function and shift data points
Status("Calibrating...", new List <string> {
taskId, "Individual Spectra Files"
});
new CalibrationEngine(myMsDataFile, acquisitionResults, CommonParameters, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
}).Run();
// do another search to evaluate calibration results
Status("Post-calibration search...", new List <string> {
taskId, "Individual Spectra Files"
});
acquisitionResults = GetDataAcquisitionResults(myMsDataFile, originalUncalibratedFilePath, variableModifications, fixedModifications, proteinList, taskId, combinedParams, combinedParams.PrecursorMassTolerance, combinedParams.ProductMassTolerance);
// stats after calibration
int postCalibrationPsmCount = acquisitionResults.Psms.Count;
double postCalibrationPrecursorErrorIqr = acquisitionResults.PsmPrecursorIqrPpmError;
double postCalibrationProductErrorIqr = acquisitionResults.PsmProductIqrPpmError;
// did the data improve? (not used for anything yet...)
bool improvement = ImprovGlobal(preCalibrationPrecursorErrorIqr, preCalibrationProductErrorIqr, prevPsmCount, postCalibrationPsmCount, postCalibrationPrecursorErrorIqr, postCalibrationProductErrorIqr);
// write toml settings for the calibrated file
var newTomlFileName = Path.Combine(OutputFolder, originalUncalibratedFilenameWithoutExtension + CalibSuffix + ".toml");
var fileSpecificParams = new FileSpecificParameters();
// carry over file-specific parameters from the uncalibrated file to the calibrated one
if (fileSettingsList[spectraFileIndex] != null)
{
fileSpecificParams = fileSettingsList[spectraFileIndex].Clone();
}
// don't write over ppm tolerances if they've been specified by the user already in the file-specific settings
// otherwise, suggest 4 * interquartile range as the ppm tolerance
if (fileSpecificParams.PrecursorMassTolerance == null)
{
fileSpecificParams.PrecursorMassTolerance = new PpmTolerance((4.0 * postCalibrationPrecursorErrorIqr) + Math.Abs(acquisitionResults.PsmPrecursorMedianPpmError));
}
if (fileSpecificParams.ProductMassTolerance == null)
{
fileSpecificParams.ProductMassTolerance = new PpmTolerance((4.0 * postCalibrationProductErrorIqr) + Math.Abs(acquisitionResults.PsmProductMedianPpmError));
}
Toml.WriteFile(fileSpecificParams, newTomlFileName, tomlConfig);
FinishedWritingFile(newTomlFileName, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
});
// write the calibrated mzML file
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, calibratedFilePath, false);
myFileManager.DoneWithFile(originalUncalibratedFilePath);
// finished calibrating this file
FinishedWritingFile(calibratedFilePath, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
});
MyTaskResults.NewSpectra.Add(calibratedFilePath);
MyTaskResults.NewFileSpecificTomls.Add(newTomlFileName);
FinishedDataFile(originalUncalibratedFilePath, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilePath
});
ReportProgress(new ProgressEventArgs(100, "Done!", new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
}));
}
// re-write experimental design (if it has been defined) with new calibrated file names
string assumedPathToExperDesign = Directory.GetParent(currentRawFileList.First()).FullName;
assumedPathToExperDesign = Path.Combine(assumedPathToExperDesign, GlobalVariables.ExperimentalDesignFileName);
List <string> newExperimentalDesignOutput = new List <string>();
if (File.Exists(assumedPathToExperDesign))
{
var lines = File.ReadAllLines(assumedPathToExperDesign);
for (int i = 0; i < lines.Length; i++)
{
// header of experimental design file
if (i == 0)
{
newExperimentalDesignOutput.Add(lines[i]);
}
else
{
var split = lines[i].Split('\t');
string newline = Path.GetFileNameWithoutExtension(split[0]) + CalibSuffix + "\t";
for (int j = 1; j < split.Length; j++)
{
newline += split[j] + "\t";
}
newExperimentalDesignOutput.Add(newline);
}
}
}
File.WriteAllLines(Path.Combine(OutputFolder, GlobalVariables.ExperimentalDesignFileName), newExperimentalDesignOutput);
// finished calibrating all files for the task
ReportProgress(new ProgressEventArgs(100, "Done!", new List <string> {
taskId, "Individual Spectra Files"
}));
return(MyTaskResults);
}
private static void Main(string[] args)
{
Console.WriteLine("Welcome to MetaMorpheus");
// EDGAR: Createing the FlashLfqEngine is unforunately required,
// otherwise the code just crashes when executed.
SpectraFileInfo mzml = new SpectraFileInfo("sliced-mzml.mzml", "a", 0, 1, 0);
var pg = new FlashLFQ.ProteinGroup("MyProtein", "gene", "org");
Identification id3 = new Identification(mzml, "EGFQVADGPLYR", "EGFQVADGPLYR",
1350.65681, 94.12193, 2, new List <FlashLFQ.ProteinGroup> {
pg
});
Identification id4 = new Identification(mzml, "EGFQVADGPLYR", "EGFQVADGPLYR",
1350.65681, 94.05811, 2, new List <FlashLFQ.ProteinGroup> {
pg
});
FlashLfqEngine engine = new FlashLfqEngine(new List <Identification> {
id3, id4
}, normalize: true);
// EDGAR: End of part required to avoid crash
//generate toml
Console.WriteLine("generating toml with {0} key-value pairs", args[1]);
var tomlData = Toml.Create();
for (int i = 0; i < int.Parse(args[1]); i++)
{
tomlData.Add(i.ToString(), i);
}
//write toml
Console.WriteLine("writing toml file {0}", args[0]);
Stopwatch stopwatch = Stopwatch.StartNew();
Toml.WriteFile(tomlData, args[0]);
stopwatch.Stop();
Console.WriteLine("Time elapsed for toml write: {0}\n", stopwatch.ElapsedMilliseconds);
//read file
Console.WriteLine("reading toml file {0}", args[0]);
stopwatch = Stopwatch.StartNew();
var tomlRead = Toml.ReadFile(args[0]);
stopwatch.Stop();
Console.WriteLine("Time elapsed for toml read: {0}\n", stopwatch.ElapsedMilliseconds);
//read mzml file
Console.WriteLine("reading mzml file {0}", args[2]);
stopwatch = Stopwatch.StartNew();
var msData = Mzml.LoadAllStaticData(args[2]);
stopwatch.Stop();
Console.WriteLine("Time elapsed for mzML read: {0}\n", stopwatch.ElapsedMilliseconds);
//write mzml file
Console.WriteLine("writing mzml file {0}", args[3]);
stopwatch = Stopwatch.StartNew();
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(msData, args[3], false);
stopwatch.Stop();
Console.WriteLine("Time elapsed for mzML write: {0}", stopwatch.ElapsedMilliseconds);
}
protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificSettings[] fileSettingsList)
{
myTaskResults = new MyTaskResults(this)
{
newSpectra = new List <string>()
};
Status("Loading modifications...", new List <string> {
taskId
});
List <ModificationWithMass> variableModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsVariable.Contains((b.modificationType, b.id))).ToList();
List <ModificationWithMass> fixedModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsFixed.Contains((b.modificationType, b.id))).ToList();
List <string> localizeableModificationTypes = CommonParameters.LocalizeAll ? GlobalVariables.AllModTypesKnown.ToList() : CommonParameters.ListOfModTypesLocalize.ToList();
Status("Loading proteins...", new List <string> {
taskId
});
var proteinList = dbFilenameList.SelectMany(b => LoadProteinDb(b.FilePath, true, UsefulProteomicsDatabases.DecoyType.Reverse, localizeableModificationTypes, b.IsContaminant, out Dictionary <string, Modification> um)).ToList();
proseCreatedWhileRunning.Append("The following calibration settings were used: ");
proseCreatedWhileRunning.Append("protease = " + CommonParameters.DigestionParams.Protease + "; ");
proseCreatedWhileRunning.Append("maximum missed cleavages = " + CommonParameters.DigestionParams.MaxMissedCleavages + "; ");
proseCreatedWhileRunning.Append("minimum peptide length = " + CommonParameters.DigestionParams.MinPeptideLength + "; ");
if (CommonParameters.DigestionParams.MaxPeptideLength == null)
{
proseCreatedWhileRunning.Append("maximum peptide length = unspecified; ");
}
else
{
proseCreatedWhileRunning.Append("maximum peptide length = " + CommonParameters.DigestionParams.MaxPeptideLength + "; ");
}
proseCreatedWhileRunning.Append("initiator methionine behavior = " + CommonParameters.DigestionParams.InitiatorMethionineBehavior + "; ");
proseCreatedWhileRunning.Append("max modification isoforms = " + CommonParameters.DigestionParams.MaxModificationIsoforms + "; ");
proseCreatedWhileRunning.Append("fixed modifications = " + string.Join(", ", fixedModifications.Select(m => m.id)) + "; ");
proseCreatedWhileRunning.Append("variable modifications = " + string.Join(", ", variableModifications.Select(m => m.id)) + "; ");
proseCreatedWhileRunning.Append("product mass tolerance = " + CommonParameters.ProductMassTolerance + " Da. ");
proseCreatedWhileRunning.Append("The combined search database contained " + proteinList.Count + " total entries including " + proteinList.Where(p => p.IsContaminant).Count() + " contaminant sequences. ");
object lock1 = new object();
ParallelOptions parallelOptions = new ParallelOptions();
if (CommonParameters.MaxParallelFilesToAnalyze.HasValue)
{
parallelOptions.MaxDegreeOfParallelism = CommonParameters.MaxParallelFilesToAnalyze.Value;
}
var myFileManager = new MyFileManager(true);
Status("Calibrating...", new List <string> {
taskId
});
Parallel.For(0, currentRawFileList.Count, parallelOptions, spectraFileIndex =>
{
var originalUncalibratedFilePath = currentRawFileList[spectraFileIndex];
var originalUncalibratedFilenameWithoutExtension = Path.GetFileNameWithoutExtension(originalUncalibratedFilePath);
ICommonParameters combinedParams = SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[spectraFileIndex]);
string calibratedFilePath = Path.Combine(OutputFolder, originalUncalibratedFilenameWithoutExtension + "-calib.mzml");
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile;
Status("Loading spectra file...", new List <string> {
taskId, "Individual Spectra Files"
});
// only load one file at a time
lock (lock1)
{
myMsDataFile = myFileManager.LoadFile(originalUncalibratedFilePath, CommonParameters.TopNpeaks, CommonParameters.MinRatio, CommonParameters.TrimMs1Peaks, CommonParameters.TrimMsMsPeaks);
}
Status("Acquiring calibration data points...", new List <string> {
taskId, "Individual Spectra Files"
});
// get datapoints to fit calibration function to
var acquisitionResults = GetDataAcquisitionResults(myMsDataFile, originalUncalibratedFilePath, variableModifications, fixedModifications, proteinList, taskId, combinedParams, combinedParams.PrecursorMassTolerance, combinedParams.ProductMassTolerance);
// stats before calibration
int prevPsmCount = acquisitionResults.Item1.Count;
var preCalibrationPrecursorErrors = acquisitionResults.Item1.Select(p => (p.ScanPrecursorMass - p.PeptideMonisotopicMass.Value) / p.PeptideMonisotopicMass.Value * 1e6).ToList();
double preCalibrationPrecursorIqr = Statistics.InterquartileRange(preCalibrationPrecursorErrors);
var preCalibrationProductErrors = acquisitionResults.Item1.SelectMany(p => p.ProductMassErrorPpm.SelectMany(v => v.Value)).ToList();
double preCalibrationProductIqr = Statistics.InterquartileRange(preCalibrationProductErrors);
// enough data points to calibrate with?
if (acquisitionResults.Item2 == null)
{
Warn("Could not find any datapoints to calibrate with!");
return;
}
if (acquisitionResults.Item2.Ms1List.Count < 4 || acquisitionResults.Item2.Ms2List.Count < 4)
{
Warn("Could not find enough MS1 datapoints to calibrate (" + acquisitionResults.Item2.Ms1List.Count + " found)");
Warn("Could not find enough MS2 datapoints to calibrate (" + acquisitionResults.Item2.Ms2List.Count + " found)");
return;
}
// generate calibration function and shift data points
Status("Calibrating...", new List <string> {
taskId, "Individual Spectra Files"
});
new CalibrationEngine(myMsDataFile, acquisitionResults.Item2, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
}).Run();
myFileManager.DoneWithFile(originalUncalibratedFilePath);
// do another search to evaluate calibration results
Status("Post-calibration search...", new List <string> {
taskId, "Individual Spectra Files"
});
acquisitionResults = GetDataAcquisitionResults(myMsDataFile, originalUncalibratedFilePath, variableModifications, fixedModifications, proteinList, taskId, combinedParams, combinedParams.PrecursorMassTolerance, combinedParams.ProductMassTolerance);
// stats after calibration
int postCalibrationPsmCount = acquisitionResults.Item1.Count;
var postCalibrationPrecursorErrors = acquisitionResults.Item1.Select(p => (p.ScanPrecursorMass - p.PeptideMonisotopicMass) / p.PeptideMonisotopicMass * 1e6).ToList();
double postCalibrationPrecursorIqr = Statistics.InterquartileRange(postCalibrationPrecursorErrors);
var postCalibrationProductErrors = acquisitionResults.Item1.SelectMany(p => p.ProductMassErrorPpm.SelectMany(v => v.Value)).ToList();
double postCalibrationProductIqr = Statistics.InterquartileRange(postCalibrationProductErrors);
// did the data improve? (not used for anything yet...)
bool improvement = ImprovGlobal(preCalibrationPrecursorIqr, preCalibrationProductIqr, prevPsmCount, postCalibrationPsmCount, postCalibrationPrecursorIqr, postCalibrationProductIqr);
// write suggested tolerances for this file
var tomlFileName = Path.Combine(OutputFolder, originalUncalibratedFilenameWithoutExtension + "-calib.toml");
FileSpecificTolerances f = new FileSpecificTolerances
{
PrecursorMassTolerance = new PpmTolerance(4.0 * postCalibrationPrecursorIqr),
ProductMassTolerance = new PpmTolerance(4.0 * postCalibrationProductIqr)
};
Toml.WriteFile(f, tomlFileName, tomlConfig);
SucessfullyFinishedWritingFile(tomlFileName, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
});
// write the calibrated MZML file
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, calibratedFilePath, false);
// all done
SucessfullyFinishedWritingFile(calibratedFilePath, new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
});
myTaskResults.newSpectra.Add(calibratedFilePath);
ReportProgress(new ProgressEventArgs(100, "Done!", new List <string> {
taskId, "Individual Spectra Files", originalUncalibratedFilenameWithoutExtension
}));
});
ReportProgress(new ProgressEventArgs(100, "Done!", new List <string> {
taskId, "Individual Spectra Files"
}));
return(myTaskResults);
}