public void test_protein_grouping_by_sequence()
{
DatabaseReference d1 = new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
});
DatabaseReference d2 = new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
});
DatabaseReference d3 = new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
});
GoTerm g1 = new GoTerm(d1);
GoTerm g2 = new GoTerm(d1);
GoTerm g3 = new GoTerm(d1);
ProteinWithGoTerms p1 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T1", new List <Tuple <string, string> > {
new Tuple <string, string>("", "")
}, new Dictionary <int, List <Modification> >(), new int?[] { 0 }, new int?[] { 0 }, new string[] { "" }, "T2", "T3", true, false, new List <DatabaseReference> {
d1
}, new List <GoTerm> {
g1
});
ProteinWithGoTerms p2 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T2", new List <Tuple <string, string> > {
new Tuple <string, string>("", "")
}, new Dictionary <int, List <Modification> >(), new int?[] { 0 }, new int?[] { 0 }, new string[] { "" }, "T2", "T3", true, false, new List <DatabaseReference> {
d2
}, new List <GoTerm> {
g2
});
ProteinWithGoTerms p3 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T3", new List <Tuple <string, string> > {
new Tuple <string, string>("", "")
}, new Dictionary <int, List <Modification> >(), new int?[] { 0 }, new int?[] { 0 }, new string[] { "" }, "T2", "T3", true, false, new List <DatabaseReference> {
d3
}, new List <GoTerm> {
g3
});
ProteinSequenceGroup psg = new ProteinSequenceGroup(new List <ProteinWithGoTerms> {
p1, p2, p3
}.OrderByDescending(p => p.IsContaminant ? 1 : 0));
Assert.AreEqual(3, psg.GoTerms.Count());
Assert.AreEqual(3, psg.GeneNames.Count());
Assert.AreEqual("T1_3G", psg.Accession);
Assert.False(psg.IsContaminant);
p3 = new ProteinWithGoTerms("MCSSSSSSSSSS", "T3", new List <Tuple <string, string> > {
new Tuple <string, string>("", "")
}, new Dictionary <int, List <Modification> >(), new int?[] { 0 }, new int?[] { 0 }, new string[] { "" }, "T2", "T3", true, false, new List <DatabaseReference> {
d3
}, new List <GoTerm> {
g3
});
ProteinSequenceGroup[] psgs = SaveState.lollipop.theoretical_database.group_proteins_by_sequence(new List <ProteinWithGoTerms> {
p1, p2, p3
});
Assert.AreEqual(2, psgs.Length);
}
public void test_protein_grouping_by_sequence_contaminant()
{
DatabaseReference d1 = new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
});
DatabaseReference d2 = new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
});
DatabaseReference d3 = new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
});
GoTerm g1 = new GoTerm(d1);
GoTerm g2 = new GoTerm(d1);
GoTerm g3 = new GoTerm(d1);
ProteinWithGoTerms p1 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T1", new List <Tuple <string, string> > {
new Tuple <string, string>("", "")
}, new Dictionary <int, List <Modification> >(), new List <ProteolysisProduct> {
new ProteolysisProduct(0, 0, "")
}, "T2", "T3", true, false, new List <DatabaseReference> {
d1
}, new List <GoTerm> {
g1
});
ProteinWithGoTerms p2 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T2", new List <Tuple <string, string> > {
new Tuple <string, string>("", "")
}, new Dictionary <int, List <Modification> >(), new List <ProteolysisProduct> {
new ProteolysisProduct(0, 0, "")
}, "T2", "T3", true, false, new List <DatabaseReference> {
d2
}, new List <GoTerm> {
g2
});
ProteinWithGoTerms p3 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T3", new List <Tuple <string, string> > {
new Tuple <string, string>("", "")
}, new Dictionary <int, List <Modification> >(), new List <ProteolysisProduct> {
new ProteolysisProduct(0, 0, "")
}, "T2", "T3", true, true, new List <DatabaseReference> {
d3
}, new List <GoTerm> {
g3
});
ProteinSequenceGroup psg = new ProteinSequenceGroup(new List <ProteinWithGoTerms> {
p1, p2, p3
}.OrderByDescending(p => p.IsContaminant ? 1 : 0));
Assert.AreEqual(3, psg.GoTerms.Count());
Assert.AreEqual(3, psg.GeneNames.Count());
Assert.AreEqual("T3_3G", psg.Accession);
Assert.True(psg.IsContaminant);
}
