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 TestMergerModel()
{
#region Example proteins
string[] testProteinSequences = new string[]
{
"PEPTIDERPEPTIDEKPEPTIDE",
"TIDERPEPTIDEKPEP",
"RPEPKTIDERPEPKTIDE",
"EDITPEPKEDITPEPR",
"PEPREDITPEPKEDIT",
"EPPIERPETPDETKTDPEPIIRDE"
};
#endregion
#region Example PSMs
List <SpectrumTuple> mergeSourcePsmSummary1 = new List <SpectrumTuple>()
{
// Group Source Spectrum Analysis Score Q List of Peptide@Charge/ScoreDivider
new SpectrumTuple("/A/1", 1, 1, 1, 12, 0, "[C2H2O1]PEPTIDE@2/1 TIDERPEPTIDEK@4/2 EPPIER@1/3"),
new SpectrumTuple("/A/1", 1, 2, 1, 23, 0, "PEPTIDER@2/1 PETPDETK@3/3 EDITPEPK@2/5"),
new SpectrumTuple("/A/1", 1, 3, 1, 34, 0, "PEPTIDEK@2/1 TIDER@1/4 PETPDETK@2/8"),
new SpectrumTuple("/A/1", 2, 1, 1, 43, 0, "PEPTIDE@2/1 E[H-2O-1]DIT[P1O4]PEPR@2/2 EPPIER@1/7"),
new SpectrumTuple("/A/1", 2, 2, 1, 32, 0, "PEPTIDER@3/1 EDITPEPK@3/4 EDITPEPR@3/5"),
new SpectrumTuple("/A/1", 2, 3, 1, 21, 0, "PEPT[P1O4]IDEK@3/1 TIDEK@1/7 PETPDETK@2/8"),
new SpectrumTuple("/A/2", 3, 1, 1, 56, 0, "TIDEK@2/1 TIDE@1/2 P[P1O4]EPTIDE@3/3"),
new SpectrumTuple("/A/2", 3, 2, 1, 45, 0, "TIDER@2/1 TIDERPEPTIDEK@4/3 PEPTIDEK@3/4"),
new SpectrumTuple("/A/2", 3, 3, 1, 34, 0, "TIDE@1/1 PEPTIDEK@3/6 TIDEK@1/7"),
new SpectrumTuple("/B/1", 4, 1, 1, 65, 0, "TIDERPEPTIDEK@4/1 PETPDETK@3/8 EDITPEPR@3/9"),
new SpectrumTuple("/B/1", 4, 2, 1, 53, 0, "E[H-2O-1]DITPEPK@2/1 PEPTIDEK@3/2 PEPTIDE@2/3"),
new SpectrumTuple("/B/1", 4, 3, 1, 42, 0, "EDIT@2/1 PEPTIDEK@3/3 EDITPEPR@2/4"),
new SpectrumTuple("/B/2", 5, 1, 1, 20, 0, "EPPIER@2/1 TIDE@1/7 PEPTIDE@2/9"),
new SpectrumTuple("/B/2", 5, 2, 1, 24, 0, "PETPDETK@2/1 PEPTIDEK@3/5 EDITPEPR@2/8"),
new SpectrumTuple("/B/2", 5, 3, 1, 24, 0, "PETPDETK@3/1 EDIT@1/4 TIDER@2/6"),
};
List <SpectrumTuple> mergeSourcePsmSummary2 = new List <SpectrumTuple>()
{
new SpectrumTuple("/A/1", 1, 1, 2, 120, 0, "TIDERPEPTIDEK@4/1 PEPTIDE@2/2 EPPIER@1/3"),
new SpectrumTuple("/A/1", 1, 2, 2, 230, 0, "PEPTIDER@2/1 PETPDETK@3/3 EDITPEPK@2/5"),
new SpectrumTuple("/A/1", 1, 3, 2, 340, 0, "PEPTIDEK@2/1 TIDER@1/4 PETPDETK@2/8"),
new SpectrumTuple("/A/1", 2, 1, 2, 430, 0, "PEPTIDE@2/1 EDITPEPR@2/2 EPPIER@1/7"),
new SpectrumTuple("/A/1", 2, 2, 2, 320, 0, "PEPTIDER@3/1 EDITPEPK@3/4 EDITPEPR@3/5"),
new SpectrumTuple("/A/1", 2, 3, 2, 210, 0, "PEPT[P1O4]IDEK@3/1 TIDEK@1/7 PETPDETK@2/8"),
new SpectrumTuple("/A/2", 3, 1, 2, 560, 0, "TIDEK@2/1 TIDE@1/2 PEPTIDE@3/3"),
new SpectrumTuple("/A/2", 3, 2, 2, 450, 0, "TIDER@2/1 TIDERPEPTIDEK@4/3 PEPTIDEK@3/4"),
new SpectrumTuple("/A/2", 3, 3, 2, 340, 0, "TIDE@1/1 PEPTIDEK@3/6 TIDEK@1/7"),
new SpectrumTuple("/B/1", 4, 1, 2, 650, 0, "TIDERPEPTIDEK@4/1 PET[P1O4]PDETK@3/8 EDITPEPR@3/9"),
new SpectrumTuple("/B/1", 4, 2, 2, 530, 0, "EDITPEPK@2/1 PEPTIDEK@3/2 PEPTIDE@2/3"),
new SpectrumTuple("/B/1", 4, 3, 2, 420, 0, "EDIT@2/1 PEPTIDEK@3/3 EDITPEPR@2/4"),
new SpectrumTuple("/B/2", 5, 1, 2, 200, 0, "E[H-2O-1]PPIER@2/1 TIDE@1/7 PEPTIDE@2/9"),
new SpectrumTuple("/B/2", 5, 2, 2, 240, 0, "PEPTIDEK@2/1 PETPDETK@2/4 EDITPEPR@2/8"),
new SpectrumTuple("/B/2", 5, 3, 2, 240, 0, "PETPDETK@3/1 EDIT@1/4 TIDER@2/6"),
};
var qonverterSettings1 = new QonverterSettings()
{
QonverterMethod = Qonverter.QonverterMethod.StaticWeighted,
DecoyPrefix = "quiRKy",
RerankMatches = true,
ScoreInfoByName = new Dictionary <string, Qonverter.Settings.ScoreInfo>()
{
{ "score1", new Qonverter.Settings.ScoreInfo()
{
Weight = 1,
Order = Qonverter.Settings.Order.Ascending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Linear
} },
{ "score2", new Qonverter.Settings.ScoreInfo()
{
Weight = 42,
Order = Qonverter.Settings.Order.Descending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Quantile
} }
}
};
var qonverterSettings2 = new QonverterSettings()
{
QonverterMethod = Qonverter.QonverterMethod.SVM,
DecoyPrefix = "___---",
RerankMatches = false,
ScoreInfoByName = new Dictionary <string, Qonverter.Settings.ScoreInfo>()
{
{ "foo", new Qonverter.Settings.ScoreInfo()
{
Weight = 7,
Order = Qonverter.Settings.Order.Ascending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Off
} },
{ "bar", new Qonverter.Settings.ScoreInfo()
{
Weight = 11,
Order = Qonverter.Settings.Order.Descending,
NormalizationMethod = Qonverter.Settings.NormalizationMethod.Off
} }
}
};
#endregion
File.Delete("testMergeSource1.idpDB");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource1.idpDB", new SessionFactoryConfig {
CreateSchema = true
}))
using (var session = sessionFactory.OpenSession())
{
TestModel.CreateTestProteins(session, testProteinSequences);
TestModel.CreateTestData(session, mergeSourcePsmSummary1);
TestModel.AddSubsetPeakData(session);
qonverterSettings1.Analysis = session.UniqueResult <Analysis>(o => o.Software.Name == "Engine 1");
session.Save(qonverterSettings1);
session.Flush();
}
File.Delete("testMergeSource2.idpDB");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource2.idpDB", new SessionFactoryConfig {
CreateSchema = true
}))
using (var session = sessionFactory.OpenSession())
{
TestModel.CreateTestProteins(session, testProteinSequences);
TestModel.CreateTestData(session, mergeSourcePsmSummary2);
TestModel.AddSubsetPeakData(session);
// copy is required because session.Save() takes ownership of the instance
var qonverterSettings2Copy = new QonverterSettings()
{
Analysis = session.UniqueResult <Analysis>(o => o.Software.Name == "Engine 2"),
QonverterMethod = qonverterSettings2.QonverterMethod,
DecoyPrefix = qonverterSettings2.DecoyPrefix,
RerankMatches = qonverterSettings2.RerankMatches,
ScoreInfoByName = qonverterSettings2.ScoreInfoByName
};
session.Save(qonverterSettings2Copy);
session.Flush();
}
// create a new merged idpDB from two idpDB files
File.Delete("testMerger.idpDB");
Merger.Merge("testMerger.idpDB", new string[] { "testMergeSource1.idpDB", "testMergeSource2.idpDB" });
var testModel = new TestModel();
// test that testMerger.idpDB passes the TestModel tests
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMerger.idpDB"))
using (var session = testModel.session = sessionFactory.OpenSession())
{
testModel.TestOverallCounts();
testModel.TestSanity();
testModel.TestProteins();
testModel.TestPeptides();
testModel.TestPeptideInstances();
testModel.TestSpectrumSourceGroups();
testModel.TestSpectrumSources(false);
testModel.TestSpectra(false);
testModel.TestAnalyses();
testModel.TestPeptideSpectrumMatches();
testModel.TestModifications();
testModel.TestQonverterSettings();
}
// create an in-memory representation of testMergeSource2
var memoryFactory = SessionFactoryFactory.CreateSessionFactory(":memory:", new SessionFactoryConfig {
CreateSchema = true
});
var memoryConnection = SessionFactoryFactory.CreateFile(":memory:");
var memorySession = memoryFactory.OpenSession(memoryConnection);
{
TestModel.CreateTestProteins(memorySession, testProteinSequences);
TestModel.CreateTestData(memorySession, mergeSourcePsmSummary2);
TestModel.AddSubsetPeakData(memorySession);
qonverterSettings2.Analysis = memorySession.UniqueResult <Analysis>(o => o.Software.Name == "Engine 2");
memorySession.Save(qonverterSettings2);
memorySession.Flush();
}
// merge the in-memory connection into the testMergeSource1 file
/*Merger.Merge("testMergeSource1.idpDB", memoryConnection as System.Data.SQLite.SQLiteConnection);
*
* // testMergeSource1.idpDB should pass just like testMerger.idpDB
* using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory("testMergeSource1.idpDB"))
* using (var session = testModel.session = sessionFactory.OpenSession())
* {
* testModel.TestOverallCounts();
* testModel.TestSanity();
* testModel.TestProteins();
* testModel.TestPeptides();
* testModel.TestPeptideInstances();
* testModel.TestSpectrumSourceGroups();
* testModel.TestSpectrumSources(false);
* testModel.TestSpectra(false);
* testModel.TestAnalyses();
* testModel.TestPeptideSpectrumMatches();
* testModel.TestModifications();
* testModel.TestQonverterSettings();
* }*/
}
