public static void AddCompIonsCommonParams()
{
CommonParameters cp = new CommonParameters(null, DissociationType.HCD, DissociationType.Unknown, true, true, 3, 12, true, true, 1,
5, 200, 0.01, null, null, false, false, true, false, null, null, null, -1, null, null, null, 1, true, 4, 1);
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int ii = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
SearchTarget = true,
};
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Test", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, new List <SilacLabel>(),
1, DecoyType.Reverse, cp, SearchParameters.MaxFragmentSize, false, new List <FileInfo>(), new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(cp.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
// without complementary ions
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
var mse = new ModernSearchEngine(allPsmsArray, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, cp, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
}
public static void TestCompIons_MatchIonsScore()
{
TestDataFile t = new TestDataFile();
Tolerance productMassTolerance = new AbsoluteTolerance(0.01);
double precursorMass = 300;
//The below theoretical does not accurately represent B-Y ions
double[] sorted_theoretical_product_masses_for_this_peptide = new double[] { precursorMass + (2 * Constants.ProtonMass) - 275.1350, precursorMass + (2 * Constants.ProtonMass) - 258.127, precursorMass + (2 * Constants.ProtonMass) - 257.1244, 50, 60, 70, 147.0764, precursorMass + (2 * Constants.ProtonMass) - 147.0764, precursorMass + (2 * Constants.ProtonMass) - 70, precursorMass + (2 * Constants.ProtonMass) - 60, precursorMass + (2 * Constants.ProtonMass) - 50, 257.1244, 258.127, 275.1350 }; //{ 50, 60, 70, 147.0764, 257.1244, 258.127, 275.1350 }
List <Product> productsWithLocalizedMassDiff = new List <Product>();
foreach (double d in sorted_theoretical_product_masses_for_this_peptide)
{
productsWithLocalizedMassDiff.Add(new Product(ProductType.b, FragmentationTerminus.Both, d, 1, 1, 0));
}
CommonParameters commonParametersNoComp = new CommonParameters {
ProductMassTolerance = new AbsoluteTolerance(0.01)
};
CommonParameters commonParametersWithComp = new CommonParameters(productMassTolerance: new AbsoluteTolerance(0.01), addCompIons: true);
MsDataScan scan = t.GetOneBasedScan(2);
var scanWithMass = new Ms2ScanWithSpecificMass(scan, precursorMass.ToMz(1), 1, "", new CommonParameters());
List <MatchedFragmentIon> matchedIons = MetaMorpheusEngine.MatchFragmentIons(scanWithMass, productsWithLocalizedMassDiff, commonParametersNoComp);
List <MatchedFragmentIon> matchedCompIons = MetaMorpheusEngine.MatchFragmentIons(scanWithMass, productsWithLocalizedMassDiff, commonParametersWithComp);
matchedCompIons.AddRange(matchedIons);
// score when the mass-diff is on this residue
double localizedScore = MetaMorpheusEngine.CalculatePeptideScore(scan, matchedIons);
double scoreNormal = MetaMorpheusEngine.CalculatePeptideScore(scan, matchedIons);
double scoreComp = MetaMorpheusEngine.CalculatePeptideScore(scan, matchedCompIons);
Assert.IsTrue(scoreNormal * 2 == scoreComp && scoreComp > scoreNormal + 1);
}
public static void TestAddCompIonsClassic()
{
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein> {
new Protein("QXQ", null)
};
var productMassTolerance = new AbsoluteTolerance(0.01);
var searchModes = new OpenSearchMode();
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Custom Protease3", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
scoreCutoff: 1,
addCompIons: false);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, CommonParameters, fsp, null, new List <string>()).Run();
CommonParameters CommonParameters2 = new CommonParameters(
digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
scoreCutoff: 1,
addCompIons: true);
var fsp2 = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp2.Add(("", CommonParameters2));
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray2, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, CommonParameters2, fsp2, null, new List <string>()).Run();
double scoreT = allPsmsArray2[0].Score;
double scoreF = allPsmsArray[0].Score;
// Single search mode
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
// Single ms2 scan
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
Assert.IsTrue(scoreT > 1);
Assert.AreEqual(allPsmsArray[0].ScanNumber, allPsmsArray2[0].ScanNumber);
Assert.IsTrue(scoreT == scoreF * 3 && scoreT > scoreF + 2);
}
public static void TestContaminantAmbiguity()
{
//create an ms file and a database for the peptide
Protein targetProtein = new Protein("PEPTIDE", "target");
string xmlName = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PEPTIDE.xml");
ProteinDbWriter.WriteXmlDatabase(null, new List <Protein> {
targetProtein
}, xmlName);
PeptideWithSetModifications pepWithSetMods = targetProtein.Digest(new DigestionParams(), null, null).First();
TestDataFile msFile = new TestDataFile(pepWithSetMods);
string mzmlName = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\PEPTIDE.mzML");
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(msFile, mzmlName, false);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestContaminantAmbiguityOutput");
//run a full modern search using two databases (the same database) but one is called a target and the other is called a contaminant
//KEEP BOTH TARGET AND CONTAMINANT
SearchParameters modernSearchParams = new SearchParameters();
modernSearchParams.SearchType = SearchType.Modern;
modernSearchParams.TCAmbiguity = TargetContaminantAmbiguity.RenameProtein;
SearchTask modernTask = new SearchTask();
modernTask.SearchParameters = modernSearchParams;
EverythingRunnerEngine engine = new EverythingRunnerEngine(new List <(string, MetaMorpheusTask)> {
("task1", modernTask)
}, new List <string> {
public static void TestAddCompIonsClassic()
{
var myMsDataFile = new TestDataFile();
var variableModifications = new List <ModificationWithMass>();
var fixedModifications = new List <ModificationWithMass>();
var proteinList = new List <Protein> {
new Protein("QXQ", null)
};
var productMassTolerance = new AbsoluteTolerance(0.01);
var searchModes = new OpenSearchMode();
bool DoPrecursorDeconvolution = true;
bool UseProvidedPrecursorInfo = true;
double DeconvolutionIntensityRatio = 4;
int DeconvolutionMaxAssumedChargeState = 10;
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, DoPrecursorDeconvolution, UseProvidedPrecursorInfo, DeconvolutionIntensityRatio, DeconvolutionMaxAssumedChargeState, DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
CommonParameters CommonParameters = new CommonParameters
{
DigestionParams = new DigestionParams
{
Protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null),
MinPeptideLength = null,
MaxMissedCleavages = 0
},
ConserveMemory = false,
ScoreCutoff = 1,
};
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, new List <ProductType> {
ProductType.B, ProductType.Y
}, searchModes, false, CommonParameters, CommonParameters.ProductMassTolerance, new List <string>()).Run();
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray2, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, new List <ProductType> {
ProductType.B, ProductType.Y
}, searchModes, true, CommonParameters, CommonParameters.ProductMassTolerance, new List <string>()).Run();
double scoreT = allPsmsArray2[0].Score;
double scoreF = allPsmsArray[0].Score;
// Single search mode
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
// Single ms2 scan
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
Assert.IsTrue(scoreT > 1);
Assert.AreEqual(allPsmsArray[0].ScanNumber, allPsmsArray2[0].ScanNumber);
Assert.IsTrue(scoreT == scoreF * 3 && scoreT > scoreF + 2);
}
public static void TestResolveAmbiguities()
{
Protease protease = new Protease("Custom Protease4", CleavageSpecificity.Full, null, null, new List <DigestionMotif> {
new DigestionMotif("K", null, 1, "")
});
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters_t = new CommonParameters(
dissociationType: MassSpectrometry.DissociationType.HCD,
digestionParams: new DigestionParams(
protease: protease.Name,
minPeptideLength: 1),
scoreCutoff: 1,
reportAllAmbiguity: true);
var fsp_t = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp_t.Add(("", CommonParameters_t));
CommonParameters CommonParameters_f = new CommonParameters(
dissociationType: MassSpectrometry.DissociationType.HCD,
digestionParams: new DigestionParams(
protease: protease.Name,
minPeptideLength: 1),
scoreCutoff: 1,
reportAllAmbiguity: false);
var fsp_f = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp_f.Add(("", CommonParameters_t));
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein> {
new Protein("MNNKNKNKQQQ", "Prot1"), new Protein("MNNNKQQQ", "Prot2")
};
var searchModes = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray_withAmbiguity = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
PeptideSpectralMatch[] allPsmsArray_withOutAmbiguity = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
bool writeSpectralLibrary = false;
new ClassicSearchEngine(allPsmsArray_withAmbiguity, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, CommonParameters_t, fsp_t, null, new List <string>(), writeSpectralLibrary).Run(); //report all ambiguity TRUE
new ClassicSearchEngine(allPsmsArray_withOutAmbiguity, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, CommonParameters_f, fsp_f, null, new List <string>(), writeSpectralLibrary).Run(); //report all ambiguity FALSE
Assert.AreEqual("QQQ", allPsmsArray_withAmbiguity[0].BaseSequence);
Assert.AreEqual("QQQ", allPsmsArray_withOutAmbiguity[0].BaseSequence);
Assert.IsTrue(allPsmsArray_withAmbiguity[0].ProteinLength == null);
Assert.IsTrue(allPsmsArray_withOutAmbiguity[0].ProteinLength != null);
Assert.IsTrue(allPsmsArray_withAmbiguity[0].OneBasedStartResidueInProtein == null);
Assert.IsTrue(allPsmsArray_withOutAmbiguity[0].OneBasedStartResidueInProtein != null);
}
//[Test]
public static void TestGetCombinedMs2Scans()
{
var myMsDataFile = new TestDataFile(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//Write prime code to combine MS2MS3
Dictionary <int, double> listOfScanPrecusor = new Dictionary <int, double>();
List <MsDataScan> ListOfSortedMsScans = new List <MsDataScan>();
List <Ms2ScanWithSpecificMass> test = new List <Ms2ScanWithSpecificMass>();
foreach (var ms2scan in myMsDataFile.GetAllScansList().Where(x => x.MsnOrder != 1))
{
if (ms2scan.MsnOrder == 2 && !listOfScanPrecusor.Contains(new KeyValuePair <int, double>(ms2scan.OneBasedPrecursorScanNumber.Value, ms2scan.SelectedIonMZ.Value)))
{
if (ms2scan.OneBasedPrecursorScanNumber.HasValue)
{
listOfScanPrecusor.Add(ms2scan.OneBasedPrecursorScanNumber.Value, ms2scan.SelectedIonMZ.Value);
List <int> currentScanMS2OneBasedScanNumber = new List <int>
{
ms2scan.OneBasedScanNumber
};
var mz2 = ms2scan.MassSpectrum.XArray.ToList();
var intensities2 = ms2scan.MassSpectrum.YArray.ToList();
for (int i = 1; i < 7; i++)
{
if (ms2scan.OneBasedScanNumber + i <= myMsDataFile.NumSpectra)
{
var x = myMsDataFile.GetOneBasedScan(ms2scan.OneBasedScanNumber + i);
//var x = myMsDataFile.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>().ElementAt(i);
if (x.MsnOrder == 2 && x.SelectedIonMZ == ms2scan.SelectedIonMZ)
{
currentScanMS2OneBasedScanNumber.Add(x.OneBasedScanNumber);
mz2.AddRange(x.MassSpectrum.XArray.ToList());
intensities2.AddRange(x.MassSpectrum.YArray.ToList());
}
if (x.MsnOrder == 3 && currentScanMS2OneBasedScanNumber.Contains(x.OneBasedPrecursorScanNumber.Value))
{
mz2.AddRange(x.MassSpectrum.XArray.ToList());
intensities2.AddRange(x.MassSpectrum.YArray.ToList());
}
}
}
var MassSpectrum2 = new MzSpectrum(mz2.ToArray(), intensities2.ToArray(), false);
ListOfSortedMsScans.Add(new MsDataScan(MassSpectrum2, ms2scan.OneBasedScanNumber, ms2scan.MsnOrder, ms2scan.IsCentroid, Polarity.Positive, ms2scan.RetentionTime,
ms2scan.ScanWindowRange, ms2scan.ScanFilter, ms2scan.MzAnalyzer, ms2scan.TotalIonCurrent, ms2scan.InjectionTime, null, "", ms2scan.SelectedIonMZ, ms2scan.SelectedIonChargeStateGuess, ms2scan.SelectedIonIntensity, ms2scan.IsolationMz, null, ms2scan.DissociationType, ms2scan.OneBasedPrecursorScanNumber, ms2scan.SelectedIonMonoisotopicGuessMz));
}
}
}
foreach (var ms2scan in ListOfSortedMsScans.Where(x => x.MsnOrder != 1))
{
test.Add(new Ms2ScanWithSpecificMass(ms2scan, ms2scan.SelectedIonMonoisotopicGuessMz.Value, ms2scan.SelectedIonChargeStateGuess.Value, "", new CommonParameters()));
}
var testToArray = test.OrderBy(b => b.PrecursorMass).ToArray();
}
public static void TestLocalization()
{
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
Protein parentProteinForMatch = new Protein("MEK", null);
DigestionParams digestionParams = new DigestionParams
{
MinPeptideLength = 1,
};
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
List <ProductType> lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.Last() as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >, pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
ps
} }
};
newPsm.MatchToProteinLinkedPeptides(matching);
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, lp, myMsDataFile, fragmentTolerance, new List <string>(), false);
f.Run();
// Was single peak!!!
Assert.AreEqual(0, newPsm.MatchedIonDictOnlyMatches[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonDictOnlyMatches[ProductType.Y].Count(b => b > 0));
// If localizing, three match!!!
Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4);
}
public static void TestPsmHeader()
{
DigestionParams digestionParams = new DigestionParams();
PeptideWithSetModifications pepWithSetMods = new Protein(
"MQQQQQQQ",
"accession1",
"org",
new List <Tuple <string, string> > {
new Tuple <string, string>("geneNameType", "geneName")
},
new Dictionary <int, List <Modification> > {
{ 2, new List <Modification> {
new Modification("mod", "mod")
} }
},
name: "name",
full_name: "fullName",
sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(2, "P", "Q", "changed this sequence")
})
.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
MsDataFile myMsDataFile = new TestDataFile(pepWithSetMods, "quadratic");
MsDataScan scann = myMsDataFile.GetOneBasedScan(2);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(scann, 4, 1, null);
PeptideSpectralMatch psm = new PeptideSpectralMatch(pepWithSetMods.CompactPeptide(TerminusType.None), 1, 2, 3, scan, digestionParams);
var t = psm.ToString();
var tabsepheader = PeptideSpectralMatch.GetTabSeparatedHeader();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ pepWithSetMods.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pepWithSetMods
} }
};
psm.MatchToProteinLinkedPeptides(matching);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Tolerance fragmentTolerance = new PpmTolerance(10);
List <ProductType> lp = new List <ProductType> {
ProductType.B
};
new LocalizationEngine(new List <PeptideSpectralMatch> {
psm
}, lp, myMsDataFile, new CommonParameters(productMassTolerance: fragmentTolerance), new List <string>()).Run();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
psm.SetFdrValues(6, 6, 6, 6, 6, 6, 0, 0, 0, true);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
}
public static void TestLocalization()
{
Protein parentProteinForMatch = new Protein("MEK", null);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
List <ProductType> lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.GetAllScansList().Last(), pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan, digestionParams);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
ps
} }
};
newPsm.MatchToProteinLinkedPeptides(matching);
CommonParameters commonParameters = new CommonParameters(productMassTolerance: fragmentTolerance);
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, lp, myMsDataFile, commonParameters, new List <string>());
f.Run();
// Was single peak!!!
Assert.AreEqual(0, newPsm.MatchedIonMassToChargeRatioDict[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonMassToChargeRatioDict[ProductType.Y].Count(b => b > 0));
Assert.AreEqual(0, newPsm.MatchedIonIntensitiesDict[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonIntensitiesDict[ProductType.Y].Count(b => b > 0));
// If localizing, three match!!!
Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4);
}
public static void TestPsmHeader()
{
CommonParameters commonParameters = new CommonParameters();
PeptideWithSetModifications pepWithSetMods = new Protein(
"MQQQQQQQ",
"accession1",
"org",
new List <Tuple <string, string> > {
new Tuple <string, string>("geneNameType", "geneName")
},
new Dictionary <int, List <Modification> > {
{ 2, new List <Modification> {
new Modification("mod", "mod")
} }
},
name: "name",
fullName: "fullName",
sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(2, "P", "Q", "changed this sequence")
})
.Digest(commonParameters.DigestionParams, new List <Modification>(), new List <Modification>()).First();
MsDataFile myMsDataFile = new TestDataFile(pepWithSetMods, "quadratic");
MsDataScan scann = myMsDataFile.GetOneBasedScan(2);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(scann, 4, 1, null, new CommonParameters());
var theoreticalIons = new List <Product>();
pepWithSetMods.Fragment(DissociationType.HCD, FragmentationTerminus.Both, theoreticalIons);
var matchedIons = MetaMorpheusEngine.MatchFragmentIons(scan, theoreticalIons, new CommonParameters());
PeptideSpectralMatch psm = new PeptideSpectralMatch(pepWithSetMods, 1, 2, 3, scan, commonParameters, matchedIons);
psm.ResolveAllAmbiguities();
var t = psm.ToString();
var tabsepheader = PeptideSpectralMatch.GetTabSeparatedHeader();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Tolerance fragmentTolerance = new PpmTolerance(10);
new LocalizationEngine(new List <PeptideSpectralMatch> {
psm
}, myMsDataFile, new CommonParameters(productMassTolerance: fragmentTolerance), null, new List <string>()).Run();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
psm.SetFdrValues(6, 6, 6, 6, 6, 0, 0, 0);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
}
public static void SingleEventArgsTest()
{
Protein parentProteinForMatch = new Protein("MEK", null);
CommonParameters commonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 1));
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", commonParameters));
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <Modification> variableModifications = new List <Modification> {
new Modification(_originalId: "21", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(commonParameters.DigestionParams, new List <Modification>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.GetAllScansList().Last(), pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null, new CommonParameters());
var theoreticalProducts = new List <Product>();
ps.Fragment(DissociationType.HCD, FragmentationTerminus.Both, theoreticalProducts);
var matchedIons = MetaMorpheusEngine.MatchFragmentIons(scan, theoreticalProducts, new CommonParameters());
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps, 0, 0, 2, scan, commonParameters, matchedIons);
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, myMsDataFile, new CommonParameters(), fsp, new List <string>());
var singleEngine = new SingleEngineEventArgs(f);
Assert.That(singleEngine.MyEngine.Equals(f));
var singleFile = new SingleFileEventArgs("", new List <string>());
Assert.That(singleFile.WrittenFile.Equals(""));
var stringList = new StringListEventArgs(new List <string>());
var rr = (stringList.StringList.DefaultIfEmpty().First());
Assert.That(stringList.StringList.DefaultIfEmpty().First() == null);
}
public static void TestLocalization()
{
Protein parentProteinForMatch = new Protein("MEK", null);
CommonParameters commonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 1));
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", commonParameters));
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <Modification> variableModifications = new List <Modification> {
new Modification(_originalId: "21", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(commonParameters.DigestionParams, new List <Modification>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.GetAllScansList().Last(), pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null, new CommonParameters());
var theoreticalProducts = new List <Product>();
ps.Fragment(DissociationType.HCD, FragmentationTerminus.Both, theoreticalProducts);
var matchedIons = MetaMorpheusEngine.MatchFragmentIons(scan, theoreticalProducts, new CommonParameters());
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps, 0, 0, 2, scan, commonParameters, matchedIons);
newPsm.ResolveAllAmbiguities();
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, myMsDataFile, commonParameters, fsp, new List <string>());
f.Run();
// single peak matches
Assert.AreEqual(1, newPsm.MatchedFragmentIons.Where(p => p.NeutralTheoreticalProduct.ProductType == ProductType.b).Count());//including b1 now
Assert.AreEqual(1, newPsm.MatchedFragmentIons.Where(p => p.NeutralTheoreticalProduct.ProductType == ProductType.y).Count());
// when localizing, three peaks match
Assert.IsTrue(newPsm.LocalizedScores[1] > 4 && newPsm.LocalizedScores[1] < 5);//we have another matched ion
}
public static void TestSilacWhenProteinIsMissing()
{
//make heavy residue and add to search task
Residue heavyLysine = new Residue("a", 'a', "a", Chemistry.ChemicalFormula.ParseFormula("C{13}6H12N{15}2O"), ModificationSites.All); //+8 lysine
Residue lightLysine = Residue.GetResidue('K');
SearchTask task = new SearchTask
{
SearchParameters = new SearchParameters
{
SilacLabels = new List <SilacLabel> {
new SilacLabel(lightLysine.Letter, heavyLysine.Letter, heavyLysine.ThisChemicalFormula.Formula, heavyLysine.MonoisotopicMass - lightLysine.MonoisotopicMass)
},
NoOneHitWonders = true
//The NoOneHitWonders=true doesn't really seem like a SILAC test, but we're testing that there's no crash if a quantified peptide's proteinGroup isn't quantified
//This happens if somebody messed with parsimony (picked TDS) or from requiring two peptides per protein (and we're only finding one). We're testing the second case here.
}
};
PeptideWithSetModifications lightPeptide = new PeptideWithSetModifications("PEPTIDEK", new Dictionary <string, Modification>());
List <double> massDifferences = new List <double> {
heavyLysine.MonoisotopicMass - lightLysine.MonoisotopicMass
};
MsDataFile myMsDataFile1 = new TestDataFile(lightPeptide, massDifferences);
string mzmlName = @"silac.mzML";
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile1, mzmlName, false);
string xmlName = "SilacDb.xml";
Protein theProtein = new Protein("PEPTIDEK", "accession1");
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), new List <Protein> {
theProtein
}, xmlName);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestSilac");
Directory.CreateDirectory(outputFolder);
var theStringResult = task.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(xmlName, false)
}, new List <string> {
mzmlName
}, "taskId1").ToString();
}
public static void TestCompIons_MatchIons()
{
TestDataFile t = new TestDataFile(0.0001);
Tolerance productMassTolerance = new AbsoluteTolerance(0.01);
double precursorMass = 402.18629720155;
//The below theoretical does not accurately represent B-Y ions
double[] sorted_theoretical_product_masses_for_this_peptide = new double[] { 50, 60, 70, 147.0764 - Constants.ProtonMass, 200, 215, 230, 245, precursorMass + Constants.ProtonMass - 147.0764, 258.127, 275.1350, precursorMass + (2 * Constants.ProtonMass) - 70, precursorMass + (2 * Constants.ProtonMass) - 60, precursorMass + (2 * Constants.ProtonMass) - 50 }; //{ 50, 60, 70, 147.0764, 257.1244, 258.127, 275.1350 }
List <double> matchedIonMassesT = new List <double>();
List <double> matchedDaErrorT = new List <double>();
List <double> matchedPpmErrorT = new List <double>();
List <double> matchedIonIntensityT = new List <double>();
List <double> matchedIonMassesF = new List <double>();
List <double> matchedDaErrorF = new List <double>();
List <double> matchedPpmErrorF = new List <double>();
List <double> matchedIonIntensityF = new List <double>();
List <int> matchedIonSeriesT = new List <int>();
List <int> matchedIonSeriesF = new List <int>();
//MetaMorpheusEngine.MatchIons(t.GetOneBasedScan(2), productMassTolerance, sorted_theoretical_product_masses_for_this_peptide, matchedIonSeriesT, matchedIonMassesT, matchedDaErrorT, matchedPpmErrorT, matchedIonIntensityT, precursorMass, ProductType.B, true);
//MetaMorpheusEngine.MatchIons(t.GetOneBasedScan(2), productMassTolerance, sorted_theoretical_product_masses_for_this_peptide, matchedIonSeriesF, matchedIonMassesF, matchedDaErrorF, matchedPpmErrorF, matchedIonIntensityF, precursorMass, ProductType.B, false);
//Test the number of series is doubled
Assert.IsTrue(matchedIonSeriesT.Count == matchedIonSeriesF.Count * 2);
//Test the number of ions is doubled
Assert.IsTrue(matchedIonMassesT.Count == matchedIonMassesF.Count * 2);
//Test the number of da errors is doubled
Assert.IsTrue(matchedDaErrorT.Count == matchedDaErrorF.Count * 2);
//test the number of ppm errors is doubled
Assert.IsTrue(matchedPpmErrorT.Count == matchedPpmErrorF.Count * 2);
//test the number of the intensity values is doubled
Assert.IsTrue(matchedIonIntensityT.Count == matchedIonIntensityF.Count * 2);
foreach (double d in matchedDaErrorF)
{
Assert.IsTrue(d <= 0.01);
}
foreach (double d in matchedDaErrorT)
{
Assert.IsTrue(d <= 0.01);
}
}
public void MoreTests(string filename, DecoyType decoyType = DecoyType.None)
{
string xmlName = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", filename);
var proteins = ProteinDbLoader.LoadProteinXML(xmlName, decoyType == DecoyType.None, decoyType, null, false, null, out var un);
var peps = proteins[1].Digest(CommonParameters.DigestionParams, null, null).ToList();
PeptideWithSetModifications pep = peps[peps.Count - 2];
string mzmlName = $"ajgdiv{filename}{decoyType.ToString()}.mzML";
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pep
});
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlName, false);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, $"TestSearchWithVariants{filename}{decoyType.ToString()}");
Directory.CreateDirectory(outputFolder);
SearchTask st = new SearchTask
{
SearchParameters = new SearchParameters
{
DoParsimony = true,
DecoyType = decoyType,
SearchTarget = decoyType == DecoyType.None,
ModPeptidesAreDifferent = false
},
CommonParameters = new CommonParameters(scoreCutoff: 1, digestionParams: new DigestionParams(minPeptideLength: 2), precursorMassTolerance: new PpmTolerance(20)),
};
st.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(xmlName, false)
}, new List <string> {
mzmlName
}, "");
var psms = File.ReadAllLines(Path.Combine(outputFolder, "AllPSMs.psmtsv"));
//Assert.IsTrue(psms.Any(line => line.Contains($"\t{variantPsmShort}\t" + (containsVariant ? variantPsmShort : "\t"))));
Directory.Delete(outputFolder, true);
File.Delete(mzmlName);
//Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"Task Settings"), true);
}
public static void TestCompIons_MatchIonsScore()
{
TestDataFile t = new TestDataFile();
Tolerance productMassTolerance = new AbsoluteTolerance(0.01);
double precursorMass = 300;
//The below theoretical does not accurately represent B-Y ions
double[] sorted_theoretical_product_masses_for_this_peptide = new double[] { precursorMass + (2 * Constants.protonMass) - 275.1350, precursorMass + (2 * Constants.protonMass) - 258.127, precursorMass + (2 * Constants.protonMass) - 257.1244, 50, 60, 70, 147.0764, precursorMass + (2 * Constants.protonMass) - 147.0764, precursorMass + (2 * Constants.protonMass) - 70, precursorMass + (2 * Constants.protonMass) - 60, precursorMass + (2 * Constants.protonMass) - 50, 257.1244, 258.127, 275.1350 }; //{ 50, 60, 70, 147.0764, 257.1244, 258.127, 275.1350 }
List <ProductType> lp = new List <ProductType> {
ProductType.B, ProductType.Y
};
double scoreT = MetaMorpheusEngine.CalculatePeptideScore(t.GetOneBasedScan(2), productMassTolerance, sorted_theoretical_product_masses_for_this_peptide, precursorMass, new List <DissociationType> {
DissociationType.HCD
}, true, 0);
double scoreF = MetaMorpheusEngine.CalculatePeptideScore(t.GetOneBasedScan(2), productMassTolerance, sorted_theoretical_product_masses_for_this_peptide, precursorMass, new List <DissociationType> {
DissociationType.HCD
}, false, 0);
Assert.IsTrue(scoreT == scoreF * 2 && scoreT > scoreF + 1);
}
public static void TestPsmHeader()
{
DigestionParams digestionParams = new DigestionParams();
PeptideWithSetModifications pepWithSetMods = new Protein("MQQQQQQQ", "accession1").Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile = new TestDataFile(pepWithSetMods, "quadratic");
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > scann = myMsDataFile.GetOneBasedScan(2) as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >;
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(scann, 4, 1, null);
PeptideSpectralMatch psm = new PeptideSpectralMatch(pepWithSetMods.CompactPeptide(TerminusType.None), 1, 2, 3, scan);
var t = psm.ToString();
var tabsepheader = PeptideSpectralMatch.GetTabSeparatedHeader();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ pepWithSetMods.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pepWithSetMods
} }
};
psm.MatchToProteinLinkedPeptides(matching);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Tolerance fragmentTolerance = new PpmTolerance(10);
List <ProductType> lp = new List <ProductType> {
ProductType.B
};
new LocalizationEngine(new List <PeptideSpectralMatch> {
psm
}, lp, myMsDataFile, fragmentTolerance, new List <string>(), false).Run();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
psm.SetFdrValues(6, 6, 6, 6, 6, 6, 0, 0, 0, false);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
}
public static void FdrTestMethod()
{
MassDiffAcceptor searchModes = new DotMassDiffAcceptor(null, new List <double> {
0, 1.0029
}, new PpmTolerance(5));
List <string> nestedIds = new List <string>();
Protein p = new Protein("MNKNNKNNNKNNNNK", null);
DigestionParams digestionParams = new DigestionParams();
var digested = p.Digest(digestionParams, new List <Modification>(), new List <Modification>()).ToList();
PeptideWithSetModifications pep1 = digested[0];
PeptideWithSetModifications pep2 = digested[1];
PeptideWithSetModifications pep3 = digested[2];
PeptideWithSetModifications pep4 = digested[3];
TestDataFile t = new TestDataFile(new List <PeptideWithSetModifications> {
pep1, pep2, pep3
});
MsDataScan mzLibScan1 = t.GetOneBasedScan(2);
Ms2ScanWithSpecificMass scan1 = new Ms2ScanWithSpecificMass(mzLibScan1, pep1.MonoisotopicMass.ToMz(1), 1, null, new CommonParameters());
PeptideSpectralMatch psm1 = new PeptideSpectralMatch(pep1, 0, 3, 0, scan1, digestionParams, new List <MatchedFragmentIon>());
MsDataScan mzLibScan2 = t.GetOneBasedScan(4);
Ms2ScanWithSpecificMass scan2 = new Ms2ScanWithSpecificMass(mzLibScan2, pep2.MonoisotopicMass.ToMz(1), 1, null, new CommonParameters());
PeptideSpectralMatch psm2 = new PeptideSpectralMatch(pep2, 1, 2, 1, scan2, digestionParams, new List <MatchedFragmentIon>());
MsDataScan mzLibScan3 = t.GetOneBasedScan(6);
Ms2ScanWithSpecificMass scan3 = new Ms2ScanWithSpecificMass(mzLibScan3, pep3.MonoisotopicMass.ToMz(1), 1, null, new CommonParameters());
PeptideSpectralMatch psm3 = new PeptideSpectralMatch(pep3, 0, 1, 2, scan3, digestionParams, new List <MatchedFragmentIon>());
psm3.AddOrReplace(pep4, 1, 1, true, new List <MatchedFragmentIon>(), 0);
var newPsms = new List <PeptideSpectralMatch> {
psm1, psm2, psm3
};
foreach (PeptideSpectralMatch psm in newPsms)
{
psm.ResolveAllAmbiguities();
}
FdrAnalysisEngine fdr = new FdrAnalysisEngine(newPsms, searchModes.NumNotches, new CommonParameters(), nestedIds);
fdr.Run();
Assert.AreEqual(2, searchModes.NumNotches);
Assert.AreEqual(0, newPsms[0].FdrInfo.CumulativeDecoyNotch);
Assert.AreEqual(1, newPsms[0].FdrInfo.CumulativeTargetNotch);
Assert.AreEqual(0, newPsms[1].FdrInfo.CumulativeDecoyNotch);
Assert.AreEqual(1, newPsms[1].FdrInfo.CumulativeTargetNotch);
Assert.AreEqual(0, newPsms[2].FdrInfo.CumulativeDecoyNotch);
Assert.AreEqual(1, newPsms[2].FdrInfo.CumulativeTargetNotch);
Assert.AreEqual(0, newPsms[0].FdrInfo.CumulativeDecoy);
Assert.AreEqual(1, newPsms[0].FdrInfo.CumulativeTarget);
Assert.AreEqual(0, newPsms[1].FdrInfo.CumulativeDecoy);
Assert.AreEqual(2, newPsms[1].FdrInfo.CumulativeTarget);
Assert.AreEqual(0, newPsms[2].FdrInfo.CumulativeDecoy);
Assert.AreEqual(3, newPsms[2].FdrInfo.CumulativeTarget);
}
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 static void TestCompIons_ModernSearch()
{
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int ii = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
SearchTarget = true,
};
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("singleN4", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams(protease: protease.Name, minPeptideLength: 1), scoreCutoff: 1);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
CommonParameters withCompIons = new CommonParameters(digestionParams: new DigestionParams(protease: protease.Name, minPeptideLength: 1), scoreCutoff: 1, addCompIons: true);
var fspComp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fspComp.Add(("", CommonParameters));
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, null, null,
1, DecoyType.Reverse, CommonParameters, fsp, SearchParameters.MaxFragmentSize, false, new List <FileInfo>(), TargetContaminantAmbiguity.RemoveContaminant, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(CommonParameters.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
// without complementary ions
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArray, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, CommonParameters, fsp, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
// with complementary ions
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArray2, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, withCompIons, fspComp, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
// Single search mode
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
// Single ms2 scan
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
Assert.That(allPsmsArray[0] != null);
Assert.That(allPsmsArray2[0] != null);
Assert.IsTrue(allPsmsArray2[0].Score > 1);
Assert.AreEqual(allPsmsArray[0].ScanNumber, allPsmsArray2[0].ScanNumber);
Assert.IsTrue(allPsmsArray2[0].Score <= allPsmsArray[0].Score * 2 && allPsmsArray2[0].Score > allPsmsArray[0].Score + 3);
}
public static void TestProteinSplitAcrossFiles()
{
SearchTask st = new SearchTask()
{
CommonParameters = new CommonParameters(
scoreCutoff: 1,
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 5,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain)),
SearchParameters = new SearchParameters
{
DoHistogramAnalysis = true,
MassDiffAcceptorType = MassDiffAcceptorType.Open,
MatchBetweenRuns = true,
DoQuantification = true
},
};
string proteinDbFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestProteinSplitAcrossFiles.xml");
string mzmlFilePath1 = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestProteinSplitAcrossFiles1.mzML");
string mzmlFilePath2 = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestProteinSplitAcrossFiles2.mzML");
ModificationMotif.TryGetMotif("D", out ModificationMotif motif);
Modification mod = new Modification(_originalId: "mod1 on D", _modificationType: "mt", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
IDictionary <int, List <Modification> > oneBasedModification = new Dictionary <int, List <Modification> >
{
{ 3, new List <Modification> {
mod
} }
};
Protein prot1 = new Protein("MEDEEK", "prot1", oneBasedModifications: oneBasedModification);
var pep1 = prot1.Digest(st.CommonParameters.DigestionParams, new List <Modification>(), new List <Modification>()).First();
var pep2 = prot1.Digest(st.CommonParameters.DigestionParams, new List <Modification>(), new List <Modification>()).Last();
List <PeptideWithSetModifications> listForFile1 = new List <PeptideWithSetModifications> {
pep1, pep2
};
List <PeptideWithSetModifications> listForFile2 = new List <PeptideWithSetModifications> {
pep2
};
MsDataFile myMsDataFile1 = new TestDataFile(listForFile1);
MsDataFile myMsDataFile2 = new TestDataFile(listForFile2);
List <Protein> proteinList = new List <Protein> {
prot1
};
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile1, mzmlFilePath1, false);
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile2, mzmlFilePath2, false);
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), proteinList, proteinDbFilePath);
string output_folder = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestProteinSplitAcrossFiles");
Directory.CreateDirectory(output_folder);
st.RunTask(
output_folder,
new List <DbForTask> {
new DbForTask(proteinDbFilePath, false)
},
new List <string> {
mzmlFilePath1, mzmlFilePath2,
},
null);
Directory.Delete(output_folder, true);
File.Delete(proteinDbFilePath);
File.Delete(mzmlFilePath1);
File.Delete(mzmlFilePath2);
Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"Task Settings"), true);
}
public static void TestBinGeneration()
{
SearchTask st = new SearchTask
{
CommonParameters = new CommonParameters(scoreCutoff: 1, digestionParams: new DigestionParams(minPeptideLength: 5, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain)),
SearchParameters = new SearchParameters
{
DoHistogramAnalysis = true,
MassDiffAcceptorType = MassDiffAcceptorType.Open,
DecoyType = DecoyType.None,
DoParsimony = true,
DoQuantification = true
},
};
string proteinDbFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "BinGenerationTest.xml");
string mzmlFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, "BinGenerationTest.mzML");
Protein prot1 = new Protein("MEDEEK", "prot1");
Protein prot2 = new Protein("MENEEK", "prot2");
ModificationMotif.TryGetMotif("D", out ModificationMotif motif);
Modification mod = new Modification(_target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
var pep1_0 = prot1.Digest(st.CommonParameters.DigestionParams, new List <Modification>(), new List <Modification>()).First();
var pep1_10 = prot1.Digest(st.CommonParameters.DigestionParams, new List <Modification>(), new List <Modification>()).Last();
Protein prot3 = new Protein("MAAADAAAAAAAAAAAAAAA", "prot3");
var pep2_0 = prot3.Digest(st.CommonParameters.DigestionParams, new List <Modification>(), new List <Modification>()).First();
var pep2_10 = prot3.Digest(st.CommonParameters.DigestionParams, new List <Modification>(), new List <Modification> {
mod
}).Last();
Protein prot4 = new Protein("MNNDNNNN", "prot4");
var pep3_10 = prot4.Digest(st.CommonParameters.DigestionParams, new List <Modification>(), new List <Modification> {
mod
}).Last();
List <PeptideWithSetModifications> pepsWithSetMods = new List <PeptideWithSetModifications> {
pep1_0, pep1_10, pep2_0, pep2_10, pep3_10
};
MsDataFile myMsDataFile = new TestDataFile(pepsWithSetMods);
List <Protein> proteinList = new List <Protein> {
prot1, prot2, prot3, prot4
};
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlFilePath, false);
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), proteinList, proteinDbFilePath);
string output_folder = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestBinGeneration");
Directory.CreateDirectory(output_folder);
st.RunTask(
output_folder,
new List <DbForTask> {
new DbForTask(proteinDbFilePath, false)
},
new List <string> {
mzmlFilePath
},
null);
Assert.AreEqual(3, File.ReadLines(Path.Combine(output_folder, @"MassDifferenceHistogram.tsv")).Count());
Directory.Delete(output_folder, true);
File.Delete(proteinDbFilePath);
File.Delete(mzmlFilePath);
Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"Task Settings"), true);
}
public static void TestMatchIonsOfAllChargesBottomUp()
{
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();
//search by new method of looking for all charges
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), true).Run();
var psm = allPsmsArray.Where(p => p != null).ToList();
Assert.That(psm[1].MatchedFragmentIons.Count == 14);
//there are ions with same product type and same fragment number but different charges
Assert.That(psm[1].MatchedFragmentIons[8].NeutralTheoreticalProduct.ProductType == psm[1].MatchedFragmentIons[9].NeutralTheoreticalProduct.ProductType &&
psm[1].MatchedFragmentIons[8].NeutralTheoreticalProduct.FragmentNumber == psm[1].MatchedFragmentIons[9].NeutralTheoreticalProduct.FragmentNumber &&
psm[1].MatchedFragmentIons[8].Charge != psm[1].MatchedFragmentIons[9].Charge);
Assert.That(psm[2].MatchedFragmentIons.Count == 14);
Assert.That(psm[4].MatchedFragmentIons.Count == 16);
//search by old method of looking for only one charge
PeptideSpectralMatch[] allPsmsArray_oneCharge = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray_oneCharge, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchMode, CommonParameters, null, null, new List <string>(), false).Run();
var psm_oneCharge = allPsmsArray_oneCharge.Where(p => p != null).ToList();
//compare 2 scores , they should have same integer part but new search has a little higher score than old search
Assert.That(psm[1].Score > psm_oneCharge[1].Score);
Assert.AreEqual(Math.Truncate(psm[1].Score), 12);
Assert.AreEqual(Math.Truncate(psm_oneCharge[1].Score), 12);
//compare 2 results and evaluate the different matched ions
var peptideTheorProducts = new List <Product>();
Assert.That(psm_oneCharge[1].MatchedFragmentIons.Count == 12);
var differences = psm[1].MatchedFragmentIons.Except(psm_oneCharge[1].MatchedFragmentIons);
psm[1].BestMatchingPeptides.First().Peptide.Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus, peptideTheorProducts);
foreach (var ion in differences)
{
foreach (var product in peptideTheorProducts)
{
if (product.Annotation.ToString().Equals(ion.NeutralTheoreticalProduct.Annotation.ToString()))
{
//to see if the different matched ions are qualified
Assert.That(CommonParameters.ProductMassTolerance.Within(ion.Mz.ToMass(ion.Charge), product.NeutralMass));
}
}
}
//test specific condition: unknown fragment mass; this only happens rarely for sequences with unknown amino acids
var myMsDataFile1 = new TestDataFile();
var variableModifications1 = new List <Modification>();
var fixedModifications1 = new List <Modification>();
var proteinList1 = new List <Protein> {
new Protein("QXQ", null)
};
var productMassTolerance = new AbsoluteTolerance(0.01);
var searchModes = new OpenSearchMode();
Tolerance DeconvolutionMassTolerance1 = new PpmTolerance(5);
var listOfSortedms2Scans1 = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Custom Protease3", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters1 = new CommonParameters(
digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
scoreCutoff: 1,
addCompIons: false);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
PeptideSpectralMatch[] allPsmsArray1 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
bool writeSpectralLibrary = true;
new ClassicSearchEngine(allPsmsArray1, listOfSortedms2Scans1, variableModifications1, fixedModifications1, null, null, null,
proteinList1, searchModes, CommonParameters1, fsp, null, new List <string>(), writeSpectralLibrary).Run();
var psm1 = allPsmsArray1.Where(p => p != null).ToList();
Assert.AreEqual(psm1.Count, 222);
}
private static Tuple <List <PeptideSpectralMatch>, Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >, MassDiffAcceptor, bool, CompactPeptideBase, CompactPeptideBase> GetInfo(bool localizeable)
{
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModificationIsoforms: 2, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain, maxModsForPeptides: 1), scoreCutoff: 1);
// Alanine = Glycine + CH2
Protein protein1 = new Protein("MA", "protein1");
Protein protein2 = new Protein("MG", "protein2");
Protein protein3;
double monoisotopicMass = Chemistry.ChemicalFormula.ParseFormula("CH2").MonoisotopicMass;
ModificationMotif.TryGetMotif("G", out ModificationMotif motif1);
ModificationMotif.TryGetMotif("A", out ModificationMotif motif2);
TerminusLocalization modificationSites = TerminusLocalization.Any;
List <ModificationWithMass> allKnownFixedModifications = new List <ModificationWithMass>
{
new ModificationWithMass("CH2 on Glycine", null, motif1, modificationSites, monoisotopicMass)
};
List <ModificationWithMass> variableModifications;
ModificationWithMass alanineMod = new ModificationWithMass("CH2 on Alanine", null, motif2, modificationSites, monoisotopicMass);
if (localizeable)
{
variableModifications = new List <ModificationWithMass>();
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
alanineMod
} }
};
protein3 = new Protein("MA", "protein3", oneBasedModifications: oneBasedModifications);
}
else
{
variableModifications = new List <ModificationWithMass>();
variableModifications = new List <ModificationWithMass> {
alanineMod
};
protein3 = new Protein("MA", "protein3");
}
var pepWithSetModifications1 = protein1.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).First();
var pepWithSetModifications2 = protein2.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).First();
var pepWithSetModifications3 = protein3.Digest(CommonParameters.DigestionParams, allKnownFixedModifications, variableModifications).Last();
CompactPeptide compactPeptide1 = new CompactPeptide(pepWithSetModifications1, TerminusType.None);
CompactPeptide compactPeptideDuplicate = new CompactPeptide(pepWithSetModifications2, TerminusType.None);
Assert.AreEqual(compactPeptide1, compactPeptideDuplicate);
CompactPeptide compactPeptide2 = new CompactPeptide(pepWithSetModifications3, TerminusType.None);
string fullFilePath = null;
int precursorCharge = 0;
TestDataFile testDataFile = new TestDataFile();
MsDataScan mzLibScan = testDataFile.GetOneBasedScan(2);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(mzLibScan, 0, precursorCharge, fullFilePath);
int scanIndex = 0;
double score = 0;
int notch = 0;
PeptideSpectralMatch psm1 = new PeptideSpectralMatch(compactPeptide1, notch, score, scanIndex, scan, CommonParameters.DigestionParams);
psm1.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
PeptideSpectralMatch psm2 = new PeptideSpectralMatch(compactPeptide1, notch, score, scanIndex, scan, CommonParameters.DigestionParams);
psm2.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
PeptideSpectralMatch psm3 = new PeptideSpectralMatch(compactPeptide2, notch, score, scanIndex, scan, CommonParameters.DigestionParams);
psm3.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
var newPsms = new List <PeptideSpectralMatch>
{
psm1,
psm2,
psm3
};
MassDiffAcceptor massDiffAcceptors = new SinglePpmAroundZeroSearchMode(5);
SequencesToActualProteinPeptidesEngine stappe = new SequencesToActualProteinPeptidesEngine(newPsms, new List <Protein> {
protein1, protein2, protein3
},
allKnownFixedModifications, variableModifications, new List <ProductType> {
ProductType.B, ProductType.Y
}, new List <DigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters.ReportAllAmbiguity, CommonParameters, new List <string>());
var haha = (SequencesToActualProteinPeptidesEngineResults)stappe.Run();
var compactPeptideToProteinPeptideMatching = haha.CompactPeptideToProteinPeptideMatching;
Assert.AreEqual(2, compactPeptideToProteinPeptideMatching.Count);
psm1.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
bool noOneHitWonders = false;
return(new Tuple <List <PeptideSpectralMatch>, Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >, MassDiffAcceptor, bool, CompactPeptideBase, CompactPeptideBase>
(
newPsms, compactPeptideToProteinPeptideMatching, massDiffAcceptors, noOneHitWonders, compactPeptide1, compactPeptide2
));
}
public static void TestDeltaValues()
{
CommonParameters CommonParameters = new CommonParameters(scoreCutoff: 1, useDeltaScore: true, digestionParams: new DigestionParams(minPeptideLength: 5));
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
};
List <Modification> variableModifications = GlobalVariables.AllModsKnown.OfType <Modification>().Where(b => CommonParameters.ListOfModsVariable.Contains((b.ModificationType, b.IdWithMotif))).ToList();
List <Modification> fixedModifications = GlobalVariables.AllModsKnown.OfType <Modification>().Where(b => CommonParameters.ListOfModsFixed.Contains((b.ModificationType, b.IdWithMotif))).ToList();
// Generate data for files
Protein TargetProtein1 = new Protein("TIDEANTHE", "accession1");
Protein TargetProtein2 = new Protein("TIDELVE", "accession2");
Protein TargetProtein3 = new Protein("TIDENIE", "accession3");
Protein TargetProteinLost = new Protein("PEPTIDEANTHE", "accession4");
Protein DecoyProteinFound = new Protein("PETPLEDQGTHE", "accessiond", isDecoy: true);
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications>
{
TargetProtein1.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein2.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein3.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
DecoyProteinFound.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0]
});
var proteinList = new List <Protein> {
TargetProtein1, TargetProtein2, TargetProtein3, TargetProteinLost, DecoyProteinFound
};
var searchModes = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//check better when using delta
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, 1, DecoyType.None, CommonParameters, 30000, false, new List <FileInfo>(), new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(CommonParameters.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
PeptideSpectralMatch[] allPsmsArrayModern = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArrayModern, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, CommonParameters, massDiffAcceptor, 0, new List <string>()).Run();
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
FdrAnalysisResults fdrResultsModernDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArrayModern.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassicDelta.PsmsWithin1PercentFdr == 3);
Assert.IsTrue(fdrResultsModernDelta.PsmsWithin1PercentFdr == 3);
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 5));
//check worse when using score
FdrAnalysisResults fdrResultsClassic = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
FdrAnalysisResults fdrResultsModern = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassic.PsmsWithin1PercentFdr == 0);
Assert.IsTrue(fdrResultsModern.PsmsWithin1PercentFdr == 0);
//check that when delta is bad, we used the score
// Generate data for files
Protein DecoyProtein1 = new Protein("TLEDAGGTHE", "accession1d", isDecoy: true);
Protein DecoyProtein2 = new Protein("TLEDLVE", "accession2d", isDecoy: true);
Protein DecoyProtein3 = new Protein("TLEDNIE", "accession3d", isDecoy: true);
Protein DecoyProteinShiny = new Protein("GGGGGG", "accessionShinyd", isDecoy: true);
myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications>
{
TargetProtein1.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein2.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein3.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
DecoyProteinShiny.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
});
proteinList = new List <Protein>
{
TargetProtein1, DecoyProtein1,
TargetProtein2, DecoyProtein2,
TargetProtein3, DecoyProtein3,
DecoyProteinShiny,
};
listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//check no change when using delta
allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
CommonParameters = new CommonParameters(useDeltaScore: true, digestionParams: new DigestionParams(minPeptideLength: 5));
indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, 1, DecoyType.None, CommonParameters, 30000, false, new List <FileInfo>(), new List <string>());
indexResults = (IndexingResults)indexEngine.Run();
massDiffAcceptor = SearchTask.GetMassDiffAcceptor(CommonParameters.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
allPsmsArrayModern = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArrayModern, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, CommonParameters, massDiffAcceptor, 0, new List <string>()).Run();
fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
fdrResultsModernDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArrayModern.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassicDelta.PsmsWithin1PercentFdr == 3);
Assert.IsTrue(fdrResultsModernDelta.PsmsWithin1PercentFdr == 3);
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 5));
//check no change when using score
fdrResultsClassic = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
fdrResultsModern = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArrayModern.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassic.PsmsWithin1PercentFdr == 3);
Assert.IsTrue(fdrResultsModern.PsmsWithin1PercentFdr == 3);
}
public static void SearchWithPeptidesAddedInParsimonyTest()
{
// Make sure can run the complete search task when multiple compact peptides may correspond to a single PWSM
SearchTask st = new SearchTask
{
SearchParameters = new SearchParameters
{
DoParsimony = true,
DecoyType = DecoyType.None,
ModPeptidesAreDifferent = false
},
CommonParameters = new CommonParameters
{
ScoreCutoff = 1,
DigestionParams = new DigestionParams
{
MinPeptideLength = 2
}
}
};
string xmlName = "andguiaheow.xml";
#region Generate protein and write to file
CommonParameters CommonParameters = new CommonParameters
{
DigestionParams = new DigestionParams
{
MaxMissedCleavages = 0,
MinPeptideLength = null,
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain,
MaxModsForPeptide = 1,
MaxModificationIsoforms = 2
},
ScoreCutoff = 1
};
ModificationMotif.TryGetMotif("A", out ModificationMotif motifA);
ModificationWithMass alanineMod = new ModificationWithMass("111", "mt", motifA, TerminusLocalization.Any, 111);
var variableModifications = new List <ModificationWithMass>();
IDictionary <int, List <Modification> > oneBasedModifications1 = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
alanineMod
} }
};
Protein protein1 = new Protein("MA", "protein1", oneBasedModifications: oneBasedModifications1);
// Alanine = Glycine + CH2
ModificationMotif.TryGetMotif("G", out ModificationMotif motif1);
ModificationWithMass glycineMod = new ModificationWithMass("CH2 on Glycine", "mt", motif1, TerminusLocalization.Any, Chemistry.ChemicalFormula.ParseFormula("CH2").MonoisotopicMass);
IDictionary <int, List <Modification> > oneBasedModifications2 = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
glycineMod
} }
};
Protein protein2 = new Protein("MG", "protein3", oneBasedModifications: oneBasedModifications2);
PeptideWithSetModifications pepMA = protein1.Digest(CommonParameters.DigestionParams, new List <ModificationWithMass>(), variableModifications).First();
PeptideWithSetModifications pepMA111 = protein1.Digest(CommonParameters.DigestionParams, new List <ModificationWithMass>(), variableModifications).Last();
var pepMG = protein2.Digest(CommonParameters.DigestionParams, new List <ModificationWithMass>(), variableModifications).First();
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), new List <Protein> {
protein1, protein2
}, xmlName);
#endregion Generate protein and write to file
string mzmlName = @"ajgdiu.mzML";
#region Generate and write the mzml
{
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepMA, pepMG, pepMA111
}, true);
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlName, false);
}
#endregion Generate and write the mzml
st.RunTask("",
new List <DbForTask> {
new DbForTask(xmlName, false)
},
new List <string> {
mzmlName
}, "");
}
public static void TestPrunedDatabase()
{
//Create Search Task
SearchTask task1 = new SearchTask
{
SearchParameters = new SearchParameters
{
WritePrunedDatabase = true,
SearchTarget = true,
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
ModsToWriteSelection = new Dictionary <string, int>
{
{ "ConnorModType", 1 }
}
},
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 5))
};
//add task to task list
List <(string, MetaMorpheusTask)> taskList = new List <(string, MetaMorpheusTask)>
{
("task1", task1)
};
ModificationMotif.TryGetMotif("P", out ModificationMotif motif);
var connorMod = new Modification(_originalId: "ConnorMod on P", _modificationType: "ConnorModType", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
GlobalVariables.AddMods(new List <Modification>
{
connorMod
}, false);
//create modification lists
List <Modification> variableModifications = GlobalVariables.AllModsKnown.OfType <Modification>()
.Where(b => task1.CommonParameters.ListOfModsVariable.Contains((b.ModificationType, b.IdWithMotif))).ToList();
//add modification to Protein object
var dictHere = new Dictionary <int, List <Modification> >();
Modification modToAdd = connorMod;
Modification modToAdd2 = connorMod;
dictHere.Add(1, new List <Modification> {
modToAdd
});
dictHere.Add(3, new List <Modification> {
modToAdd2
});
//protein Creation (One with mod and one without)
Protein TestProteinWithMod = new Protein("PEPTID", "accession1", "organism", new List <Tuple <string, string> >(), dictHere);
//First Write XML Database
string xmlName = "okkk.xml";
//Add Mod to list and write XML input database
Dictionary <string, HashSet <Tuple <int, Modification> > > modList = new Dictionary <string, HashSet <Tuple <int, Modification> > >();
var Hash = new HashSet <Tuple <int, Modification> >
{
new Tuple <int, Modification>(3, modToAdd)
};
modList.Add("test", Hash);
ProteinDbWriter.WriteXmlDatabase(modList, new List <Protein> {
TestProteinWithMod
}, xmlName);
//now write MZML file
var protein = ProteinDbLoader.LoadProteinXML(xmlName, true,
DecoyType.Reverse, new List <Modification>(), false, new List <string>(), out Dictionary <string, Modification> ok);
//Dictionary 'ok' contains unknown modifications. There are no unknown modifications in this test.
Assert.AreEqual(0, ok.Count);
//One protein is read from the .xml database and one decoy is created. Therefore, the list of proteins contains 2 entries.
Assert.AreEqual(2, protein.Count);
//The original database had two localized mods on the protein. Therefore. both protein and decoy should have two mods.
Assert.AreEqual(2, protein[0].OneBasedPossibleLocalizedModifications.Count);
List <int> foundResidueIndicies = protein[0].OneBasedPossibleLocalizedModifications.Select(k => k.Key).ToList();
List <int> expectedResidueIndices = new List <int>()
{
1, 3
};
Assert.That(foundResidueIndicies, Is.EquivalentTo(expectedResidueIndices));
Assert.AreEqual(2, protein[1].OneBasedPossibleLocalizedModifications.Count);
foundResidueIndicies = protein[1].OneBasedPossibleLocalizedModifications.Select(k => k.Key).ToList();
expectedResidueIndices = new List <int>()
{
4, 6
}; //originally modified residues are now at the end in the decoy
Assert.That(foundResidueIndicies, Is.EquivalentTo(expectedResidueIndices));
var thisOk = ok; //for debugging
var commonParamsAtThisPoint = task1.CommonParameters.DigestionParams; //for debugging
var digestedList = protein[0].Digest(task1.CommonParameters.DigestionParams, new List <Modification> {
},
variableModifications).ToList();
Assert.AreEqual(4, digestedList.Count);
//Set Peptide with 1 mod at position 3
PeptideWithSetModifications pepWithSetMods1 = digestedList[1];
//Finally Write MZML file
Assert.AreEqual("PEP[ConnorModType:ConnorMod on P]TID", pepWithSetMods1.FullSequence);//this might be base sequence
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetMods1
});
string mzmlName = @"hello.mzML";
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlName, false);
//run!
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestPrunedDatabase");
var engine = new EverythingRunnerEngine(taskList, new List <string> {
mzmlName
},
new List <DbForTask> {
new DbForTask(xmlName, false)
}, outputFolder);
engine.Run();
string final = Path.Combine(MySetUpClass.outputFolder, "task1", "okkkpruned.xml");
var proteins = ProteinDbLoader.LoadProteinXML(final, true, DecoyType.Reverse, new List <Modification>(), false, new List <string>(), out ok);
//check length
Assert.AreEqual(1, proteins[0].OneBasedPossibleLocalizedModifications.Count);
//check location (key)
Assert.AreEqual(true, proteins[0].OneBasedPossibleLocalizedModifications.ContainsKey(3));
List <Modification> listOfMods = proteins[0].OneBasedPossibleLocalizedModifications[3];
//check Type, count, ID
Assert.AreEqual(listOfMods[0].ModificationType, "ConnorModType");
Assert.AreEqual(listOfMods[0].IdWithMotif, "ConnorMod on P");
Assert.AreEqual(listOfMods.Count, 1);
Directory.Delete(outputFolder, true);
File.Delete(xmlName);
File.Delete(mzmlName);
}
public static void TestAnalysisEngineTests()
{
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Custom Protease5", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(
protease: protease.Name,
maxMissedCleavages: 0,
minPeptideLength: 1,
maxModificationIsoforms: 1042),
scoreCutoff: 1,
productMassTolerance: new PpmTolerance(10));
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
List <Modification> localizeableModifications = new List <Modification>();
List <Modification> variableModifications = new List <Modification>();
List <Modification> fixedModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int i = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", "accession")
};
var modPep = proteinList.First().Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).Last();
HashSet <PeptideWithSetModifications> value1 = new HashSet <PeptideWithSetModifications> {
modPep
};
PeptideWithSetModifications compactPeptide1 = value1.First();
Assert.AreEqual("QQQ", value1.First().BaseSequence);
var modPep2 = proteinList.First().Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).First();
HashSet <PeptideWithSetModifications> value2 = new HashSet <PeptideWithSetModifications> {
modPep2
};
PeptideWithSetModifications compactPeptide2 = value2.First();
Assert.AreEqual("MNNNK", value2.First().BaseSequence);
var modPep3 = proteinList.First().Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[1];
HashSet <PeptideWithSetModifications> value3 = new HashSet <PeptideWithSetModifications> {
modPep3
};
PeptideWithSetModifications compactPeptide3 = value3.First();
Assert.AreEqual("NNNK", value3.First().BaseSequence);
Ms2ScanWithSpecificMass scanA = new Ms2ScanWithSpecificMass(new MsDataScan(new MzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 2, 1, true, Polarity.Positive, double.NaN, null, null, MZAnalyzerType.Orbitrap, double.NaN, null, null, "scan=1", double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 1, null), 1, 1, null, new CommonParameters());
Ms2ScanWithSpecificMass scanB = new Ms2ScanWithSpecificMass(new MsDataScan(new MzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 3, 1, true, Polarity.Positive, double.NaN, null, null, MZAnalyzerType.Orbitrap, double.NaN, null, null, "scan=2", double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 1, null), 2 + 132.040, 1, null, new CommonParameters());
Ms2ScanWithSpecificMass scanC = new Ms2ScanWithSpecificMass(new MsDataScan(new MzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 4, 1, true, Polarity.Positive, double.NaN, null, null, MZAnalyzerType.Orbitrap, double.NaN, null, null, "scan=3", double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 1, null), 3, 1, null, new CommonParameters());
PeptideSpectralMatch matchA = new PeptideSpectralMatch(compactPeptide1, 0, 0, 0, scanA, CommonParameters, new List <MatchedFragmentIon>());
PeptideSpectralMatch matchB = new PeptideSpectralMatch(compactPeptide2, 0, 0, 0, scanB, CommonParameters, new List <MatchedFragmentIon>());
PeptideSpectralMatch matchC = new PeptideSpectralMatch(compactPeptide3, 0, 0, 0, scanC, CommonParameters, new List <MatchedFragmentIon>());
var newPsms = new List <PeptideSpectralMatch> {
matchA, matchB, matchC
};
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
value1.First(), value2.First(), value3.First()
});
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Action <List <PeptideSpectralMatch>, string, List <string> > action2 = (List <PeptideSpectralMatch> l, string s, List <string> sdf) => {; };
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var arrayOfMs2ScansSortedByMass = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
Action <BinTreeStructure, string> action1 = (BinTreeStructure l, string s) =>
{
Assert.AreEqual(1, l.FinalBins.Count);
};
FdrAnalysisEngine engine = new FdrAnalysisEngine(newPsms, searchMode.NumNotches, CommonParameters, fsp, new List <string> {
"ff"
});
engine.Run();
}
public static void SearchWithPeptidesAddedInParsimonyTest()
{
// Make sure can run the complete search task when multiple compact peptides may correspond to a single PWSM
SearchTask st = new SearchTask
{
SearchParameters = new SearchParameters
{
DoParsimony = true,
DecoyType = DecoyType.None,
ModPeptidesAreDifferent = false
},
CommonParameters = new CommonParameters(scoreCutoff: 1, digestionParams: new DigestionParams(minPeptideLength: 2)),
};
string xmlName = "andguiaheow.xml";
CommonParameters CommonParameters = new CommonParameters(
scoreCutoff: 1,
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 1,
maxModificationIsoforms: 2,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain,
maxModsForPeptides: 1));
ModificationMotif.TryGetMotif("A", out ModificationMotif motifA);
Modification alanineMod = new Modification(_originalId: "111", _modificationType: "mt", _target: motifA, _locationRestriction: "Anywhere.", _monoisotopicMass: 111);
var variableModifications = new List <Modification>();
IDictionary <int, List <Modification> > oneBasedModifications1 = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
alanineMod
} }
};
Protein protein1 = new Protein("MA", "protein1", oneBasedModifications: oneBasedModifications1);
// Alanine = Glycine + CH2
ModificationMotif.TryGetMotif("G", out ModificationMotif motif1);
Modification glycineMod = new Modification(_originalId: "CH2 on Glycine", _modificationType: "mt", _target: motif1, _locationRestriction: "Anywhere.", _monoisotopicMass: Chemistry.ChemicalFormula.ParseFormula("CH2").MonoisotopicMass);
IDictionary <int, List <Modification> > oneBasedModifications2 = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
glycineMod
} }
};
Protein protein2 = new Protein("MG", "protein3", oneBasedModifications: oneBasedModifications2);
PeptideWithSetModifications pepMA = protein1.Digest(CommonParameters.DigestionParams, new List <Modification>(), variableModifications).First();
PeptideWithSetModifications pepMA111 = protein1.Digest(CommonParameters.DigestionParams, new List <Modification>(), variableModifications).Last();
var pepMG = protein2.Digest(CommonParameters.DigestionParams, new List <Modification>(), variableModifications).First();
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), new List <Protein> {
protein1, protein2
}, xmlName);
string mzmlName = @"ajgdiu.mzML";
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepMA, pepMG, pepMA111
});
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlName, false);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestSearchWithPeptidesAddedInParsimony");
Directory.CreateDirectory(outputFolder);
st.RunTask(outputFolder,
new List <DbForTask> {
new DbForTask(xmlName, false)
},
new List <string> {
mzmlName
}, "");
Directory.Delete(outputFolder, true);
File.Delete(mzmlName);
File.Delete(xmlName);
Directory.Delete(Path.Combine(TestContext.CurrentContext.TestDirectory, @"Task Settings"), true);
}
