public static void TopPickedFdrTest()
{
//Test that the decoy beats out the target for FDR, but that the target still gets written.
Protein fillerProtein = new Protein("FILLR", "filler");
Protein targetProtein = new Protein("KFDSA", "protein");
Protein decoyProtein = new Protein("ASDFK", "DECOY_protein", isDecoy: true);
IEnumerable <Modification> allKnownFixedModifications = new List <Modification>();
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 5);
List <Modification> variableModifications = new List <Modification>();
PeptideWithSetModifications fillerPep = fillerProtein.Digest(digestionParams, allKnownFixedModifications, variableModifications).First();
PeptideWithSetModifications targetPep = targetProtein.Digest(digestionParams, allKnownFixedModifications, variableModifications).First();
PeptideWithSetModifications decoyPep = decoyProtein.Digest(digestionParams, allKnownFixedModifications, variableModifications).First();
// build the dictionary for input to parsimony
MsDataScan dfb = 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(dfb, 2, 0, "File", new CommonParameters());
List <PeptideSpectralMatch> psms = new List <PeptideSpectralMatch>
{
new PeptideSpectralMatch(fillerPep, 0, 30, 0, scan, new DigestionParams(), new List <MatchedFragmentIon>()),
new PeptideSpectralMatch(decoyPep, 0, 15.11, 0, scan, new DigestionParams(), new List <MatchedFragmentIon>()),
new PeptideSpectralMatch(targetPep, 0, 15.1, 0, scan, new DigestionParams(), new List <MatchedFragmentIon>())
};
psms.ForEach(p => p.ResolveAllAmbiguities());
psms.ForEach(p => p.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0));
// apply parsimony
ProteinParsimonyEngine pae = new ProteinParsimonyEngine(psms, false, new CommonParameters(), new List <string>());
ProteinParsimonyResults proteinParsimonyResult = (ProteinParsimonyResults)pae.Run();
ProteinScoringAndFdrEngine proteinScoringEngine = new ProteinScoringAndFdrEngine(proteinParsimonyResult.ProteinGroups, psms, false, true, true, new CommonParameters(), new List <string>());
ProteinScoringAndFdrResults results = (ProteinScoringAndFdrResults)proteinScoringEngine.Run();
Assert.IsTrue(results.SortedAndScoredProteinGroups.Count == 3);
Assert.IsTrue(results.SortedAndScoredProteinGroups[1].QValue == 0.5);
}
public static void TryFailSequenceCoverage()
{
var prot1 = new Protein("MMKMMK", "prot1");
ModificationMotif.TryGetMotif("M", out ModificationMotif motifM);
Modification mod1 = new Modification(_originalId: "mod1", _modificationType: "mt", _target: motifM, _locationRestriction: "N-terminal.", _monoisotopicMass: 10);
Modification mod2 = new Modification(_originalId: "mod2", _modificationType: "mt", _target: motifM, _locationRestriction: "Peptide N-terminal.", _monoisotopicMass: 10);
Modification mod3 = new Modification(_originalId: "mod3", _modificationType: "mt", _target: motifM, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
ModificationMotif.TryGetMotif("K", out ModificationMotif motifK);
Modification mod4 = new Modification(_originalId: "mod4", _modificationType: "mt", _target: motifK, _locationRestriction: "Peptide C-terminal.", _monoisotopicMass: 10);
Modification mod5 = new Modification(_originalId: "mod5", _modificationType: "mt", _target: motifK, _locationRestriction: "C-terminal.", _monoisotopicMass: 10);
Dictionary <int, Modification> modsFor1 = new Dictionary <int, Modification>
{
{ 1, mod1 },
{ 3, mod3 },
{ 5, mod4 },
};
Dictionary <int, Modification> modsFor2 = new Dictionary <int, Modification>
{
{ 1, mod2 },
{ 5, mod5 },
};
Dictionary <int, Modification> modsFor3 = new Dictionary <int, Modification>
{
{ 1, mod1 },
{ 5, mod3 },
{ 8, mod5 }
};
DigestionParams digestionParams = new DigestionParams();
var pwsm1 = new PeptideWithSetModifications(prot1, digestionParams, 1, 3, CleavageSpecificity.Unknown, "", 0, modsFor1, 0);
var pwsm2 = new PeptideWithSetModifications(prot1, digestionParams, 4, 6, CleavageSpecificity.Unknown, "", 0, modsFor2, 0);
var pwsm3 = new PeptideWithSetModifications(prot1, digestionParams, 1, 6, CleavageSpecificity.Unknown, "", 0, modsFor3, 0);
HashSet <PeptideWithSetModifications> peptides = new HashSet <PeptideWithSetModifications>
{
pwsm1,
pwsm2,
pwsm3,
};
IScan scan = new ThisTestScan();
var psm1 = new PeptideSpectralMatch(pwsm1, 0, 1, 0, scan, digestionParams, new List <MatchedFragmentIon>());
psm1.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
var psm2 = new PeptideSpectralMatch(pwsm2, 0, 1, 0, scan, digestionParams, new List <MatchedFragmentIon>());
psm2.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
var psm3 = new PeptideSpectralMatch(pwsm3, 0, 1, 0, scan, digestionParams, new List <MatchedFragmentIon>());
psm3.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
List <PeptideSpectralMatch> newPsms = new List <PeptideSpectralMatch>
{
psm1,
psm2,
psm3,
};
newPsms.ForEach(p => p.ResolveAllAmbiguities());
ProteinParsimonyEngine ppe = new ProteinParsimonyEngine(newPsms, true, new CommonParameters(), new List <string>());
ProteinParsimonyResults fjkd = (ProteinParsimonyResults)ppe.Run();
ProteinScoringAndFdrEngine psafe = new ProteinScoringAndFdrEngine(fjkd.ProteinGroups, newPsms, true, true, true, new CommonParameters(), new List <string>());
psafe.Run();
fjkd.ProteinGroups.First().CalculateSequenceCoverage();
var firstSequenceCoverageDisplayList = fjkd.ProteinGroups.First().SequenceCoverageDisplayList.First();
Assert.AreEqual("MMKMMK", firstSequenceCoverageDisplayList);
var firstSequenceCoverageDisplayListWithMods = fjkd.ProteinGroups.First().SequenceCoverageDisplayListWithMods.First();
Assert.AreEqual("[mod1 on M]-MM[mod3 on M]KM[mod3 on M]MK-[mod5 on K]", firstSequenceCoverageDisplayListWithMods);
var firstModInfo = fjkd.ProteinGroups.First().ModsInfo.First();
Assert.IsTrue(firstModInfo.Contains(@"#aa1[mod1 on M,info:occupancy=1.00(2/2)]"));
Assert.IsTrue(firstModInfo.Contains(@"#aa2[mod3 on M,info:occupancy=0.50(1/2)]"));
Assert.IsFalse(firstModInfo.Contains(@"#aa3"));
Assert.IsTrue(firstModInfo.Contains(@"#aa4[mod3 on M,info:occupancy=0.50(1/2)]"));
Assert.IsFalse(firstModInfo.Contains(@"#aa5"));
Assert.IsTrue(firstModInfo.Contains(@"#aa6[mod5 on K,info:occupancy=1.00(2/2)]"));
}
public static void TryFailSequenceCoverage()
{
var prot1 = new Protein("MMKMMK", "prot1");
ModificationMotif.TryGetMotif("M", out ModificationMotif motifM);
ModificationWithMass mod1 = new ModificationWithMass("mod1", "mt", motifM, TerminusLocalization.NProt, 10);
ModificationWithMass mod2 = new ModificationWithMass("mod2", "mt", motifM, TerminusLocalization.NPep, 10);
ModificationWithMass mod3 = new ModificationWithMass("mod3", "mt", motifM, TerminusLocalization.Any, 10);
ModificationMotif.TryGetMotif("K", out ModificationMotif motifK);
ModificationWithMass mod4 = new ModificationWithMass("mod4", "mt", motifK, TerminusLocalization.PepC, 10);
ModificationWithMass mod5 = new ModificationWithMass("mod5", "mt", motifK, TerminusLocalization.ProtC, 10);
Dictionary <int, ModificationWithMass> modsFor1 = new Dictionary <int, ModificationWithMass>
{
{ 1, mod1 },
{ 3, mod3 },
{ 5, mod4 },
};
Dictionary <int, ModificationWithMass> modsFor2 = new Dictionary <int, ModificationWithMass>
{
{ 1, mod2 },
{ 5, mod5 },
};
Dictionary <int, ModificationWithMass> modsFor3 = new Dictionary <int, ModificationWithMass>
{
{ 1, mod1 },
{ 5, mod3 },
{ 8, mod5 }
};
DigestionParams digestionParams = new DigestionParams();
var pwsm1 = new PeptideWithSetModifications(protein: prot1, digestionParams: digestionParams, oneBasedStartResidueInProtein: 1, oneBasedEndResidueInProtein: 3, peptideDescription: "", missedCleavages: 0, allModsOneIsNterminus: modsFor1, numFixedMods: 0);
var pwsm2 = new PeptideWithSetModifications(protein: prot1, digestionParams: digestionParams, oneBasedStartResidueInProtein: 4, oneBasedEndResidueInProtein: 6, peptideDescription: "", missedCleavages: 0, allModsOneIsNterminus: modsFor2, numFixedMods: 0);
var pwsm3 = new PeptideWithSetModifications(protein: prot1, digestionParams: digestionParams, oneBasedStartResidueInProtein: 1, oneBasedEndResidueInProtein: 6, peptideDescription: "", missedCleavages: 0, allModsOneIsNterminus: modsFor3, numFixedMods: 0);
HashSet <PeptideWithSetModifications> peptides = new HashSet <PeptideWithSetModifications>
{
pwsm1,
pwsm2,
pwsm3,
};
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ pwsm1.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pwsm1
} },
{ pwsm2.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pwsm2
} },
{ pwsm3.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pwsm3
} },
};
IScan scan = new ThisTestScan();
var psm1 = new PeptideSpectralMatch(pwsm1.CompactPeptide(TerminusType.None), 0, 1, 0, scan, digestionParams);
psm1.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
psm1.MatchToProteinLinkedPeptides(matching);
var psm2 = new PeptideSpectralMatch(pwsm2.CompactPeptide(TerminusType.None), 0, 1, 0, scan, digestionParams);
psm2.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
psm2.MatchToProteinLinkedPeptides(matching);
var psm3 = new PeptideSpectralMatch(pwsm3.CompactPeptide(TerminusType.None), 0, 1, 0, scan, digestionParams);
psm3.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
psm3.MatchToProteinLinkedPeptides(matching);
List <PeptideSpectralMatch> newPsms = new List <PeptideSpectralMatch>
{
psm1,
psm2,
psm3,
};
ProteinParsimonyEngine ppe = new ProteinParsimonyEngine(matching, true, new CommonParameters(), new List <string>());
ProteinParsimonyResults fjkd = (ProteinParsimonyResults)ppe.Run();
ProteinScoringAndFdrEngine psafe = new ProteinScoringAndFdrEngine(fjkd.ProteinGroups, newPsms, true, true, true, new CommonParameters(), new List <string>());
psafe.Run();
fjkd.ProteinGroups.First().CalculateSequenceCoverage();
var firstSequenceCoverageDisplayList = fjkd.ProteinGroups.First().SequenceCoverageDisplayList.First();
Assert.AreEqual("MMKMMK", firstSequenceCoverageDisplayList);
var firstSequenceCoverageDisplayListWithMods = fjkd.ProteinGroups.First().SequenceCoverageDisplayListWithMods.First();
Assert.AreEqual("[mod1]-MM[mod3]KM[mod3]MK-[mod5]", firstSequenceCoverageDisplayListWithMods);
var firstModInfo = fjkd.ProteinGroups.First().ModsInfo.First();
Assert.IsTrue(firstModInfo.Contains(@"#aa1[mod1,info:occupancy=1.00(2/2)]"));
Assert.IsTrue(firstModInfo.Contains(@"#aa2[mod3,info:occupancy=0.50(1/2)]"));
Assert.IsFalse(firstModInfo.Contains(@"#aa3"));
Assert.IsTrue(firstModInfo.Contains(@"#aa4[mod3,info:occupancy=0.50(1/2)]"));
Assert.IsFalse(firstModInfo.Contains(@"#aa5"));
Assert.IsTrue(firstModInfo.Contains(@"#aa6[mod5,info:occupancy=1.00(2/2)]"));
}
