public void TestStaticQonverter()
{
#region Example with forward and reverse proteins
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEK",
"TIDERPEPTIDEKPEP",
"DERPEPTIDEKPEPTI",
"THEQUICKBRWNFXUMPSVERTHELZYDG",
"KEDITPEPREDITPEP",
"PEPKEDITPEPREDIT",
"ITPEPKEDITPEPRED",
"GDYZLEHTREVSPMUXFNWRBKCIUQEHT"
};
const string decoyPrefix = "r-";
const int analysisCount = 2;
const int sourceCount = 2;
const int chargeCount = 2;
File.Delete("testStaticQonversion.idpDB");
var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testStaticQonversion.idpDB", new SessionFactoryConfig {
CreateSchema = true
});
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
session.Clear();
// add decoy prefix to the second half of the proteins
for (long i = testProteinSequences.LongLength / 2; i < testProteinSequences.LongLength; ++i)
{
var pro = session.Get <Protein>(i + 1);
pro.Accession = decoyPrefix + pro.Accession;
session.Update(pro);
}
#endregion
#region Example PSMs
// For each combination of 2 engines, 2 sources, and 2 charges,
// we test qonversion on this scenario:
//
// Scan Score DecoyState Targets Decoys Ambiguous -> Expected QValue
// 50 6 T 1 0 0 0
// 30 5 T 2 0 0 0
// 40 4 T 3 0 0 0
// 10 3 D 3 1 0 2/4
// 20 2 D 3 2 0 4/5
// 60 1 T 4 2 0 4/6
double q = PeptideSpectrumMatch.DefaultQValue;
for (int analysis = 1; analysis <= analysisCount; ++analysis)
{
for (int source = 1; source <= sourceCount; ++source)
{
for (int charge = 1; charge <= chargeCount; ++charge)
{
List <SpectrumTuple> testPsmSummary = new List <SpectrumTuple>()
{
// Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
new SpectrumTuple("/", source, 5, analysis, 6, q, String.Format("TIDERPEPTIDEK@{0}/1 PEPTIDER@{0}/8", charge)),
new SpectrumTuple("/", source, 3, analysis, 5, q, String.Format("TIDERPEPTIDEK@{0}/1 PEPTIDER@{0}/2", charge)),
new SpectrumTuple("/", source, 4, analysis, 4, q, String.Format("EDITPEP@{0}/1 THEQUICKBR@{0}/4", charge)),
new SpectrumTuple("/", source, 1, analysis, 3, q, String.Format("PEPTIDEKPEP@{0}/1 PEPTIDEK@{0}/2", charge)),
new SpectrumTuple("/", source, 2, analysis, 2, q, String.Format("TIDER@{0}/1 PEPTIDER@{0}/2", charge)),
new SpectrumTuple("/", source, 6, analysis, 1, q, String.Format("EDITPEPR@{0}/1 TIDERPEPTIDEK@{0}/3", charge))
};
TestModel.CreateTestData(session, testPsmSummary);
}
}
}
List <SpectrumTuple> testPsmSummaryWithoutScores = new List <SpectrumTuple>()
{
new SpectrumTuple("/", 1, 1, analysisCount + 1, null, 0.01, "TIDERPEPTIDEK@1/1 PEPTIDER@3/8"),
new SpectrumTuple("/", 1, 2, analysisCount + 1, null, 0.02, "KEDITPEPR@2/1 PEPTIDEK@2/8"),
new SpectrumTuple("/", 1, 3, analysisCount + 1, null, 0.03, "THEQUICKBR@3/1 THELZYDG@1/8"),
};
TestModel.CreateTestData(session, testPsmSummaryWithoutScores);
// force all peptide instances to fully specific
foreach (PeptideInstance pi in session.Query <PeptideInstance>())
{
pi.NTerminusIsSpecific = pi.CTerminusIsSpecific = true;
session.Update(pi);
}
session.Flush();
session.Close(); // close the connection
sessionFactory.Close();
#endregion
var qonverter = new IDPicker.Qonverter()
{
SettingsByAnalysis = new Dictionary <int, Qonverter.Settings>()
};
for (int i = 1; i <= analysisCount + 1; ++i)
{
qonverter.SettingsByAnalysis[i] = new Qonverter.Settings()
{
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
ChargeStateHandling = Qonverter.ChargeStateHandling.Ignore,
TerminalSpecificityHandling = Qonverter.TerminalSpecificityHandling.Ignore,
MassErrorHandling = Qonverter.MassErrorHandling.Ignore,
MissedCleavagesHandling = Qonverter.MissedCleavagesHandling.Ignore,
DecoyPrefix = decoyPrefix,
ScoreInfoByName = new Dictionary <string, Qonverter.Settings.ScoreInfo>()
{
{ "score1", new Qonverter.Settings.ScoreInfo()
{
Weight = 1
} },
{ "score2", new Qonverter.Settings.ScoreInfo()
{
Weight = 0
} }
}
}
}
;
var progressTester = new QonversionProgressTest()
{
Qonverter = qonverter,
ExpectedTotalAnalyses = analysisCount * sourceCount // engine 3 is ignored
};
File.Copy("testStaticQonversion.idpDB", "testStaticQonversion2.idpDB", true);
// test without progress monitor
qonverter.Qonvert("testStaticQonversion2.idpDB");
qonverter.QonversionProgress += new IDPicker.Qonverter.QonversionProgressEventHandler(progressTester.qonverter_QonversionProgress);
File.Copy("testStaticQonversion.idpDB", "testStaticQonversion3.idpDB", true);
// test progress monitor with cancelling
// (must before a full qonversion since the QValue test doesn't expect cancellation)
progressTester.ExpectedQonvertedAnalyses = 0;
progressTester.CancelAtCount = 4;
qonverter.Qonvert("testStaticQonversion3.idpDB");
// test progress monitor without cancelling
progressTester.ExpectedQonvertedAnalyses = 0;
progressTester.CancelAtCount = int.MaxValue;
qonverter.Qonvert("testStaticQonversion.idpDB");
sessionFactory = SessionFactoryFactory.CreateSessionFactory("testStaticQonversion.idpDB");
session = sessionFactory.OpenSession();
session.Clear();
#region QValue test
Dictionary <long, double> expectedQValues = new Dictionary <long, double>()
{
// with high scoring decoys, Q values can spike and gradually go down again;
// we squash these spikes such that Q value is monotonically increasing;
// then we convert Q values to FDR scores using linear interpolation
// targets decoys ambiguous unadjusted-Q-value adjusted-Q-value FDR-score
{ 4, 0 }, // 1 0 0 0 0 0
{ 2, 0.2 }, // 2 0 0 0 0 0.2
{ 3, 0.4 }, // 2 1 0 0.666 0.4 0.4
{ 0, 0.488 }, // 3 1 0 0.5 0.4 0.488
{ 1, 0.577 }, // 4 1 0 0.4 0.4 0.577
{ 5, 0.666 }, // 4 2 0 0.666 0.666 0.666
};
for (long engine = 1; engine <= 2; ++engine)
{
for (long source = 1; source <= 2; ++source)
{
for (int charge = 1; charge <= 2; ++charge)
{
foreach (var itr in expectedQValues)
{
var topRankedMatch = session.CreateQuery("SELECT psm " +
"FROM PeptideSpectrumMatch psm " +
"WHERE psm.Analysis.id = ? " +
" AND psm.Spectrum.Source.id = ? " +
" AND psm.Spectrum.Index = ? " +
" AND psm.Charge = ? " +
" AND psm.Rank = 1" +
"GROUP BY psm.Spectrum.id ")
.SetParameter(0, engine)
.SetParameter(1, source)
.SetParameter(2, itr.Key)
.SetParameter(3, charge)
.List <PeptideSpectrumMatch>().First();
Assert.AreEqual(session.Get <Analysis>(engine), topRankedMatch.Analysis);
Assert.AreEqual(session.Get <SpectrumSource>(source), topRankedMatch.Spectrum.Source);
Assert.AreEqual(charge, topRankedMatch.Charge);
Assert.AreEqual(itr.Value, topRankedMatch.QValue, 1e-3);
}
}
}
}
var scorelessMatches = session.CreateQuery("SELECT psm " +
"FROM PeptideSpectrumMatch psm " +
"WHERE psm.Analysis.id = 3 " +
" AND psm.Rank = 1")
.List <PeptideSpectrumMatch>();
Assert.AreEqual(3, scorelessMatches.Count);
Assert.AreEqual(0.01, scorelessMatches[0].QValue, 1e-12);
Assert.AreEqual(0.02, scorelessMatches[1].QValue, 1e-12);
Assert.AreEqual(0.03, scorelessMatches[2].QValue, 1e-12);
#endregion
}
public void TestStaticQonverter ()
{
#region Example with forward and reverse proteins
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEK",
"TIDERPEPTIDEKPEP",
"DERPEPTIDEKPEPTI",
"THEQUICKBRWNFXUMPSVERTHELZYDG",
"KEDITPEPREDITPEP",
"PEPKEDITPEPREDIT",
"ITPEPKEDITPEPRED",
"GDYZLEHTREVSPMUXFNWRBKCIUQEHT"
};
const string decoyPrefix = "r-";
const int analysisCount = 2;
const int sourceCount = 2;
const int chargeCount = 2;
File.Delete("testStaticQonversion.idpDB");
var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testStaticQonversion.idpDB", new SessionFactoryConfig { CreateSchema = true });
var session = sessionFactory.OpenSession();
TestModel.CreateTestProteins(session, testProteinSequences);
session.Clear();
// add decoy prefix to the second half of the proteins
for (long i = testProteinSequences.LongLength / 2; i < testProteinSequences.LongLength; ++i)
{
var pro = session.Get<Protein>(i + 1);
pro.Accession = decoyPrefix + pro.Accession;
session.Update(pro);
}
#endregion
#region Example PSMs
// For each combination of 2 engines, 2 sources, and 2 charges,
// we test qonversion on this scenario:
//
// Scan Score DecoyState Targets Decoys Ambiguous -> Expected QValue
// 50 6 T 1 0 0 0
// 30 5 T 2 0 0 0
// 40 4 T 3 0 0 0
// 10 3 D 3 1 0 2/4
// 20 2 D 3 2 0 4/5
// 60 1 T 4 2 0 4/6
double q = PeptideSpectrumMatch.DefaultQValue;
for (int analysis = 1; analysis <= analysisCount; ++analysis)
for (int source = 1; source <= sourceCount; ++source)
for (int charge = 1; charge <= chargeCount; ++charge)
{
List<SpectrumTuple> testPsmSummary = new List<SpectrumTuple>()
{
// Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
new SpectrumTuple("/", source, 5, analysis, 6, q, String.Format("TIDERPEPTIDEK@{0}/1 PEPTIDER@{0}/8", charge)),
new SpectrumTuple("/", source, 3, analysis, 5, q, String.Format("TIDERPEPTIDEK@{0}/1 PEPTIDER@{0}/2", charge)),
new SpectrumTuple("/", source, 4, analysis, 4, q, String.Format("EDITPEP@{0}/1 THEQUICKBR@{0}/4", charge)),
new SpectrumTuple("/", source, 1, analysis, 3, q, String.Format("PEPTIDEKPEP@{0}/1 PEPTIDEK@{0}/2", charge)),
new SpectrumTuple("/", source, 2, analysis, 2, q, String.Format("TIDER@{0}/1 PEPTIDER@{0}/2", charge)),
new SpectrumTuple("/", source, 6, analysis, 1, q, String.Format("EDITPEPR@{0}/1 TIDERPEPTIDEK@{0}/3", charge))
};
TestModel.CreateTestData(session, testPsmSummary);
}
List<SpectrumTuple> testPsmSummaryWithoutScores = new List<SpectrumTuple>()
{
new SpectrumTuple("/", 1, 1, analysisCount+1, null, 0.01, "TIDERPEPTIDEK@1/1 PEPTIDER@3/8"),
new SpectrumTuple("/", 1, 2, analysisCount+1, null, 0.02, "KEDITPEPR@2/1 PEPTIDEK@2/8"),
new SpectrumTuple("/", 1, 3, analysisCount+1, null, 0.03, "THEQUICKBR@3/1 THELZYDG@1/8"),
};
TestModel.CreateTestData(session, testPsmSummaryWithoutScores);
// force all peptide instances to fully specific
foreach (PeptideInstance pi in session.Query<PeptideInstance>())
{
pi.NTerminusIsSpecific = pi.CTerminusIsSpecific = true;
session.Update(pi);
}
session.Flush();
session.Close(); // close the connection
sessionFactory.Close();
#endregion
var qonverter = new IDPicker.Qonverter()
{
SettingsByAnalysis = new Dictionary<int, Qonverter.Settings>()
};
for (int i = 1; i <= analysisCount + 1; ++i)
qonverter.SettingsByAnalysis[i] = new Qonverter.Settings()
{
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
ChargeStateHandling = Qonverter.ChargeStateHandling.Ignore,
TerminalSpecificityHandling = Qonverter.TerminalSpecificityHandling.Ignore,
MassErrorHandling = Qonverter.MassErrorHandling.Ignore,
MissedCleavagesHandling = Qonverter.MissedCleavagesHandling.Ignore,
DecoyPrefix = decoyPrefix,
ScoreInfoByName = new Dictionary<string, Qonverter.Settings.ScoreInfo>()
{
{ "score1", new Qonverter.Settings.ScoreInfo() { Weight = 1 } },
{ "score2", new Qonverter.Settings.ScoreInfo() { Weight = 0 } }
}
};
var progressTester = new QonversionProgressTest()
{
Qonverter = qonverter,
ExpectedTotalAnalyses = analysisCount * sourceCount // engine 3 is ignored
};
File.Copy("testStaticQonversion.idpDB", "testStaticQonversion2.idpDB", true);
// test without progress monitor
qonverter.Qonvert("testStaticQonversion2.idpDB");
qonverter.QonversionProgress += new IDPicker.Qonverter.QonversionProgressEventHandler(progressTester.qonverter_QonversionProgress);
File.Copy("testStaticQonversion.idpDB", "testStaticQonversion3.idpDB", true);
// test progress monitor with cancelling
// (must before a full qonversion since the QValue test doesn't expect cancellation)
progressTester.ExpectedQonvertedAnalyses = 0;
progressTester.CancelAtCount = 4;
qonverter.Qonvert("testStaticQonversion3.idpDB");
// test progress monitor without cancelling
progressTester.ExpectedQonvertedAnalyses = 0;
progressTester.CancelAtCount = int.MaxValue;
qonverter.Qonvert("testStaticQonversion.idpDB");
sessionFactory = SessionFactoryFactory.CreateSessionFactory("testStaticQonversion.idpDB");
session = sessionFactory.OpenSession();
session.Clear();
#region QValue test
Dictionary<long, double> expectedQValues = new Dictionary<long, double>()
{
// with high scoring decoys, Q values can spike and gradually go down again;
// we squash these spikes such that Q value is monotonically increasing;
// then we convert Q values to FDR scores using linear interpolation
// targets decoys ambiguous unadjusted-Q-value adjusted-Q-value FDR-score
{ 4, 0 }, // 1 0 0 0 0 0
{ 2, 0.2 }, // 2 0 0 0 0 0.2
{ 3, 0.4 }, // 2 1 0 0.666 0.4 0.4
{ 0, 0.488 }, // 3 1 0 0.5 0.4 0.488
{ 1, 0.577 }, // 4 1 0 0.4 0.4 0.577
{ 5, 0.666 }, // 4 2 0 0.666 0.666 0.666
};
for (long engine = 1; engine <= 2; ++engine)
for (long source = 1; source <= 2; ++source)
for (int charge = 1; charge <= 2; ++charge)
foreach (var itr in expectedQValues)
{
var topRankedMatch = session.CreateQuery("SELECT psm " +
"FROM PeptideSpectrumMatch psm " +
"WHERE psm.Analysis.id = ? " +
" AND psm.Spectrum.Source.id = ? " +
" AND psm.Spectrum.Index = ? " +
" AND psm.Charge = ? " +
" AND psm.Rank = 1" +
"GROUP BY psm.Spectrum.id ")
.SetParameter(0, engine)
.SetParameter(1, source)
.SetParameter(2, itr.Key)
.SetParameter(3, charge)
.List<PeptideSpectrumMatch>().First();
Assert.AreEqual(session.Get<Analysis>(engine), topRankedMatch.Analysis);
Assert.AreEqual(session.Get<SpectrumSource>(source), topRankedMatch.Spectrum.Source);
Assert.AreEqual(charge, topRankedMatch.Charge);
Assert.AreEqual(itr.Value, topRankedMatch.QValue, 1e-3);
}
var scorelessMatches = session.CreateQuery("SELECT psm " +
"FROM PeptideSpectrumMatch psm " +
"WHERE psm.Analysis.id = 3 " +
" AND psm.Rank = 1")
.List<PeptideSpectrumMatch>();
Assert.AreEqual(3, scorelessMatches.Count);
Assert.AreEqual(0.01, scorelessMatches[0].QValue, 1e-12);
Assert.AreEqual(0.02, scorelessMatches[1].QValue, 1e-12);
Assert.AreEqual(0.03, scorelessMatches[2].QValue, 1e-12);
#endregion
}