public void test_construct_target_and_decoy_families() { SaveState.lollipop = new Lollipop(); SaveState.lollipop.neucode_labeled = true; ExperimentalProteoform pf1 = ConstructorsForTesting.ExperimentalProteoform("E1", 1000, 5, true); ExperimentalProteoform pf2 = ConstructorsForTesting.ExperimentalProteoform("E2", 1020, 5, true); ExperimentalProteoform pf3 = ConstructorsForTesting.ExperimentalProteoform("E3", 1040, 8, true); ExperimentalProteoform pf4 = ConstructorsForTesting.ExperimentalProteoform("E4", 1050, 5, true); TheoreticalProteoform t1 = ConstructorsForTesting.make_a_theoretical("t1", 1000, 5); TheoreticalProteoform decoy1 = ConstructorsForTesting.make_a_theoretical("Decoy1", 1020, 5); TestProteoformCommunityRelate.prepare_for_et(new List <double>() { 0 }); SaveState.lollipop.target_proteoform_community = new ProteoformCommunity(); SaveState.lollipop.target_proteoform_community.experimental_proteoforms = new ExperimentalProteoform[4] { pf1, pf2, pf3, pf4 }; SaveState.lollipop.target_proteoform_community.theoretical_proteoforms = new TheoreticalProteoform[1] { t1 }; SaveState.lollipop.decoy_proteoform_communities.Add(SaveState.lollipop.decoy_community_name_prefix + "0", new ProteoformCommunity()); SaveState.lollipop.decoy_proteoform_communities[SaveState.lollipop.decoy_community_name_prefix + "0"].experimental_proteoforms = SaveState.lollipop.target_proteoform_community.experimental_proteoforms.Select(e => new ExperimentalProteoform(e)).ToArray(); SaveState.lollipop.decoy_proteoform_communities[SaveState.lollipop.decoy_community_name_prefix + "0"].theoretical_proteoforms = new TheoreticalProteoform[1] { decoy1 }; SaveState.lollipop.et_relations = SaveState.lollipop.target_proteoform_community.relate(SaveState.lollipop.target_proteoform_community.experimental_proteoforms, SaveState.lollipop.target_proteoform_community.theoretical_proteoforms, ProteoformComparison.ExperimentalTheoretical, true, TestContext.CurrentContext.TestDirectory, true); SaveState.lollipop.ee_relations = SaveState.lollipop.target_proteoform_community.relate(SaveState.lollipop.target_proteoform_community.experimental_proteoforms, SaveState.lollipop.target_proteoform_community.experimental_proteoforms, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, true); SaveState.lollipop.relate_ed(); SaveState.lollipop.relate_ef(); foreach (ProteoformRelation pr in SaveState.lollipop.et_relations) { pr.set_nearby_group(SaveState.lollipop.et_relations, SaveState.lollipop.et_relations.Select(r => r.InstanceId).ToList()); } foreach (ProteoformRelation pr in SaveState.lollipop.ee_relations) { pr.set_nearby_group(SaveState.lollipop.ee_relations, SaveState.lollipop.ee_relations.Select(r => r.InstanceId).ToList()); } SaveState.lollipop.et_peaks = SaveState.lollipop.target_proteoform_community.accept_deltaMass_peaks(SaveState.lollipop.et_relations, SaveState.lollipop.ed_relations); SaveState.lollipop.ee_peaks = SaveState.lollipop.target_proteoform_community.accept_deltaMass_peaks(SaveState.lollipop.ee_relations, SaveState.lollipop.ef_relations); //one ED relation Assert.AreEqual(1, SaveState.lollipop.ed_relations.Values.SelectMany(v => v).Count()); Assert.AreEqual(1, SaveState.lollipop.decoy_proteoform_communities[SaveState.lollipop.decoy_community_name_prefix + "0"].theoretical_proteoforms.SelectMany(t => t.relationships).Count()); //peak is unaccepted --> relation should be unaccepted, peak added to relation Assert.IsFalse(SaveState.lollipop.ed_relations.First().Value.FirstOrDefault().Accepted); //should be false if peak unaccepted Assert.AreEqual(1, SaveState.lollipop.et_peaks.Count); Assert.IsNotNull(SaveState.lollipop.ed_relations.Values.SelectMany(v => v).First().peak); //peak is accepted --> relation should be accepted, peak added to relation SaveState.lollipop.clear_et(); SaveState.lollipop.min_peak_count_et = 1; SaveState.lollipop.et_relations = SaveState.lollipop.target_proteoform_community.relate(SaveState.lollipop.target_proteoform_community.experimental_proteoforms, SaveState.lollipop.target_proteoform_community.theoretical_proteoforms, ProteoformComparison.ExperimentalTheoretical, true, TestContext.CurrentContext.TestDirectory, true); SaveState.lollipop.relate_ed(); foreach (ProteoformRelation pr in SaveState.lollipop.et_relations) { pr.set_nearby_group(SaveState.lollipop.et_relations, SaveState.lollipop.et_relations.Select(r => r.InstanceId).ToList()); } foreach (ProteoformRelation pr in SaveState.lollipop.ee_relations) { pr.set_nearby_group(SaveState.lollipop.ee_relations, SaveState.lollipop.ee_relations.Select(r => r.InstanceId).ToList()); } SaveState.lollipop.et_peaks = SaveState.lollipop.target_proteoform_community.accept_deltaMass_peaks(SaveState.lollipop.et_relations, SaveState.lollipop.ed_relations); SaveState.lollipop.et_peaks = SaveState.lollipop.target_proteoform_community.accept_deltaMass_peaks(SaveState.lollipop.et_relations, SaveState.lollipop.ed_relations); Assert.IsTrue(SaveState.lollipop.ed_relations.First().Value.FirstOrDefault().Accepted); //should be true if peak accepted Assert.IsNotNull(SaveState.lollipop.ed_relations.Values.SelectMany(v => v).First().peak); Assert.AreEqual(1, SaveState.lollipop.ed_relations.Values.SelectMany(v => v).Count(r => r.Accepted)); //only 1 relation is in delta mass range of accepted peak - only 1 accepted //2 ef relations, unaccepted because peak unaccepted Assert.AreEqual(3, SaveState.lollipop.ef_relations.Values.SelectMany(v => v).Count()); //2 ef relations Assert.AreEqual(0, SaveState.lollipop.ef_relations.Values.SelectMany(v => v).Count(r => r.Accepted)); //all peaks accepted are false, so relation accepted should be false //one peak accepted --> one of the EF relations falls into range of peak and should be accepted SaveState.lollipop.clear_ee(); SaveState.lollipop.min_peak_count_ee = 1; SaveState.lollipop.ee_relations = SaveState.lollipop.target_proteoform_community.relate(SaveState.lollipop.target_proteoform_community.experimental_proteoforms, SaveState.lollipop.target_proteoform_community.experimental_proteoforms, ProteoformComparison.ExperimentalExperimental, true, TestContext.CurrentContext.TestDirectory, true); SaveState.lollipop.relate_ef(); SaveState.lollipop.ee_peaks = SaveState.lollipop.target_proteoform_community.accept_deltaMass_peaks(SaveState.lollipop.ee_relations, SaveState.lollipop.ef_relations); Assert.AreEqual(3, SaveState.lollipop.ee_peaks.Count(p => p.Accepted)); Assert.AreEqual(3, SaveState.lollipop.ee_relations.Count); Assert.AreEqual(1, SaveState.lollipop.ef_relations.Values.SelectMany(v => v).Count(r => r.Accepted)); //only 1 relation is in delta mass range of accepted peak - only 1 accepted SaveState.lollipop.construct_target_and_decoy_families(); //should be 2 target families and 3 decoy families //only make decoy relations out of accepted relations --> 1 family with accepted relations Assert.AreEqual(2, SaveState.lollipop.target_proteoform_community.families.Count); Assert.AreEqual(3, SaveState.lollipop.decoy_proteoform_communities[SaveState.lollipop.decoy_community_name_prefix + "0"].families.Count); Assert.AreEqual(1, SaveState.lollipop.decoy_proteoform_communities[SaveState.lollipop.decoy_community_name_prefix + "0"].families.Count(f => f.relations.Count > 0)); Assert.AreEqual(2, SaveState.lollipop.decoy_proteoform_communities[SaveState.lollipop.decoy_community_name_prefix + "0"].families.SelectMany(f => f.relations).Count()); }
public void TestDeltaMassPeakConstructorWithNotches() { Sweet.lollipop = new Lollipop(); Sweet.lollipop.et_use_notch = true; Sweet.lollipop.enter_input_files(new string[] { Path.Combine(TestContext.CurrentContext.TestDirectory, "ptmlist.txt") }, Lollipop.acceptable_extensions[2], Lollipop.file_types[2], Sweet.lollipop.input_files, false); ConstructorsForTesting.read_mods(); Sweet.lollipop.et_high_mass_difference = 250; Sweet.lollipop.et_low_mass_difference = -250; ExperimentalProteoform pf1 = ConstructorsForTesting.ExperimentalProteoform("acession1"); TheoreticalProteoform pf2 = ConstructorsForTesting.make_a_theoretical(); pf1.modified_mass = 1000; ProteoformComparison relation_type = ProteoformComparison.ExperimentalTheoretical; double delta_mass = 1 - 1e-7; ExperimentalProteoform pf3 = ConstructorsForTesting.ExperimentalProteoform("acession3"); TheoreticalProteoform pf4 = ConstructorsForTesting.make_a_theoretical(); pf3.modified_mass = 1000; ProteoformComparison relation_type2 = ProteoformComparison.ExperimentalTheoretical; double delta_mass2 = 1; ExperimentalProteoform pf5 = ConstructorsForTesting.ExperimentalProteoform("acession5"); TheoreticalProteoform pf6 = ConstructorsForTesting.make_a_theoretical(); pf5.modified_mass = 1000; ProteoformComparison relation_type3 = ProteoformComparison.ExperimentalTheoretical; double delta_mass3 = 1 + 1e-7; ExperimentalProteoform pf55 = ConstructorsForTesting.ExperimentalProteoform("acession5"); TheoreticalProteoform pf65 = ConstructorsForTesting.make_a_theoretical(); pf55.modified_mass = 1000; ProteoformComparison relation_type35 = ProteoformComparison.ExperimentalTheoretical; double delta_mass35 = 1 + 2e-7; TestProteoformCommunityRelate.prepare_for_et(new List <double>() { 1 }); List <ProteoformRelation> theList = new List <ProteoformRelation>(); theList.Add(new ProteoformRelation(pf1, pf2, relation_type, delta_mass, TestContext.CurrentContext.TestDirectory)); theList.Add(new ProteoformRelation(pf3, pf4, relation_type2, delta_mass2, TestContext.CurrentContext.TestDirectory)); theList.Add(new ProteoformRelation(pf5, pf6, relation_type3, delta_mass3, TestContext.CurrentContext.TestDirectory)); theList.Add(new ProteoformRelation(pf55, pf65, relation_type35, delta_mass35, TestContext.CurrentContext.TestDirectory)); ProteoformRelation base_relation = new ProteoformRelation(pf3, pf4, relation_type2, delta_mass2, TestContext.CurrentContext.TestDirectory); //base_relation.nearby_relations = base_relation.set_nearby_group(theList, theList.Select(r => r.InstanceId).ToList()); Console.WriteLine("Creating deltaMassPeak"); DeltaMassPeak deltaMassPeak = new DeltaMassPeak(base_relation, new HashSet <ProteoformRelation>(theList)); Console.WriteLine("Created deltaMassPeak"); Assert.AreEqual(0, deltaMassPeak.peak_group_fdr); Assert.AreEqual(4, deltaMassPeak.grouped_relations.Count); Assert.AreEqual("[fake1]", deltaMassPeak.possiblePeakAssignments_string); Assert.AreEqual(1.0, deltaMassPeak.DeltaMass); Dictionary <string, List <ProteoformRelation> > decoy_relations = new Dictionary <string, List <ProteoformRelation> >(); decoy_relations["decoyDatabase1"] = new List <ProteoformRelation>(); ExperimentalProteoform pf7 = ConstructorsForTesting.ExperimentalProteoform("experimental1"); TheoreticalProteoform pf8 = ConstructorsForTesting.make_a_theoretical(); pf7.modified_mass = 1000; ProteoformComparison relation_type4 = ProteoformComparison.ExperimentalDecoy; double delta_mass4 = 1; ProteoformRelation decoy_relation = new ProteoformRelation(pf7, pf8, relation_type4, delta_mass4, TestContext.CurrentContext.TestDirectory); decoy_relations["decoyDatabase1"].Add(decoy_relation); deltaMassPeak.calculate_fdr(decoy_relations); Assert.AreEqual(0.25, deltaMassPeak.peak_group_fdr); // 1 decoy database, (1 decoy relation, median=1), 4 target relations decoy_relations["decoyDatabase2"] = new List <ProteoformRelation>(); decoy_relations["decoyDatabase2"].Add(decoy_relation); decoy_relations["decoyDatabase2"].Add(decoy_relation); deltaMassPeak.calculate_fdr(decoy_relations); Assert.AreEqual(0.375, deltaMassPeak.peak_group_fdr); // 2 decoy databases (1 & 2 decoy relations, median=1.5), 4 target relations }
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); }