public static void TestGptmdEngine(string proteinSequence, string accession, string sequenceVariantDescription, int numModifiedResidues)
{
List <PeptideSpectralMatch> allResultingIdentifications = null;
ModificationMotif.TryGetMotif("N", out ModificationMotif motifN);
var gptmdModifications = new List <Modification> {
new Modification(_originalId: "21", _modificationType: "mt", _target: motifN, _locationRestriction: "Anywhere.", _monoisotopicMass: 21.981943)
};
IEnumerable <Tuple <double, double> > combos = new List <Tuple <double, double> >();
Tolerance precursorMassTolerance = new PpmTolerance(10);
allResultingIdentifications = new List <PeptideSpectralMatch>();
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", new CommonParameters()));
var engine = new GptmdEngine(allResultingIdentifications, gptmdModifications, combos, new Dictionary <string, Tolerance> {
{ "filepath", precursorMassTolerance }
}, new CommonParameters(), fsp, new List <string>());
var res = (GptmdResults)engine.Run();
Assert.AreEqual(0, res.Mods.Count);
var parentProtein = new Protein(proteinSequence, accession, sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(1, "N", "A", sequenceVariantDescription)
});
var variantProteins = parentProtein.GetVariantProteins();
CommonParameters commonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 5));
List <Modification> variableModifications = new List <Modification>();
var modPep = variantProteins.SelectMany(p => p.Digest(commonParameters.DigestionParams, new List <Modification>(), variableModifications)).First();
//PsmParent newPsm = new TestParentSpectrumMatch(588.22520189093 + 21.981943);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(new MsDataScan(new MzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 0, 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, 0, null), (new Proteomics.AminoAcidPolymer.Peptide(modPep.BaseSequence).MonoisotopicMass + 21.981943).ToMz(1), 1, "filepath", new CommonParameters());
var peptidesWithSetModifications = new List <PeptideWithSetModifications> {
modPep
};
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(peptidesWithSetModifications.First(), 0, 0, 0, scan, commonParameters, new List <MatchedFragmentIon>());
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
newPsm.SetFdrValues(1, 0, 0, 1, 0, 0, 0, 0);
allResultingIdentifications.Add(newPsm);
engine = new GptmdEngine(allResultingIdentifications, gptmdModifications, combos, new Dictionary <string, Tolerance> {
{ "filepath", precursorMassTolerance }
}, new CommonParameters(), null, new List <string>());
res = (GptmdResults)engine.Run();
Assert.AreEqual(1, res.Mods.Count);
Assert.AreEqual(numModifiedResidues, res.Mods["accession"].Count);
}
public static void TestCombos(string proteinSequence, string accession, string variantAA, string sequenceVariantDescription, int numModHashes, int numModifiedResidues, int numModifiedResiduesN, int numModifiedResiduesP, int numModifiedResiduesNP)
{
List <PeptideSpectralMatch> allIdentifications = null;
ModificationMotif.TryGetMotif("N", out ModificationMotif motifN);
ModificationMotif.TryGetMotif("P", out ModificationMotif motifP);
var gptmdModifications = new List <Modification> {
new Modification(_originalId: "21", _modificationType: "mt", _target: motifN, _locationRestriction: "Anywhere.", _monoisotopicMass: 21.981943),
new Modification(_originalId: "16", _modificationType: "mt", _target: motifP, _locationRestriction: "Anywhere.", _monoisotopicMass: 15.994915)
};
IEnumerable <Tuple <double, double> > combos = new List <Tuple <double, double> > {
new Tuple <double, double>(21.981943, 15.994915)
};
Tolerance precursorMassTolerance = new PpmTolerance(10);
var parentProtein = new Protein(proteinSequence, accession, sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(1, "N", variantAA, sequenceVariantDescription)
});
var variantProteins = parentProtein.GetVariantProteins();
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 5);
List <Modification> variableModifications = new List <Modification>();
var modPep = variantProteins.SelectMany(p => p.Digest(digestionParams, new List <Modification>(), variableModifications)).First();
MsDataScan dfd = new MsDataScan(new MzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 0, 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, 0, null);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(dfd, (new Proteomics.AminoAcidPolymer.Peptide(modPep.BaseSequence).MonoisotopicMass + 21.981943 + 15.994915).ToMz(1), 1, "filepath", new CommonParameters());
var peptidesWithSetModifications = new List <PeptideWithSetModifications> {
modPep
};
PeptideSpectralMatch match = new PeptideSpectralMatch(peptidesWithSetModifications.First(), 0, 0, 0, scan, digestionParams, new List <MatchedFragmentIon>());
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(peptidesWithSetModifications.First(), 0, 0, 0, scan, digestionParams, new List <MatchedFragmentIon>());
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
match.SetFdrValues(1, 0, 0, 1, 0, 0, 0, 0);
allIdentifications = new List <PeptideSpectralMatch> {
match
};
var engine = new GptmdEngine(allIdentifications, gptmdModifications, combos, new Dictionary <string, Tolerance> {
{ "filepath", precursorMassTolerance }
}, new CommonParameters(), new List <string>());
var res = (GptmdResults)engine.Run();
Assert.AreEqual(numModHashes, res.Mods.Count);
Assert.AreEqual(numModifiedResidues, res.Mods["accession"].Count);
Assert.AreEqual(numModifiedResiduesN, res.Mods["accession"].Where(b => b.Item2.OriginalId.Equals("21")).Count());
Assert.AreEqual(numModifiedResiduesP, res.Mods["accession"].Where(b => b.Item2.OriginalId.Equals("16")).Count());
res.Mods.TryGetValue("accession_N1P", out var hash);
Assert.AreEqual(numModifiedResiduesNP, (hash ?? new HashSet <Tuple <int, Modification> >()).Count);
}
public static void TestProteinPrunedWithModSelectionAndVariants()
{
var modToWrite = GlobalVariables.AllModsKnown.Where(p => p.ModificationType == "UniProt" && p.Target.ToString() == "T").First();
var modToNotWrite = GlobalVariables.AllModsKnown.Where(p => p.ModificationType == "Common Artifact" && p.Target.ToString() == "X").First();
Dictionary <int, List <Modification> > variantMods = new Dictionary <int, List <Modification> >();
variantMods.Add(1, new List <Modification>()
{
modToNotWrite
});
List <SequenceVariation> variants = new List <SequenceVariation> {
new SequenceVariation(4, 4, "V", "T", @"20\t41168825\t.\tT\tC\t14290.77\t.\tANN=C|missense_variant|MODERATE|PLCG1|ENSG00000124181|transcript|ENST00000244007.7|protein_coding|22/33|c.2438T>C|p.Ile813Thr|2635/5285|2438/3876|813/1291||\tGT:AD:DP:GQ:PL\t1/1:1,392:393:99:14319,1142,0", variantMods)
};
var protein1 = new Protein("PEPVIDEKPEPT", "1", oneBasedModifications: new Dictionary <int, List <Modification> > {
{ 1, new List <Modification> {
modToNotWrite
} }, { 12, new List <Modification> {
modToWrite
} }
}, sequenceVariations: variants);
var protein2 = new Protein("PEPIDPEPT", "2", oneBasedModifications: new Dictionary <int, List <Modification> > {
{ 1, new List <Modification> {
modToNotWrite
} }, { 9, new List <Modification> {
modToWrite
} }
});
var protein1Variants = protein1.GetVariantProteins(1, 0);
string path = @"temp";
var proteinList = new List <Protein> {
protein1, protein2
};
proteinList.AddRange(protein1Variants);
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), proteinList, path);
Directory.CreateDirectory(Path.Combine(TestContext.CurrentContext.TestDirectory, @"PrunedDbTestVariant"));
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>(1, modToWrite),
new Tuple <int, Modification>(2, modToNotWrite),
};
var db = ProteinDbWriter.WriteXmlDatabase(modList, proteinList, Path.Combine(TestContext.CurrentContext.TestDirectory, @"PrunedDbTestVariant/fakeDb.xml"));
var peptideObserved = protein1Variants.First().Digest(new DigestionParams(minPeptideLength: 1), new List <Modification>(), new List <Modification>())
.Where(p => p.BaseSequence == "PEPT").First();
PostSearchAnalysisParameters testPostTaskParameters = new PostSearchAnalysisParameters();
CommonParameters commonParam = new CommonParameters(useDeltaScore: false);
double[,] noiseData = new double[10000, 10000];
noiseData[0, 0] = 1.0;
List <Proteomics.Fragmentation.MatchedFragmentIon> matchedFragmentIons = new List <Proteomics.Fragmentation.MatchedFragmentIon>()
{
};
MzSpectrum spectrum = new MzSpectrum(noiseData);
MsDataScan scan = new MsDataScan(spectrum, 1, 1, true, Polarity.Unknown, 2, new MzLibUtil.MzRange(10, 1000), "", MZAnalyzerType.Orbitrap, 10000, null, noiseData, "");
testPostTaskParameters.ProteinList = proteinList;
testPostTaskParameters.AllPsms = new List <PeptideSpectralMatch> {
new PeptideSpectralMatch(peptideObserved, 0, 20, 1, new Ms2ScanWithSpecificMass(scan, 100, 1, @"", commonParam), commonParam, matchedFragmentIons)
};
testPostTaskParameters.SearchParameters = new SearchParameters();
testPostTaskParameters.SearchParameters.WritePrunedDatabase = true;
testPostTaskParameters.SearchParameters.DoQuantification = false;
testPostTaskParameters.SearchParameters.WriteMzId = false;
testPostTaskParameters.DatabaseFilenameList = new List <DbForTask>()
{
new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"PrunedDbTest/fakeDb.xml"), false)
};
testPostTaskParameters.OutputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"PrunedDbTest");
Directory.CreateDirectory(Path.Combine(TestContext.CurrentContext.TestDirectory, @"PrunedDbTest/individual"));
testPostTaskParameters.IndividualResultsOutputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"PrunedDbTest/individual");
int[] stuffForSpectraFile = new int[2];
stuffForSpectraFile[0] = 10;
stuffForSpectraFile[1] = 10;
Dictionary <string, int[]> numSpectraPerFile = new Dictionary <string, int[]>();
numSpectraPerFile.Add("", stuffForSpectraFile);
testPostTaskParameters.NumMs2SpectraPerFile = numSpectraPerFile;
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications>
{
peptideObserved
});
string mzmlName = @"newMzml.mzML";
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, mzmlName, false);
modList.Add("test", Hash);
testPostTaskParameters.CurrentRawFileList = new List <string>()
{
mzmlName
};
SearchTask task5 = new SearchTask
{
SearchParameters = new SearchParameters
{
WritePrunedDatabase = true,
SearchTarget = true,
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
},
CommonParameters = new CommonParameters()
};
var test = task5.RunTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"PrunedDbTest"), new List <DbForTask>()
{
new DbForTask(Path.Combine(TestContext.CurrentContext.TestDirectory, @"PrunedDbTest/fakeDb.xml"), false)
}, new List <string>()
{
mzmlName
}, "name");
testPostTaskParameters.SearchTaskResults = test;
PostSearchAnalysisTask testPostTask = new PostSearchAnalysisTask();
testPostTask.Parameters = testPostTaskParameters;
testPostTask.CommonParameters = commonParam;
testPostTask.FileSpecificParameters = new List <(string FileName, CommonParameters Parameters)> {
("newMzMl.mzml", commonParam)
};
testPostTask.Run();
var proteinsLoaded = ProteinDbLoader.LoadProteinXML(path, true, DecoyType.None, GlobalVariables.AllModsKnown, false, new List <string>(), out var unknownMods);
// assert that mods on proteins are the same before/after task is run
Assert.AreEqual(protein1Variants.First().Accession, proteinsLoaded.First().Accession);
Assert.AreEqual(protein1Variants.First().OneBasedPossibleLocalizedModifications.Count(), proteinsLoaded.First().OneBasedPossibleLocalizedModifications.Count());
Assert.AreEqual(protein2.OneBasedPossibleLocalizedModifications.Count(), proteinsLoaded.ElementAt(1).OneBasedPossibleLocalizedModifications.Count());
// assert that protein pruned DB has correct proteins mods
var proteinPruned = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, @"PrunedDbTest/fakeDbproteinPruned.xml"), true, DecoyType.None, GlobalVariables.AllModsKnown, false, new List <string>(), out var unknownMods1);
Assert.That(proteinPruned.Count().Equals(1));
Assert.That(proteinPruned.FirstOrDefault().OneBasedPossibleLocalizedModifications.Count().Equals(1));
// assert that mod-pruned DB has correct proteins and mods
var modPruned = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, @"PrunedDbTest/fakeDbpruned.xml"), true, DecoyType.None, GlobalVariables.AllModsKnown, false, new List <string>(), out var unknownMods2);
Assert.That(modPruned.Count().Equals(2));
Assert.That(modPruned.ElementAt(0).OneBasedPossibleLocalizedModifications.Count().Equals(1));
Assert.That(modPruned.ElementAt(1).OneBasedPossibleLocalizedModifications.Count().Equals(1));
}
public static void TestComputePEPValue()
{
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML");
MyFileManager myFileManager = new MyFileManager(true);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams());
var myMsDataFile = myFileManager.LoadFile(origDataFile, CommonParameters);
var searchModes = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\hela_snip_for_unitTest.fasta"), true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors, -1);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML", CommonParameters).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.Where(p => p != null).ToList(), 1, CommonParameters, new List <string>()).Run());
var nonNullPsms = allPsmsArray.Where(p => p != null).ToList();
var nonNullPsmsOriginalCopy = allPsmsArray.Where(p => p != null).ToList();
var maxScore = nonNullPsms.Select(n => n.Score).Max();
PeptideSpectralMatch maxScorePsm = nonNullPsms.Where(n => n.Score == maxScore).First();
Dictionary <string, int> sequenceToPsmCount = new Dictionary <string, int>();
List <string> sequences = new List <string>();
foreach (PeptideSpectralMatch psm in nonNullPsms)
{
var ss = psm.BestMatchingPeptides.Select(b => b.Peptide.FullSequence).ToList();
sequences.Add(String.Join("|", ss));
}
var s = sequences.GroupBy(i => i);
foreach (var grp in s)
{
sequenceToPsmCount.Add(grp.Key, grp.Count());
}
Dictionary <string, Dictionary <int, Tuple <double, double> > > fileSpecificRetTimeHI_behavior = new Dictionary <string, Dictionary <int, Tuple <double, double> > >();
Dictionary <string, Dictionary <int, Tuple <double, double> > > fileSpecificRetTemHI_behaviorModifiedPeptides = new Dictionary <string, Dictionary <int, Tuple <double, double> > >();
//average hydrophobicity, standard deviation hydrophobicity
Tuple <double, double> at = new Tuple <double, double>(33.0, 1.0);
Dictionary <int, Tuple <double, double> > HI_Time_avg_dev = new Dictionary <int, Tuple <double, double> >
{
{ 154, at }
};
fileSpecificRetTimeHI_behavior.Add(@"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML", HI_Time_avg_dev);
string[] trainingVariables = new[] { "HydrophobicityZScore", "Intensity", "ScanPrecursorCharge", "DeltaScore", "Notch", "PsmCount", "ModsCount", "MissedCleavagesCount", "Ambiguity", "LongestFragmentIonSeries", "IsVariantPeptide" };
int chargeStateMode = 4;
var(notch, pwsm) = maxScorePsm.BestMatchingPeptides.First();
var maxPsmData = PEP_Analysis.CreateOnePsmDataEntry(maxScorePsm, sequenceToPsmCount, fileSpecificRetTimeHI_behavior, fileSpecificRetTemHI_behaviorModifiedPeptides, chargeStateMode, pwsm, trainingVariables, notch, !pwsm.Protein.IsDecoy);
Assert.That(maxScorePsm.PeptidesToMatchingFragments.Count - 1, Is.EqualTo(maxPsmData.Ambiguity));
Assert.That(maxScorePsm.DeltaScore, Is.EqualTo(maxPsmData.DeltaScore).Within(0.05));
Assert.That((float)(maxScorePsm.Score - (int)maxScorePsm.Score), Is.EqualTo(maxPsmData.Intensity).Within(0.05));
Assert.That(maxPsmData.HydrophobicityZScore, Is.EqualTo(5.170955).Within(0.05));
Assert.That(maxScorePsm.BestMatchingPeptides.Select(p => p.Peptide).First().MissedCleavages, Is.EqualTo(maxPsmData.MissedCleavagesCount));
Assert.That(maxScorePsm.BestMatchingPeptides.Select(p => p.Peptide).First().AllModsOneIsNterminus.Values.Count(), Is.EqualTo(maxPsmData.ModsCount));
Assert.That(maxScorePsm.Notch ?? 0, Is.EqualTo(maxPsmData.Notch));
Assert.That(maxScorePsm.PsmCount, Is.EqualTo(maxPsmData.PsmCount));
Assert.That(-Math.Abs(chargeStateMode - maxScorePsm.ScanPrecursorCharge), Is.EqualTo(maxPsmData.PrecursorChargeDiffToMode));
Assert.AreEqual((float)0, maxPsmData.IsVariantPeptide);
PEP_Analysis.ComputePEPValuesForAllPSMsGeneric(nonNullPsms);
int trueCount = 0;
foreach (var item in allPsmsArray.Where(p => p != null))
{
var b = item.FdrInfo.PEP;
if (b >= 0.5)
{
trueCount++;
}
}
List <PeptideSpectralMatch> moreNonNullPSMs = new List <PeptideSpectralMatch>();
for (int i = 0; i < 3; i++)
{
foreach (PeptideSpectralMatch psm in nonNullPsms)
{
moreNonNullPSMs.Add(psm);
}
}
string expectedMetrics = "************************************************************\r\n* Metrics for Determination of PEP Using Binary Classification \r\n" +
"*-----------------------------------------------------------\r\n* Accuracy: 1\r\n* Area Under Curve: 1\r\n* Area under Precision recall Curve: 1\r\n* F1Score: 1\r\n" +
"* LogLoss: 2.60551851621861E-10\r\n* LogLossReduction: 0.999999999599165\r\n* PositivePrecision: 1\r\n* PositiveRecall: 1\r\n* NegativePrecision: 1\r\n" +
"* NegativeRecall: 1\r\n* Count of Ambiguous Peptides Removed: 0\r\n************************************************************\r\n";
string metrics = PEP_Analysis.ComputePEPValuesForAllPSMsGeneric(moreNonNullPSMs);
Assert.AreEqual(expectedMetrics, metrics);
Assert.GreaterOrEqual(32, trueCount);
//Test Variant Peptide as Input is identified as such as part of PEP calculation input much of the next several lines simply necessry to create a psm.
var anMzSpectrum = new MzSpectrum(new double[] { 1, 1 }, new double[] { 2, 2 }, true);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(new MsDataScan(anMzSpectrum, 1, 1, true, Polarity.Negative, 2, null, "", MZAnalyzerType.Orbitrap, 2, null, null, null), 1, 1, "path", new CommonParameters());
Protein variantProtein = new Protein("MPEPPPTIDE", "protein3", sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(4, 6, "PPP", "P", @"1\t50000000\t.\tA\tG\t.\tPASS\tANN=G||||||||||||||||\tGT:AD:DP\t1/1:30,30:30", null)
});
PeptideWithSetModifications varPep = variantProtein.GetVariantProteins().SelectMany(p => p.Digest(CommonParameters.DigestionParams, null, null)).FirstOrDefault();
PeptideSpectralMatch variantPSM = new PeptideSpectralMatch(varPep, 0, maxScorePsm.Score, maxScorePsm.ScanIndex, scan, new DigestionParams(), null);
sequenceToPsmCount = new Dictionary <string, int>();
sequences = new List <string>();
nonNullPsms.Add(variantPSM);
foreach (PeptideSpectralMatch psm in nonNullPsms)
{
var ss = psm.BestMatchingPeptides.Select(b => b.Peptide.FullSequence).ToList();
sequences.Add(String.Join("|", ss));
}
s = sequences.GroupBy(i => i);
foreach (var grp in s)
{
sequenceToPsmCount.Add(grp.Key, grp.Count());
}
var(vnotch, vpwsm) = variantPSM.BestMatchingPeptides.First();
PsmData variantPsmData = PEP_Analysis.CreateOnePsmDataEntry(variantPSM, sequenceToPsmCount, fileSpecificRetTimeHI_behavior, fileSpecificRetTemHI_behaviorModifiedPeptides, chargeStateMode, vpwsm, trainingVariables, vnotch, !maxScorePsm.IsDecoy);
Assert.AreEqual((float)1, variantPsmData.IsVariantPeptide);
}
