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();
* }*/
}
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();
}*/
}
