public static TheoreticalProteoform make_a_theoretical(string a, double mass, int lysine_count)
{
ModificationMotif motif;
ModificationMotif.TryGetMotif("X", out motif);
Modification unmodification = new Modification("Unmodified", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 0);
ProteinWithGoTerms p1 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T1", new List <Tuple <string, string> > {
new Tuple <string, string>("", "")
}, new Dictionary <int, List <Modification> > {
{ 0, new List <Modification> {
unmodification
} }
}, new List <ProteolysisProduct> {
new ProteolysisProduct(1, 12, "")
}, "T2", "T3", true, false, new List <DatabaseReference> {
new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
})
}, new List <GoTerm> {
new GoTerm(new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
}))
});
PtmSet set = new PtmSet(new List <Ptm> {
new Ptm()
});
var t = new TheoreticalProteoform(a, "", p1.BaseSequence, new List <ProteinWithGoTerms> {
p1
}, mass, lysine_count, set, true, false, new Dictionary <InputFile, Protein[]>());
t.modified_mass = mass;
return(t);
}
public static TheoreticalProteoform make_a_theoretical(string a, string d, double mass, ProteinWithGoTerms p, Dictionary <InputFile, Protein[]> dict)
{
ModificationMotif motif;
ModificationMotif.TryGetMotif("X", out motif);
string mod_title = "oxidation";
Modification m = new Modification(mod_title, _modificationType: "modtype", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1);
ProteinWithGoTerms p1 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T1", new List <Tuple <string, string> > {
new Tuple <string, string>("ordered locus", "GENE")
}, new Dictionary <int, List <Modification> > {
{ 1, new List <Modification> {
m
} }
}, new List <ProteolysisProduct> {
new ProteolysisProduct(1, 12, "")
}, "T2", "T3", true, false, new List <DatabaseReference> {
new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
})
}, new List <GoTerm> {
new GoTerm(new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
}))
});
PtmSet set = new PtmSet(new List <Ptm> {
new Ptm(0, m)
});
return(new TheoreticalProteoform(a, d, p1.BaseSequence, new List <ProteinWithGoTerms> {
p
}, mass, 0, set, true, false, dict));
}
public static TheoreticalProteoform make_a_theoretical(string a, string d, double mass, ProteinWithGoTerms p, Dictionary <InputFile, Protein[]> dict)
{
ModificationMotif motif;
ModificationMotif.TryGetMotif("K", out motif);
string mod_title = "oxidation";
ModificationWithMass m = new ModificationWithMass(mod_title, new Tuple <string, string>("", mod_title), motif, ModificationSites.K, 1, new Dictionary <string, IList <string> >(), new List <double>(), new List <double>(), "");
ProteinWithGoTerms p1 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T1", new List <Tuple <string, string> > {
new Tuple <string, string>("ordered locus", "GENE")
}, new Dictionary <int, List <Modification> > {
{ 1, new List <Modification> {
m
} }
}, new int?[] { 0 }, new int?[] { 0 }, new string[] { "" }, "T2", "T3", true, false, new List <DatabaseReference> {
new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
})
}, new List <GoTerm> {
new GoTerm(new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
}))
});
PtmSet set = new PtmSet(new List <Ptm> {
new Ptm(0, m)
});
return(new TheoreticalProteoform(a, d, new List <ProteinWithGoTerms> {
p
}, mass, 0, set, true, false, dict));
}
//MAKE THEORETICAL
public static TheoreticalProteoform make_a_theoretical(string a, ProteinWithGoTerms p, Dictionary <InputFile, Protein[]> dict)
{
ModificationMotif motif;
ModificationMotif.TryGetMotif("K", out motif);
PtmSet set = new PtmSet(p.OneBasedPossibleLocalizedModifications.SelectMany(m => m.Value.OfType <ModificationWithMass>().SelectMany(mmm => new List <Ptm> {
new Ptm(0, mmm)
})).ToList());
return(new TheoreticalProteoform(a, "", new List <ProteinWithGoTerms> {
p
}, 100, 0, set, true, true, dict));
}
//MAKE THEORETICAL
public static TheoreticalProteoform make_a_theoretical(string a, ProteinWithGoTerms p, Dictionary <InputFile, Protein[]> dict)
{
ModificationMotif motif;
ModificationMotif.TryGetMotif("X", out motif);
PtmSet set = new PtmSet(p.OneBasedPossibleLocalizedModifications.SelectMany(m => m.Value.SelectMany(mmm => new List <Ptm> {
new Ptm(0, mmm)
})).ToList());
TheoreticalProteoform t = new TheoreticalProteoform(a, "", p.BaseSequence, new List <ProteinWithGoTerms> {
p
}, 100, 0, set, true, true, dict);
t.begin = 1;
t.end = 4;
return(t);
}
public void test_same_ptmset()
{
PtmSet set1 = new PtmSet(new List <Ptm>()
{
new Ptm(1, ConstructorsForTesting.get_modWithMass("id1", 5)),
new Ptm(2, ConstructorsForTesting.get_modWithMass("id2", 6)),
new Ptm(2, ConstructorsForTesting.get_modWithMass("id4", 6))
});
PtmSet set2 = new PtmSet(new List <Ptm>()
{
new Ptm(1, ConstructorsForTesting.get_modWithMass("id1", 5)),
new Ptm(2, ConstructorsForTesting.get_modWithMass("id2", 6)),
new Ptm(2, ConstructorsForTesting.get_modWithMass("id4", 6))
});
Assert.IsTrue(set1.same_ptmset(set2, true));
Assert.IsTrue(set1.same_ptmset(set2, false));
set2 = new PtmSet(new List <Ptm>()
{
new Ptm(1, ConstructorsForTesting.get_modWithMass("id1", 5)),
new Ptm(2, ConstructorsForTesting.get_modWithMass("id2", 6)),
new Ptm(2, ConstructorsForTesting.get_modWithMass("id3", 6))
});
Assert.IsFalse(set1.same_ptmset(set2, true));
Assert.IsFalse(set1.same_ptmset(set2, false));
Assert.IsFalse(set2.same_ptmset(set1, true));
Assert.IsFalse(set2.same_ptmset(set1, false));
set2 = new PtmSet(new List <Ptm>()
{
new Ptm(1, ConstructorsForTesting.get_modWithMass("id1", 5)),
new Ptm(2, ConstructorsForTesting.get_modWithMass("id2", 6)),
});
Assert.IsFalse(set1.same_ptmset(set2, true));
Assert.IsFalse(set1.same_ptmset(set2, false));
Assert.IsFalse(set2.same_ptmset(set1, true));
Assert.IsFalse(set2.same_ptmset(set1, false));
}
public static TheoreticalProteoform make_a_theoretical(string a, double mass, int lysine_count)
{
ModificationWithMass unmodification = new ModificationWithMass("Unmodified", new Tuple <string, string>("N/A", "Unmodified"), null, ModificationSites.Any, 0, null, null, null, null);
ProteinWithGoTerms p1 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T1", new List <Tuple <string, string> > {
new Tuple <string, string>("", "")
}, new Dictionary <int, List <Modification> > {
{ 0, new List <Modification> {
unmodification
} }
}, new int?[] { 0 }, new int?[] { 0 }, new string[] { "" }, "T2", "T3", true, false, new List <DatabaseReference> {
new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
})
}, new List <GoTerm> {
new GoTerm(new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
}))
});
PtmSet set = new PtmSet(new List <Ptm>());
return(new TheoreticalProteoform(a, "", new List <ProteinWithGoTerms> {
p1
}, mass, lysine_count, set, true, false, new Dictionary <InputFile, Protein[]>()));
}
public void TestRelateTD()
{
Sweet.lollipop = new Lollipop();
Sweet.lollipop.neucode_labeled = false;
Sweet.lollipop.maximum_missed_monos = 1;
Sweet.lollipop.agg_minBiorepsWithObservations = 0;
InputFile f = new InputFile("path", Purpose.Identification);
Sweet.lollipop.input_files.Add(f);
// Two proteoforms; lysine count equal; mass difference < 250 -- return 1
Component c1 = new Component();
c1.weighted_monoisotopic_mass = 1000.0;
c1.rt_apex = 45;
c1.accepted = true;
c1.id = 1.ToString();
c1.intensity_sum = 1e6;
c1.input_file = f;
c1.charge_states = new List <ChargeState>()
{
new ChargeState(1, c1.intensity_sum, c1.weighted_monoisotopic_mass)
};
Component c2 = new Component();
c2.weighted_monoisotopic_mass = 1000.0;
c2.rt_apex = 85;
c2.accepted = true;
c2.input_file = f;
c2.intensity_sum = 1e6;
c2.charge_states = new List <ChargeState>()
{
new ChargeState(1, c2.intensity_sum, c2.weighted_monoisotopic_mass)
};
c2.id = 2.ToString();
Component c3 = new Component();
c3.weighted_monoisotopic_mass = 1131.04;
c3.rt_apex = 45;
c3.accepted = true;
c3.input_file = f;
c3.intensity_sum = 1e6;
c3.charge_states = new List <ChargeState>()
{
new ChargeState(1, c3.intensity_sum, c3.weighted_monoisotopic_mass)
};
c3.id = 3.ToString();
Component c4 = new Component();
c4.weighted_monoisotopic_mass = 2000.00;
c4.rt_apex = 45;
c4.accepted = true;
c4.input_file = new InputFile("path", Purpose.Identification);
c4.intensity_sum = 1e6;
c4.charge_states = new List <ChargeState>()
{
new ChargeState(1, c4.intensity_sum, c4.weighted_monoisotopic_mass)
};
c4.id = 4.ToString();
Component c5 = new Component();
c5.weighted_monoisotopic_mass = 1001.0;
c5.rt_apex = 45;
c5.accepted = true;
c5.input_file = f;
c5.intensity_sum = 1e6;
c5.charge_states = new List <ChargeState>()
{
new ChargeState(1, c5.intensity_sum, c5.weighted_monoisotopic_mass)
};
c5.id = 2.ToString();
List <IAggregatable> components = new List <IAggregatable>()
{
c1, c2, c3, c4, c5
};
Sweet.lollipop.raw_experimental_components = components.OfType <Component>().ToList();
TopDownProteoform td1 = ConstructorsForTesting.TopDownProteoform("ACCESSION_1", 1000.0, 45);
TopDownProteoform td2 = ConstructorsForTesting.TopDownProteoform("ACCESSION_2", 1001.0, 85);
TopDownProteoform td3 = ConstructorsForTesting.TopDownProteoform("ACCESSION_3", 1131.04, 45);
TheoreticalProteoform t1 = ConstructorsForTesting.make_a_theoretical("ACCESSION", 1000.0, 1);
//need to make theoretical accession database
TestProteoformCommunityRelate.prepare_for_et(new List <double>()
{
0
});
Sweet.lollipop.target_proteoform_community.community_number = -100;
Sweet.lollipop.theoretical_database.theoreticals_by_accession = new Dictionary <int, Dictionary <string, List <TheoreticalProteoform> > >();
Sweet.lollipop.theoretical_database.theoreticals_by_accession.Add(-100, new Dictionary <string, List <TheoreticalProteoform> >());
Sweet.lollipop.theoretical_database.theoreticals_by_accession[-100].Add(t1.accession, new List <TheoreticalProteoform>()
{
t1
});
//need to make decon error top "deconvolution error"
ModificationMotif motif;
ModificationMotif.TryGetMotif("S", out motif);
Modification m = new Modification("id", _modificationType: "modtype", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1);
Sweet.lollipop.theoretical_database.all_mods_with_mass.Add(m);
PtmSet set = new PtmSet(new List <Ptm> {
new Ptm(-1, m)
});
Sweet.lollipop.theoretical_database.all_possible_ptmsets.Add(set);
Sweet.lollipop.modification_ranks.Add(-1.0023, 2);
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary.Add(-1.0, new List <PtmSet>()
{
set
});
//need missing error
Modification m2 = new Modification("id", _modificationType: "modtype", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1);
Sweet.lollipop.theoretical_database.all_mods_with_mass.Add(m2);
PtmSet set2 = new PtmSet(new List <Ptm> {
new Ptm(-1, m2)
});
Sweet.lollipop.theoretical_database.all_possible_ptmsets.Add(set2);
Sweet.lollipop.modification_ranks.Add(-87.03, 2);
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary.Add(-87.0, new List <PtmSet>()
{
set2
});
Sweet.lollipop.target_proteoform_community.theoretical_proteoforms = new List <TheoreticalProteoform>()
{
t1
}.ToArray();
Sweet.lollipop.topdown_proteoforms = new List <TopDownProteoform> {
td1, td2, td3
};
Sweet.lollipop.add_td_proteoforms = true;
Sweet.lollipop.aggregate_proteoforms(Sweet.lollipop.validate_proteoforms, Sweet.lollipop.raw_neucode_pairs, Sweet.lollipop.raw_experimental_components, Sweet.lollipop.raw_quantification_components, 0);
List <ProteoformRelation> relations = Sweet.lollipop.target_proteoform_community.relate(Sweet.lollipop.target_proteoform_community.experimental_proteoforms, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms, ProteoformComparison.ExperimentalTheoretical, true, Environment.CurrentDirectory, true);
List <DeltaMassPeak> peaks = Sweet.lollipop.target_proteoform_community.accept_deltaMass_peaks(relations, new Dictionary <string, List <ProteoformRelation> >());
//should have 4 experimental proteoforms -- 3 topdown, 1 not topdown experimental
Assert.AreEqual(3, Sweet.lollipop.target_proteoform_community.experimental_proteoforms.Count(e => e.topdown_id));
Assert.AreEqual(4, Sweet.lollipop.target_proteoform_community.experimental_proteoforms.Count());
Assert.AreEqual(1, relations.Count);
Assert.AreEqual(1, relations.Count(r => r.RelationType == ProteoformComparison.ExperimentalTheoretical && (r.connected_proteoforms[0] as ExperimentalProteoform).topdown_id));
Assert.AreEqual(1, td1.relationships.Count(r => r.RelationType == ProteoformComparison.ExperimentalTheoretical && (r.connected_proteoforms[0] as ExperimentalProteoform).topdown_id));
Assert.AreEqual(0, td2.relationships.Count());
Assert.AreEqual(0, td3.relationships.Count());
//accession 3 has higher score... gets td
Sweet.lollipop.clear_td();
td3 = ConstructorsForTesting.TopDownProteoform("ACCESSION_3", 1000.0, 45);
TopDownHit h3 = new TopDownHit();
h3.score = 100;
td3.topdown_hits = new List <TopDownHit>()
{
h3
};
TopDownHit h4 = new TopDownHit();
h4.score = 1;
TopDownProteoform td4 = ConstructorsForTesting.TopDownProteoform("ACCESSION_4", 1001.0, 45);
td4.topdown_hits = new List <TopDownHit>()
{
h4
};
Sweet.lollipop.topdown_proteoforms = new List <TopDownProteoform> {
td4, td3
};
Sweet.lollipop.topdown_proteoforms.OrderBy(p => p.modified_mass);
Sweet.lollipop.aggregate_proteoforms(Sweet.lollipop.validate_proteoforms, Sweet.lollipop.raw_neucode_pairs, Sweet.lollipop.raw_experimental_components, Sweet.lollipop.raw_quantification_components, 0);
Assert.AreEqual(0, Math.Round(td3.modified_mass - td3.matching_experimental.modified_mass, 0));
Assert.IsNull(td4.matching_experimental);
}
