######################################################################### # MacSyFinder - Detection of macromolecular systems in protein dataset # # using systems modelling and similarity search. # # Authors: Sophie Abby, Bertrand Neron # # Copyright (c) 2014-2024 Institut Pasteur (Paris) and CNRS. # # See the COPYRIGHT file for details # # # # This file is part of MacSyFinder package. # # # # MacSyFinder is free software: you can redistribute it and/or modify # # it under the terms of the GNU General Public License as published by # # the Free Software Foundation, either version 3 of the License, or # # (at your option) any later version. # # # # MacSyFinder is distributed in the hope that it will be useful, # # but WITHOUT ANY WARRANTY; without even the implied warranty of # # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # GNU General Public License for more details . # # # # You should have received a copy of the GNU General Public License # # along with MacSyFinder (COPYING). # # If not, see . # ######################################################################### import os import argparse from macsypy.hit import CoreHit, ModelHit, Loner, MultiSystem, LonerMultiSystem, HitWeight from macsypy.config import Config, MacsyDefaults from macsypy.gene import CoreGene, ModelGene, Exchangeable, GeneStatus from macsypy.profile import ProfileFactory from macsypy.model import Model from macsypy.registries import ModelLocation from macsypy.cluster import Cluster from macsypy.system import System, HitSystemTracker from macsypy.error import MacsypyError from tests import MacsyTest class SystemTest(MacsyTest): def setUp(self) -> None: args = argparse.Namespace() args.sequence_db = self.find_data("base", "test_1.fasta") args.db_type = 'gembase' args.models_dir = self.find_data('models') args.verbosity = 3 self.cfg = Config(MacsyDefaults(), args) self.model_name = 'foo' self.model_location = ModelLocation(path=os.path.join(args.models_dir, self.model_name)) self.profile_factory = ProfileFactory(self.cfg) self.hit_weights = HitWeight(**self.cfg.hit_weights()) def test_init(self): model = Model("foo/T2SS", 10) # test if id is well incremented c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model) model.add_mandatory_gene(gene_gspd) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) model.add_accessory_gene(gene_sctj) hit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_1 = ModelHit(hit_1, gene_gspd, GeneStatus.MANDATORY) hit_2 = CoreHit(c_gene_sctj, "hit_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_2 = ModelHit(hit_2, gene_sctj, GeneStatus.ACCESSORY) system_1 = System(model, [Cluster([v_hit_1, v_hit_2], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertTrue(system_1.id.startswith('replicon_id_T2SS_')) system_2 = System(model, [Cluster([v_hit_1, v_hit_2], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(int(system_2.id.split('_')[-1]), int(system_1.id.split('_')[-1]) + 1) def test_hits(self): model = Model("foo/T2SS", 10) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model) model.add_mandatory_gene(gene_gspd) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) model.add_accessory_gene(gene_sctj) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model) model.add_accessory_gene(gene_sctn) hit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_1 = ModelHit(hit_1, gene_gspd, GeneStatus.MANDATORY) hit_2 = CoreHit(c_gene_sctj, "hit_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_2 = ModelHit(hit_2, gene_sctj, GeneStatus.ACCESSORY) hit_3 = CoreHit(c_gene_sctn, "hit_3", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_3 = ModelHit(hit_3, gene_sctn, GeneStatus.ACCESSORY) system_1 = System(model, [Cluster([v_hit_1, v_hit_2], model, self.hit_weights), Cluster([v_hit_3], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(system_1.hits, [v_hit_1, v_hit_2, v_hit_3]) def test_position(self): model = Model("foo/mod1", 10) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model) model.add_mandatory_gene(gene_gspd) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) model.add_accessory_gene(gene_sctj) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model, loner=True) model.add_accessory_gene(gene_sctn) hit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 10, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_1 = ModelHit(hit_1, gene_gspd, GeneStatus.MANDATORY) hit_2 = CoreHit(c_gene_sctj, "hit_2", 803, "replicon_id", 20, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_2 = ModelHit(hit_2, gene_sctj, GeneStatus.ACCESSORY) hit_3 = CoreHit(c_gene_sctn, "hit_3", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_3 = ModelHit(hit_3, gene_sctn, GeneStatus.ACCESSORY) system_1 = System(model, [Cluster([v_hit_1, v_hit_2], model, self.hit_weights), Cluster([v_hit_3], model, self.hit_weights)], self.cfg.redundancy_penalty()) # loner are not to take in account to compute position if system contains none loner hit self.assertEqual(system_1.position, (10, 20)) model = Model("foo/mod2", 10) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model, loner=True) model.add_mandatory_gene(gene_gspd) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model, loner=True) model.add_accessory_gene(gene_sctj) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model, loner=True) model.add_accessory_gene(gene_sctn) hit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 10, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_1 = ModelHit(hit_1, gene_gspd, GeneStatus.MANDATORY) hit_2 = CoreHit(c_gene_sctj, "hit_2", 803, "replicon_id", 20, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_2 = ModelHit(hit_2, gene_sctj, GeneStatus.ACCESSORY) hit_3 = CoreHit(c_gene_sctn, "hit_3", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_3 = ModelHit(hit_3, gene_sctn, GeneStatus.ACCESSORY) system_1 = System(model, [Cluster([v_hit_1, v_hit_2], model, self.hit_weights), Cluster([v_hit_3], model, self.hit_weights)], self.cfg.redundancy_penalty()) # loner are not to take in account to compute position if system contains none loner hit self.assertEqual(system_1.position, (1, 20)) # def test_multi_loci(self): # model = Model("foo/T2SS", 10) # c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) # gene_gspd = ModelGene(c_gene_gspd, model) # model.add_mandatory_gene(gene_gspd) # c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) # gene_sctj = ModelGene(c_gene_sctj, model) # model.add_accessory_gene(gene_sctj) # c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) # gene_sctn = ModelGene(c_gene_sctn, model) # model.add_accessory_gene(gene_sctn) # # hit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) # v_hit_1 = ModelHit(hit_1, gene_gspd, GeneStatus.MANDATORY) # hit_2 = CoreHit(c_gene_sctj, "hit_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) # v_hit_2 = ModelHit(hit_2, gene_sctj, GeneStatus.ACCESSORY) # hit_3 = CoreHit(c_gene_sctn, "hit_3", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) # v_hit_3 = ModelHit(hit_3, gene_sctn, GeneStatus.ACCESSORY) # c1 = Cluster([v_hit_1, v_hit_2], model, self.hit_weights) # c2 = Cluster([v_hit_1, v_hit_3], model, self.hit_weights) # sys_single_locus = System(model, [c1]) # self.assertFalse(sys_single_locus.multi_loci) # sys_multi_loci = System(model, [c1, c2]) # self.assertTrue(sys_multi_loci.multi_loci) # c1 = Cluster([v_hit_1, v_hit_2], model, self.hit_weights) # c3 = Cluster([v_hit_3], model, self.hit_weights) # sys_single_locus_plus_loner = System(model, [c1, c3], self.cfg.redundancy_penalty()) # self.assertFalse(sys_single_locus_plus_loner.multi_loci) def test_loci_nb(self): model = Model("foo/T2SS", 10) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model) model.add_mandatory_gene(gene_gspd) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) model.add_accessory_gene(gene_sctj) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model, loner=True) model.add_accessory_gene(gene_sctn) hit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) m_hit_1 = ModelHit(hit_1, gene_gspd, GeneStatus.MANDATORY) hit_2 = CoreHit(c_gene_sctj, "hit_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) m_hit_2 = ModelHit(hit_2, gene_sctj, GeneStatus.ACCESSORY) hit_3 = CoreHit(c_gene_sctn, "hit_3", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) m_hit_3 = ModelHit(hit_3, gene_sctn, GeneStatus.ACCESSORY) c1 = Cluster([m_hit_1, m_hit_2], model, self.hit_weights) c2 = Cluster([m_hit_1, m_hit_3], model, self.hit_weights) sys_single_locus = System(model, [c1], self.cfg.redundancy_penalty()) self.assertEqual(sys_single_locus.loci_nb, 1) sys_multi_loci = System(model, [c1, c2], self.cfg.redundancy_penalty()) self.assertEqual(sys_multi_loci.loci_nb, 2) c1 = Cluster([m_hit_1, m_hit_2], model, self.hit_weights) h_loner = Loner(hit_3, gene_sctn, GeneStatus.ACCESSORY) c3 = Cluster([h_loner], model, self.hit_weights) sys_single_locus_plus_loner = System(model, [c1, c3], self.cfg.redundancy_penalty()) self.assertEqual(sys_single_locus_plus_loner.loci_nb, 1) # if max_gene_requird == 1 we authorize cluster with one gene c4 = Cluster([m_hit_1], model, self.hit_weights) sys_single_locus_of_one_hit_not_loner = System(model, [c4], self.cfg.redundancy_penalty()) self.assertEqual(sys_single_locus_of_one_hit_not_loner.loci_nb, 1) def test_loci_num(self): model = Model("foo/T2SS", 10) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model) model.add_mandatory_gene(gene_gspd) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) model.add_accessory_gene(gene_sctj) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model, loner=True) model.add_accessory_gene(gene_sctn) hit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_1 = ModelHit(hit_1, gene_gspd, GeneStatus.MANDATORY) hit_2 = CoreHit(c_gene_sctj, "hit_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_2 = ModelHit(hit_2, gene_sctj, GeneStatus.ACCESSORY) hit_3 = CoreHit(c_gene_sctn, "hit_3", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_3 = ModelHit(hit_3, gene_sctn, GeneStatus.ACCESSORY) c1 = Cluster([v_hit_1, v_hit_2], model, self.hit_weights) c2 = Cluster([v_hit_1, v_hit_3], model, self.hit_weights) sys_single_locus = System(model, [c1], self.cfg.redundancy_penalty()) self.assertListEqual(sys_single_locus.loci_num, [1]) sys_multi_loci = System(model, [c1, c2], self.cfg.redundancy_penalty()) self.assertListEqual(sys_multi_loci.loci_num, [1, 2]) c1 = Cluster([v_hit_1, v_hit_2], model, self.hit_weights) h_loner = Loner(hit_3, gene_sctn, GeneStatus.ACCESSORY) c3 = Cluster([h_loner], model, self.hit_weights) sys_single_locus_plus_loner = System(model, [c1, c3], self.cfg.redundancy_penalty()) self.assertListEqual(sys_single_locus_plus_loner.loci_num, [1, -1]) c4 = Cluster([v_hit_1], model, self.hit_weights) sys_single_locus_of_one_hit_not_loner = System(model, [c4], self.cfg.redundancy_penalty()) self.assertEqual(sys_single_locus_of_one_hit_not_loner.loci_num, [1]) def test_wholeness(self): model_1 = Model("foo/T2SS", 10) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model_1) model_1.add_mandatory_gene(gene_gspd) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model_1) model_1.add_accessory_gene(gene_sctj) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model_1, loner=True) model_1.add_accessory_gene(gene_sctn) hit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) m1_v_hit_1 = ModelHit(hit_1, gene_gspd, GeneStatus.MANDATORY) hit_2 = CoreHit(c_gene_sctj, "hit_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) m1_v_hit_2 = ModelHit(hit_2, gene_sctj, GeneStatus.ACCESSORY) hit_3 = CoreHit(c_gene_sctn, "hit_3", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) m1_v_hit_3 = ModelHit(hit_3, gene_sctn, GeneStatus.ACCESSORY) c1 = Cluster([m1_v_hit_1, m1_v_hit_2], model_1, self.hit_weights) c2 = Cluster([m1_v_hit_1, m1_v_hit_3], model_1, self.hit_weights) s = System(model_1, [c1]) self.assertEqual(s.wholeness, 2 / 3) s = System(model_1, [c1, c2]) self.assertEqual(s.wholeness, 3 / 3) model_2 = Model("foo/T2SS", 10, max_nb_genes=2) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) m2_gene_gspd = ModelGene(c_gene_gspd, model_2) model_2.add_mandatory_gene(gene_gspd) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) m2_gene_sctj = ModelGene(c_gene_sctj, model_2) model_2.add_accessory_gene(gene_sctj) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) m2_gene_sctn = ModelGene(c_gene_sctn, model_2, loner=True) model_2.add_accessory_gene(gene_sctn) m2_v_hit_1 = ModelHit(hit_1, m2_gene_gspd, GeneStatus.MANDATORY) m2_v_hit_2 = ModelHit(hit_2, m2_gene_sctj, GeneStatus.ACCESSORY) c3 = Cluster([m2_v_hit_1, m2_v_hit_2], model_2, self.hit_weights) s = System(model_2, [c3]) self.assertEqual(s.wholeness, 1) def test_occurrence(self): model = Model("foo/T2SS", 10) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model) model.add_mandatory_gene(gene_gspd) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) model.add_accessory_gene(gene_sctj) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model, loner=True) model.add_accessory_gene(gene_sctn) hit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_1 = ModelHit(hit_1, gene_gspd, GeneStatus.MANDATORY) hit_2 = CoreHit(c_gene_sctj, "hit_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_2 = ModelHit(hit_2, gene_sctj, GeneStatus.ACCESSORY) hit_3 = CoreHit(c_gene_sctn, "hit_3", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_3 = ModelHit(hit_3, gene_sctn, GeneStatus.ACCESSORY) c = Cluster([v_hit_1, v_hit_2, v_hit_3], model, self.hit_weights) s = System(model, [c]) self.assertEqual(s.occurrence(), 1) c1 = Cluster([v_hit_1, v_hit_2, v_hit_3], model, self.hit_weights) c2 = Cluster([v_hit_2, v_hit_3], model, self.hit_weights) s = System(model, [c1, c2], self.cfg.redundancy_penalty()) # The estimation of occurrence number is based on mandatory only self.assertEqual(s.occurrence(), 1) c1 = Cluster([v_hit_1, v_hit_2, v_hit_3], model, self.hit_weights) c2 = Cluster([v_hit_1, v_hit_3], model, self.hit_weights) s = System(model, [c1, c2], self.cfg.redundancy_penalty()) self.assertEqual(s.occurrence(), 2) ########################## # with multi system gene # ########################## # the multi_system genes should not count in the occurence model = Model("foo/T2SS", 10) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model) model.add_mandatory_gene(gene_gspd) c_gene_tadz = CoreGene(self.model_location, "tadZ", self.profile_factory) gene_tadz = ModelGene(c_gene_tadz, model) model.add_mandatory_gene(gene_tadz) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) model.add_mandatory_gene(gene_sctj) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model, multi_system=True) model.add_mandatory_gene(gene_sctn) hit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_1 = ModelHit(hit_1, gene_gspd, GeneStatus.MANDATORY) hit_2 = CoreHit(c_gene_tadz, "hit_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_2 = ModelHit(hit_2, gene_tadz, GeneStatus.MANDATORY) hit_3_1 = CoreHit(c_gene_sctj, "hit_3_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_3_1 = ModelHit(hit_3_1, gene_sctj, GeneStatus.MANDATORY) hit_3_2 = CoreHit(c_gene_sctj, "hit_3_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_3_2 = ModelHit(hit_3_2, gene_sctj, GeneStatus.MANDATORY) hit_4_1 = CoreHit(c_gene_sctn, "hit_4_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_4_1 = ModelHit(hit_4_1, gene_sctn, GeneStatus.MANDATORY) hit_4_2 = CoreHit(c_gene_sctn, "hit_4_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_4_2 = ModelHit(hit_4_2, gene_sctn, GeneStatus.MANDATORY) hit_4_3 = CoreHit(c_gene_sctn, "hit_4_3", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) v_hit_4_3 = ModelHit(hit_4_3, gene_sctn, GeneStatus.MANDATORY) c = Cluster([v_hit_1, v_hit_2, v_hit_3_1, v_hit_3_2, v_hit_4_1, v_hit_4_2, v_hit_4_3], model, self.hit_weights) s = System(model, [c], self.cfg.redundancy_penalty()) self.assertEqual(s.occurrence(), 1) def test_score(self): model = Model("foo/T2SS", 10) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model) model.add_mandatory_gene(gene_gspd) c_gene_tadZ = CoreGene(self.model_location, "tadZ", self.profile_factory) gene_tadZ = ModelGene(c_gene_tadZ, model) model.add_mandatory_gene(gene_tadZ) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) c_gene_sctJ_FLG = CoreGene(self.model_location, "sctJ_FLG", self.profile_factory) sctJ_FLG = Exchangeable(c_gene_sctJ_FLG, gene_sctj) gene_sctj.add_exchangeable(sctJ_FLG) model.add_accessory_gene(gene_sctj) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model, loner=True) c_gene_sctn_FLG = CoreGene(self.model_location, "sctN_FLG", self.profile_factory) sctn_FLG = Exchangeable(c_gene_sctn_FLG, gene_sctj) gene_sctn.add_exchangeable(sctn_FLG) model.add_accessory_gene(gene_sctn) c_gene_abc = CoreGene(self.model_location, "abc", self.profile_factory) gene_abc = ModelGene(c_gene_abc, model) model.add_neutral_gene(gene_abc) c_gene_flie = CoreGene(self.model_location, "fliE", self.profile_factory) gene_flie = ModelGene(c_gene_flie, model, loner=True) model.add_mandatory_gene(gene_flie) c_gene_flgb = CoreGene(self.model_location, "flgB", self.profile_factory) gene_flgb = ModelGene(c_gene_flgb, model, multi_system=True) model.add_accessory_gene(gene_flgb) c_gene_flgc = CoreGene(self.model_location, "flgC", self.profile_factory) gene_flgc = ModelGene(c_gene_flgb, model, loner=True, multi_system=True) model.add_accessory_gene(gene_flgc) h_gspd = CoreHit(c_gene_gspd, "h_gspd", 10, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) mh_gspd = ModelHit(h_gspd, gene_gspd, GeneStatus.MANDATORY) h_tadz = CoreHit(c_gene_tadZ, "h_tadz", 20, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) mh_tadz = ModelHit(h_tadz, gene_tadZ, GeneStatus.MANDATORY) h_sctj = CoreHit(c_gene_sctj, "h_sctj", 30, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) mh_sctj = ModelHit(h_sctj, gene_sctj, GeneStatus.ACCESSORY) h_sctj_an = CoreHit(c_gene_sctJ_FLG, "h_sctj_an", 30, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) mh_sctj_an = ModelHit(h_sctj_an, sctJ_FLG, GeneStatus.ACCESSORY) h_sctn = CoreHit(c_gene_sctn, "sctn", 40, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) mh_sctn = ModelHit(h_sctn, gene_sctn, GeneStatus.ACCESSORY) l_sctn = Loner(h_sctn, gene_sctn, GeneStatus.ACCESSORY) h_sctn_hom = CoreHit(c_gene_sctn_FLG, "h_scth_hom", 30, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) mh_sctn_hom = ModelHit(h_sctn_hom, sctn_FLG, GeneStatus.ACCESSORY) l_sctn_hom = ModelHit(h_sctn_hom, sctn_FLG, GeneStatus.ACCESSORY) h_abc = CoreHit(c_gene_abc, "h_abc", 50, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) mh_abc = ModelHit(h_abc, gene_abc, GeneStatus.NEUTRAL) h_flie_1 = CoreHit(c_gene_flie, "h_flie_1", 150, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_flie_2 = CoreHit(c_gene_flie, "h_flie_2", 300, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) # mh_flie_1 is a false loner (gene tag as loner hit in cluster) mh_flie_1 = ModelHit(h_flie_1, gene_flie, GeneStatus.MANDATORY) mh_flie_2 = ModelHit(h_flie_2, gene_flie, GeneStatus.MANDATORY) # l_h_flie_1 is a True Loner gene tag as loner, hit outside cluster # mh_flie_2 is a counterpart of l_h_flie_1 l_h_flie_1 = Loner(h_flie_1, gene_flie, GeneStatus.MANDATORY, counterpart=[mh_flie_2]) l_h_flie_2 = Loner(h_flie_2, gene_flie, GeneStatus.MANDATORY, counterpart=[mh_flie_1]) # mh_flie_3 is used as False loner (loner in cluster) h_flie_3 = CoreHit(c_gene_flie, "h_flie_3", 25, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) mh_flie_3 = ModelHit(h_flie_3, gene_flie, GeneStatus.MANDATORY) # mh_flgb is used as multi_system in cluster h_flgb = CoreHit(c_gene_flgb, "h_flgb", 60, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) mh_flgb = MultiSystem(h_flgb, gene_flgb, GeneStatus.ACCESSORY) # mh_flgc is used as multi_system in cluster h_flgc = CoreHit(c_gene_flgc, "h_flgc", 80, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) mh_flgc = LonerMultiSystem(h_flgc, gene_flgc, GeneStatus.ACCESSORY) # system with # 1 cluster # 2 mandatory, 2 accessory no analog/homolog sctn is a loner included in cluster # 2 * 1 + 2 * 0.5 = 3 s = System(model, [Cluster([mh_gspd, mh_tadz, mh_sctj, mh_sctn], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 3) # system with # 2 clusters # 2 mandatory, 2 accessory no analog/homolog no duplicates # [1 + 0.5] + [1 + 0.5] = 3 s = System(model, [Cluster([mh_gspd, mh_tadz], model, self.hit_weights), Cluster([mh_sctj, mh_sctn], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 3) # system with # 1 cluster # 2 mandatory gspd + tadZ + 1 mandatory duplicated 1 time gspd # 1 accessory sctj + sctn + 1 accessory duplicated 1 times sctn # no analog/homolog # 1 + 1 + 0 + 0.5 + 0.5 + 0 = 3 s = System(model, [Cluster([mh_gspd, mh_tadz, mh_sctj, mh_sctn, mh_gspd, mh_sctn], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 3) # system with 2 clusters # 1rst cluster 1 mandatory gspd + 1 accessory sctj # 1 + 0.5 # 2nd cluster 1 mandatory tadZ + 1 accessory sctj already in first cluster # 1 + 0.5 # [1 + .5] + [1 + .5] # 3 - (2 - 1) * 1.5 = 1.5 s = System(model, [Cluster([mh_gspd, mh_sctj], model, self.hit_weights), Cluster([mh_tadz, mh_sctj], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 1.5) # system with 1 cluster # 2 mandatory gspd + tadZ # 1 accessory sctn + 1 accessory exchangeable sctj_an # 1 + 1 + .5 + (.5 * .8) = 2.9 s = System(model, [Cluster([mh_gspd, mh_tadz, mh_sctj_an, mh_sctn], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 2.9) # system with 2 clusters # 1 mandatory + 1 accessory # 1 + 0.5 # 1 mandatory + 1 accessory exchangeable same role as cluster_1 accessory # 1 + 0.4 # system penalty due to 2 genes with same role in 2 clusters: -1.5 # 2.9 - 1.5 = 1.8 s = System(model, [Cluster([mh_gspd, mh_sctj], model, self.hit_weights), Cluster([mh_tadz, mh_sctj_an], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 1.4) # system with 2 cluster # 1 mandatory + 1 accessory + 1 neutral + same gene as accessory # gspd sctj abc sctj # 1 + 0.5 0 0 # 1 mandatory true loner (loner alone) # flie_1 # + (1 * 0.7) # system penalty: 0 # 2.2 s = System(model, [Cluster([mh_gspd, mh_sctj, mh_abc, mh_sctj], model, self.hit_weights), Cluster([l_h_flie_1], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 2.2) # system with 2 cluster # 1 mandatory + 1 accessory + 1 neutral + same gene as accessory + mandatory "faux loner" # 1 + 0.5 0 0 + 1 # 1 cluster of true loner already in first cluster # + 0 # system penalty: 0 # 2.5 s = System(model, [Cluster([mh_gspd, mh_sctj, mh_abc, mh_sctj, mh_flie_1], model, self.hit_weights), Cluster([l_h_flie_2], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 2.5) # system with 2 clusters # 1 mandatory gspd + 1 accessory sctj # 1 0.5 # 1 mandatory tadz + 1 accessory multisystems (in this cluster) # 1 0.5 # system penalty: 0 # 3.0 s = System(model, [Cluster([mh_gspd, mh_sctj], model, self.hit_weights), Cluster([mh_tadz, mh_flgb], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 3.0) # system with 1 cluster + 1 multi system out of cluster # 1 mandatory gspd + 1 accessory sctj # 1 0.5 # 1 accessory multisystems flgb (out of cluster) # 0.5 * 0.7 = 0.35 # system penalty: 0 # 1.85 s = System(model, [Cluster([mh_gspd, mh_sctj], model, self.hit_weights), Cluster([mh_flgb], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 1.85) # system with 1 cluster + 1 Loner multi system (out of cluster) # 1 mandatory gspd + 1 accessory sctj # 1 0.5 # 1 accessory multisystems flgc (out of cluster) # 0.5 * 0.7 = 0.35 # system penalty: 0 # 1.85 s = System(model, [Cluster([mh_gspd, mh_sctj], model, self.hit_weights), Cluster([mh_flgc], model, self.hit_weights)], self.cfg.redundancy_penalty()) self.assertEqual(s.score, 1.85) def test_is_compatible(self): model_A = Model("foo/A", 10) model_B = Model("foo/B", 10) model_C = Model("foo/C", 10) model_D = Model("foo/D", 10) model_E = Model("foo/E", 10) model_F = Model("foo/F", 10) cg_sctn_flg = CoreGene(self.model_location, "sctN_FLG", self.profile_factory) cg_sctj_flg = CoreGene(self.model_location, "sctJ_FLG", self.profile_factory) cg_flgB = CoreGene(self.model_location, "flgB", self.profile_factory) cg_tadZ = CoreGene(self.model_location, "tadZ", self.profile_factory) cg_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) cg_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) cg_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) cg_abc = CoreGene(self.model_location, "abc", self.profile_factory) mg_A_sctn = ModelGene(cg_sctn, model_A, multi_system=True) mg_A_sctn_hom = Exchangeable(cg_sctn_flg, mg_A_sctn, multi_system=True) mg_A_sctn.add_exchangeable(mg_A_sctn_hom) mg_A_sctj = ModelGene(cg_sctj, model_A) mg_A_sctj_an = Exchangeable(cg_sctj_flg, mg_A_sctj) mg_A_sctj.add_exchangeable(mg_A_sctj_an) mg_A_gspd = ModelGene(cg_gspd, model_A) mg_A_gspd_an = Exchangeable(cg_flgB, mg_A_gspd) mg_A_gspd.add_exchangeable(mg_A_gspd_an) mg_A_abc = ModelGene(cg_abc, model_A) mg_A_abc_ho = Exchangeable(cg_tadZ, mg_A_abc) mg_A_abc.add_exchangeable(mg_A_abc_ho) mg_B_sctn_flg = ModelGene(cg_sctn_flg, model_B) mg_B_sctj_flg = ModelGene(cg_sctj_flg, model_B) mg_B_flgB = ModelGene(cg_flgB, model_B) mg_B_tadZ = ModelGene(cg_tadZ, model_B, loner=True) mg_C_sctn_flg = ModelGene(cg_sctn_flg, model_C) mg_C_sctj_flg = ModelGene(cg_sctj_flg, model_C) mg_C_flgB = ModelGene(cg_flgB, model_C) mg_C_tadZ = ModelGene(cg_tadZ, model_C) mg_C_gspd = ModelGene(cg_gspd, model_C) mg_D_abc = ModelGene(cg_abc, model_D) mg_D_sctn = ModelGene(cg_sctn, model_D, multi_system=True) mg_E_abc = ModelGene(cg_abc, model_E) mg_E_sctn = ModelGene(cg_sctn, model_E, multi_model=True) mg_F_abc = ModelGene(cg_abc, model_F) mg_F_sctn = ModelGene(cg_sctn, model_F, multi_model=True) model_A.add_mandatory_gene(mg_A_sctn) # multi system model_A.add_mandatory_gene(mg_A_sctj) model_A.add_accessory_gene(mg_A_gspd) model_A.add_forbidden_gene(mg_A_abc) model_B.add_mandatory_gene(mg_B_sctn_flg) model_B.add_mandatory_gene(mg_B_sctj_flg) model_B.add_accessory_gene(mg_B_flgB) model_B.add_accessory_gene(mg_B_tadZ) # loner model_C.add_mandatory_gene(mg_C_sctn_flg) model_C.add_mandatory_gene(mg_C_sctj_flg) model_C.add_mandatory_gene(mg_C_flgB) model_C.add_accessory_gene(mg_C_tadZ) model_C.add_accessory_gene(mg_C_gspd) model_D.add_mandatory_gene(mg_D_abc) model_D.add_accessory_gene(mg_D_sctn) model_E.add_mandatory_gene(mg_E_abc) model_E.add_accessory_gene(mg_E_sctn) model_F.add_mandatory_gene(mg_F_abc) model_F.add_accessory_gene(mg_F_sctn) ch_sctj = CoreHit(cg_sctj, "hit_sctj", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) ch_sctn = CoreHit(cg_sctn, "hit_sctn", 803, "replicon_id", 2, 1.0, 1.0, 1.0, 1.0, 10, 20) ch_gspd = CoreHit(cg_gspd, "hit_gspd", 803, "replicon_id", 3, 1.0, 1.0, 1.0, 1.0, 10, 20) ch_sctj_flg = CoreHit(cg_sctj_flg, "hit_sctj_flg", 803, "replicon_id", 4, 1.0, 1.0, 1.0, 1.0, 10, 20) ch_flgB = CoreHit(cg_flgB, "hit_flgB", 803, "replicon_id", 5, 1.0, 1.0, 1.0, 1.0, 10, 20) ch_tadZ = CoreHit(cg_tadZ, "hit_tadZ", 803, "replicon_id", 6, 1.0, 1.0, 1.0, 1.0, 10, 20) ch_abc = CoreHit(cg_abc, "hit_abc", 803, "replicon_id", 7, 1.0, 1.0, 1.0, 1.0, 10, 20) ch_sctj_2 = CoreHit(cg_sctj, "hit_sctj_2", 803, "replicon_id", 20, 1.0, 1.0, 1.0, 1.0, 10, 20) ch_sctn_2 = CoreHit(cg_sctn, "hit_sctn_2", 803, "replicon_id", 21, 1.0, 1.0, 1.0, 1.0, 10, 20) ch_gspd_2 = CoreHit(cg_gspd, "hit_gspd_2", 803, "replicon_id", 22, 1.0, 1.0, 1.0, 1.0, 10, 20) ch_abc_2 = CoreHit(cg_abc, "hit_abc_2", 803, "replicon_id", 23, 1.0, 1.0, 1.0, 1.0, 10, 20) model_A._min_mandatory_genes_required = 2 model_A._min_genes_required = 2 c1_A = Cluster([ModelHit(ch_sctj, mg_A_sctj, GeneStatus.MANDATORY), MultiSystem(ch_sctn, mg_A_sctn, GeneStatus.MANDATORY), ModelHit(ch_gspd, mg_A_gspd, GeneStatus.ACCESSORY) ], model_A, self.hit_weights) c2_A = Cluster([ModelHit(ch_sctj, mg_A_sctj, GeneStatus.MANDATORY), MultiSystem(ch_sctn, mg_A_sctn, GeneStatus.MANDATORY)], model_A, self.hit_weights) c3_A = Cluster([ModelHit(ch_sctj_2, mg_A_sctj, GeneStatus.MANDATORY), MultiSystem(ch_sctn_2, mg_A_sctn, GeneStatus.MANDATORY), ModelHit(ch_gspd_2, mg_A_gspd, GeneStatus.ACCESSORY) ], model_A, self.hit_weights) c4_A = Cluster([ModelHit(ch_sctj, mg_A_sctj, GeneStatus.MANDATORY), MultiSystem(ch_sctn_2, mg_A_sctn, GeneStatus.MANDATORY), ModelHit(ch_gspd_2, mg_A_gspd, GeneStatus.ACCESSORY) ], model_A, self.hit_weights) c5_A = Cluster([ModelHit(ch_sctj_2, mg_A_sctj, GeneStatus.MANDATORY), MultiSystem(ch_sctn_2, mg_A_sctn, GeneStatus.MANDATORY), ModelHit(ch_gspd, mg_A_gspd, GeneStatus.ACCESSORY) ], model_A, self.hit_weights) model_B._min_mandatory_genes_required = 1 model_B._min_genes_required = 2 c6_B = Cluster([ModelHit(ch_sctj_flg, mg_B_sctj_flg, GeneStatus.MANDATORY), ModelHit(ch_tadZ, mg_B_tadZ, GeneStatus.ACCESSORY), ModelHit(ch_flgB, mg_B_flgB, GeneStatus.ACCESSORY)], model_B, self.hit_weights) model_C._min_mandatory_genes_required = 1 model_C._min_genes_required = 2 c7_C = Cluster([ModelHit(ch_sctj_flg, mg_C_sctj_flg, GeneStatus.MANDATORY), ModelHit(ch_tadZ, mg_C_tadZ, GeneStatus.ACCESSORY), ModelHit(ch_flgB, mg_C_flgB, GeneStatus.MANDATORY), ModelHit(ch_gspd, mg_C_gspd, GeneStatus.ACCESSORY)], model_C, self.hit_weights) model_D._min_mandatory_genes_required = 1 model_D._min_genes_required = 1 c8_D = Cluster([ModelHit(ch_abc, mg_D_abc, GeneStatus.MANDATORY), MultiSystem(ch_sctn, mg_D_sctn, GeneStatus.ACCESSORY)], model_D, self.hit_weights) model_E._min_mandatory_genes_required = 1 model_E._min_genes_required = 1 c9_E = Cluster([ModelHit(ch_abc, mg_E_abc, GeneStatus.MANDATORY), ModelHit(ch_sctn, mg_E_sctn, GeneStatus.ACCESSORY)], model_E, self.hit_weights) model_F._min_mandatory_genes_required = 1 model_F._min_genes_required = 1 c10_F = Cluster([ModelHit(ch_abc_2, mg_F_abc, GeneStatus.MANDATORY), ModelHit(ch_sctn, mg_F_sctn, GeneStatus.ACCESSORY)], model_F, self.hit_weights) sys_A1 = System(model_A, [c1_A, c2_A], self.cfg.redundancy_penalty()) # we need to tweek the replicon_id to have stable results # whatever the number of tests ran # or the tests order sys_A1.id = "replicon_id_A1" sys_A2 = System(model_A, [c3_A], self.cfg.redundancy_penalty()) sys_A2.id = "replicon_id_A2" sys_A3 = System(model_A, [c4_A], self.cfg.redundancy_penalty()) sys_A3.id = "replicon_id_A3" sys_A4 = System(model_A, [c5_A], self.cfg.redundancy_penalty()) sys_A4.id = "replicon_id_A4" sys_B = System(model_B, [c6_B], self.cfg.redundancy_penalty()) sys_B.id = "replicon_id_B" sys_C = System(model_C, [c7_C], self.cfg.redundancy_penalty()) sys_C.id = "replicon_id_C" sys_D = System(model_D, [c8_D], self.cfg.redundancy_penalty()) sys_D.id = "replicon_id_D" sys_E = System(model_E, [c9_E], self.cfg.redundancy_penalty()) sys_E.id = "replicon_id_E" sys_F = System(model_F, [c10_F], self.cfg.redundancy_penalty()) sys_F.id = "replicon_id_F" self.assertFalse(sys_A1.is_compatible(sys_A3)) # False: same model: share sctj (not multi_system) self.assertTrue(sys_A3.is_compatible(sys_A4)) # True: same model: share sctn (multi_system) self.assertTrue(sys_A1.is_compatible(sys_A2)) # True: same model: do not share any hit self.assertTrue(sys_A1.is_compatible(sys_B)) # True: different models: do not share any hit self.assertFalse(sys_A1.is_compatible(sys_C)) # False: diffrent models: share h_gspd self.assertFalse(sys_A1.is_compatible(sys_D)) # False: different models: share h_sctn (which is multi_system im model A but not multi model) self.assertFalse(sys_D.is_compatible(sys_E)) # False: different modesls: share sctn but sctn is multi_model only in E self.assertTrue(sys_E.is_compatible(sys_F)) # True: different Model: share sctn which is multi_model in E and F def test_HitSystemTracker(self): model_1 = Model("foo/T2SS", 10) model_2 = Model("foo/T3SS", 10) c_gene_sctn_flg = CoreGene(self.model_location, "sctN_FLG", self.profile_factory) gene_sctn_flg = ModelGene(c_gene_sctn_flg, model_2) c_gene_sctj_flg = CoreGene(self.model_location, "sctJ_FLG", self.profile_factory) gene_sctj_flg = ModelGene(c_gene_sctj_flg, model_2) c_gene_flgB = CoreGene(self.model_location, "flgB", self.profile_factory) gene_flgB = ModelGene(c_gene_flgB, model_2) c_gene_tadZ = CoreGene(self.model_location, "tadZ", self.profile_factory) gene_tadZ = ModelGene(c_gene_tadZ, model_2) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model_1) gene_sctn_hom = Exchangeable(c_gene_sctn_flg, gene_sctn) gene_sctn.add_exchangeable(gene_sctn_hom) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model_1) gene_sctj_an = Exchangeable(c_gene_sctj_flg, gene_sctj) gene_sctj.add_exchangeable(gene_sctj_an) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model_1) gene_gspd_an = Exchangeable(c_gene_flgB, gene_gspd) gene_gspd.add_exchangeable(gene_gspd_an) c_gene_abc = CoreGene(self.model_location, "abc", self.profile_factory) gene_abc = ModelGene(c_gene_abc, model_1) gene_abc_ho = Exchangeable(c_gene_tadZ, gene_abc) gene_abc.add_exchangeable(gene_abc_ho) model_1.add_mandatory_gene(gene_sctn) model_1.add_mandatory_gene(gene_sctj) model_1.add_accessory_gene(gene_gspd) model_1.add_forbidden_gene(gene_abc) model_2.add_mandatory_gene(gene_sctn_flg) model_2.add_mandatory_gene(gene_sctj_flg) model_2.add_accessory_gene(gene_flgB) model_2.add_accessory_gene(gene_tadZ) h_sctj = CoreHit(c_gene_sctj, "hit_sctj", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_sctn = CoreHit(c_gene_sctn, "hit_sctn", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_gspd = CoreHit(c_gene_gspd, "hit_gspd", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_sctj_flg = CoreHit(c_gene_sctj_flg, "hit_sctj_flg", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_flgB = CoreHit(c_gene_flgB, "hit_flgB", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_tadZ = CoreHit(c_gene_tadZ, "hit_tadZ", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) model_1._min_mandatory_genes_required = 2 model_1._min_genes_required = 2 c1 = Cluster([ModelHit(h_sctj, gene_sctj, GeneStatus.MANDATORY), ModelHit(h_sctn, gene_sctn, GeneStatus.MANDATORY), ModelHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY) ], model_1, self.hit_weights) c2 = Cluster([ModelHit(h_sctj, gene_sctj, GeneStatus.MANDATORY), ModelHit(h_sctn, gene_sctn, GeneStatus.MANDATORY), ModelHit(h_flgB, gene_gspd, GeneStatus.ACCESSORY)], model_1, self.hit_weights) model_2._min_mandatory_genes_required = 1 model_2._min_genes_required = 2 c3 = Cluster([ModelHit(h_sctj_flg, gene_sctj_flg, GeneStatus.MANDATORY), ModelHit(h_tadZ, gene_tadZ, GeneStatus.ACCESSORY), ModelHit(h_flgB, gene_flgB, GeneStatus.ACCESSORY)], model_2, self.hit_weights) s1 = System(model_1, [c1], self.cfg.redundancy_penalty()) s2 = System(model_1, [c1, c2], self.cfg.redundancy_penalty()) s3 = System(model_2, [c3], self.cfg.redundancy_penalty()) track_multi_systems_hit = HitSystemTracker([s1, s2, s3]) self.assertSetEqual({s1, s2}, track_multi_systems_hit[h_sctj]) self.assertSetEqual({s1, s2}, track_multi_systems_hit[h_gspd]) self.assertSetEqual({s3}, track_multi_systems_hit[h_tadZ]) self.assertSetEqual({s2, s3}, track_multi_systems_hit[h_flgB]) def test_count(self): model = Model("foo/T2SS", 10) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model) c_gene_sctn_flg = CoreGene(self.model_location, "sctN_FLG", self.profile_factory) gene_sctn_flg = Exchangeable(c_gene_sctn_flg, gene_sctn) gene_sctn.add_exchangeable(gene_sctn_flg) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) c_gene_sctj_flg = CoreGene(self.model_location, "sctJ_FLG", self.profile_factory) gene_sctj_flg = Exchangeable(c_gene_sctj_flg, gene_sctj) gene_sctj.add_exchangeable(gene_sctj_flg) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model) c_gene_flgB = CoreGene(self.model_location, "flgB", self.profile_factory) gene_gspd_an = Exchangeable(c_gene_flgB, gene_gspd) gene_gspd.add_exchangeable(gene_gspd_an) c_gene_abc = CoreGene(self.model_location, "abc", self.profile_factory) gene_abc = ModelGene(c_gene_abc, model) c_gene_tadZ = CoreGene(self.model_location, "tadZ", self.profile_factory) gene_abc_ho = Exchangeable(c_gene_tadZ, gene_abc) gene_abc.add_exchangeable(gene_abc_ho) c_gene_toto = CoreGene(self.model_location, "toto", self.profile_factory) gene_toto = ModelGene(c_gene_toto, model) c_gene_totote = CoreGene(self.model_location, "totote", self.profile_factory) gene_toto_ho = Exchangeable(c_gene_totote, gene_toto) gene_toto.add_exchangeable(gene_toto_ho) c_gene_not_in_model = CoreGene(self.model_location, "toto", self.profile_factory) gene_not_in_model = ModelGene(c_gene_not_in_model, model) model.add_mandatory_gene(gene_sctn) model.add_mandatory_gene(gene_sctj) model.add_accessory_gene(gene_gspd) model.add_neutral_gene(gene_toto) model.add_forbidden_gene(gene_abc) h_sctj = CoreHit(c_gene_sctj, "hit_sctj", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_sctn = CoreHit(c_gene_sctn, "hit_sctn", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_gspd = CoreHit(c_gene_gspd, "hit_gspd", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_gspd_an = CoreHit(c_gene_flgB, "hit_gspd_an", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_abc = CoreHit(c_gene_abc, "hit_abc", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_toto = CoreHit(c_gene_toto, "hit_toto", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_toto_ho = CoreHit(c_gene_totote, "hit_toto_ho", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_not_in_model = CoreHit(c_gene_not_in_model, "hit_not_in_model", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) model._min_mandatory_genes_required = 2 model._min_genes_required = 1 mh_sctj = ModelHit(h_sctj, gene_sctj, GeneStatus.MANDATORY) mh_sctn = ModelHit(h_sctn, gene_sctn, GeneStatus.MANDATORY) mh_gspd = ModelHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY) mh_abc = ModelHit(h_abc, gene_abc, GeneStatus.FORBIDDEN) mh_toto = ModelHit(h_toto, gene_toto, GeneStatus.NEUTRAL) c1 = Cluster([mh_sctj, mh_sctn, mh_gspd, mh_abc, mh_toto], model, self.hit_weights) s1 = System(model, [c1], self.cfg.redundancy_penalty()) self.assertDictEqual(s1.mandatory_occ, {'sctJ': [mh_sctj], 'sctN': [mh_sctn]}) self.assertDictEqual(s1.accessory_occ, {'gspD': [mh_gspd]}) self.assertDictEqual(s1.neutral_occ, {'toto': [mh_toto]}) # test with homolog and analog mh_sctj = ModelHit(h_sctj, gene_sctj, GeneStatus.MANDATORY) mh_sctn = ModelHit(h_sctn, gene_sctn, GeneStatus.MANDATORY) mh_gspd = ModelHit(h_gspd_an, gene_gspd, GeneStatus.ACCESSORY) mh_abc = ModelHit(h_abc, gene_abc, GeneStatus.FORBIDDEN) mh_toto = ModelHit(h_toto_ho, gene_toto, GeneStatus.NEUTRAL) c1 = Cluster([mh_sctj, mh_sctn, mh_gspd, mh_abc, mh_toto], model, self.hit_weights) s1 = System(model, [c1], self.cfg.redundancy_penalty()) self.assertDictEqual(s1.mandatory_occ, {'sctJ': [mh_sctj], 'sctN': [mh_sctn]}) self.assertDictEqual(s1.accessory_occ, {'gspD': [mh_gspd]}) self.assertDictEqual(s1.neutral_occ, {'toto': [mh_toto]}) mh_sctj = ModelHit(h_sctj, gene_sctj, GeneStatus.MANDATORY) mh_not_in_model = ModelHit(h_not_in_model, gene_not_in_model, GeneStatus.MANDATORY) c1 = Cluster([mh_sctj, mh_not_in_model], model, self.hit_weights) with self.assertRaises(MacsypyError) as ctx: s1 = System(model, [c1], self.cfg.redundancy_penalty()) self.assertEqual(str(ctx.exception), "gene 'toto' does not belong to 'mandatory' genes in model 'T2SS'") def test_multi_loci(self): model = Model("foo/T2SS", 10) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model) c_gene_sctn_flg = CoreGene(self.model_location, "sctN_FLG", self.profile_factory) gene_sctn_flg = Exchangeable(c_gene_sctn_flg, gene_sctn) gene_sctn.add_exchangeable(gene_sctn_flg) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) c_gene_sctj_flg = CoreGene(self.model_location, "sctJ_FLG", self.profile_factory) gene_sctj_flg = Exchangeable(c_gene_sctj_flg, gene_sctj) gene_sctj.add_exchangeable(gene_sctj_flg) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model, loner=True) c_gene_flgB = CoreGene(self.model_location, "flgB", self.profile_factory) gene_gspd_an = Exchangeable(c_gene_flgB, gene_gspd, loner=True) gene_gspd.add_exchangeable(gene_gspd_an) c_gene_abc = CoreGene(self.model_location, "abc", self.profile_factory) gene_abc = ModelGene(c_gene_abc, model) c_gene_tadZ = CoreGene(self.model_location, "tadZ", self.profile_factory) gene_abc_ho = Exchangeable(c_gene_tadZ, gene_abc) gene_abc.add_exchangeable(gene_abc_ho) c_gene_toto = CoreGene(self.model_location, "toto", self.profile_factory) gene_toto = ModelGene(c_gene_toto, model) c_gene_totote = CoreGene(self.model_location, "totote", self.profile_factory) gene_toto_ho = Exchangeable(c_gene_totote, gene_toto) gene_toto.add_exchangeable(gene_toto_ho) model.add_mandatory_gene(gene_sctn) model.add_mandatory_gene(gene_sctj) model.add_accessory_gene(gene_gspd) model.add_neutral_gene(gene_toto) model.add_forbidden_gene(gene_abc) h_sctj = CoreHit(c_gene_sctj, "hit_sctj", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_sctn = CoreHit(c_gene_sctn, "hit_sctn", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_gspd = CoreHit(c_gene_gspd, "hit_gspd", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_toto = CoreHit(c_gene_toto, "hit_toto", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) model._min_mandatory_genes_required = 2 model._min_genes_required = 1 mh_sctj = ModelHit(h_sctj, gene_sctj, GeneStatus.MANDATORY) mh_sctn = ModelHit(h_sctn, gene_sctn, GeneStatus.MANDATORY) mh_gspd = ModelHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY) l_h_gspd = Loner(h_gspd, gene_gspd, GeneStatus.ACCESSORY) mh_toto = ModelHit(h_toto, gene_toto, GeneStatus.NEUTRAL) c1 = Cluster([mh_sctj, mh_sctn, mh_gspd, mh_toto], model, self.hit_weights) # 1 cluster s1 = System(model, [c1], self.cfg.redundancy_penalty()) self.assertFalse(s1.multi_loci) c2 = Cluster([mh_sctj, mh_sctn], model, self.hit_weights) c3 = Cluster([mh_gspd, mh_toto], model, self.hit_weights) # 2 clusters of 2 hits each s2 = System(model, [c2, c3], self.cfg.redundancy_penalty()) self.assertTrue(s2.multi_loci) # c2 contains 2 hits # c4 one hit one loner c4 = Cluster([l_h_gspd], model, self.hit_weights) s3 = System(model, [c2, c4], self.cfg.redundancy_penalty()) self.assertFalse(s3.multi_loci) # c2 contains (2 hits) # c5 contains one hit not loner model._min_mandatory_genes_required = 1 model._min_genes_required = 1 c5 = Cluster([mh_toto], model, self.hit_weights) s4 = System(model, [c2, c5], self.cfg.redundancy_penalty()) self.assertTrue(s4.multi_loci) def test_get_loners(self): model = Model("foo/T2SS", 10) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model) c_gene_sctn_flg = CoreGene(self.model_location, "sctN_FLG", self.profile_factory) gene_sctn_flg = Exchangeable(c_gene_sctn_flg, gene_sctn) gene_sctn.add_exchangeable(gene_sctn_flg) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) c_gene_sctj_flg = CoreGene(self.model_location, "sctJ_FLG", self.profile_factory) gene_sctj_flg = Exchangeable(c_gene_sctj_flg, gene_sctj) gene_sctj.add_exchangeable(gene_sctj_flg) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model, loner=True) c_gene_flgB = CoreGene(self.model_location, "flgB", self.profile_factory) gene_gspd_an = Exchangeable(c_gene_flgB, gene_gspd) gene_gspd.add_exchangeable(gene_gspd_an) c_gene_abc = CoreGene(self.model_location, "abc", self.profile_factory) gene_abc = ModelGene(c_gene_abc, model, loner=True, multi_system=True) c_gene_tadZ = CoreGene(self.model_location, "tadZ", self.profile_factory) gene_abc_ho = Exchangeable(c_gene_tadZ, gene_abc) gene_abc.add_exchangeable(gene_abc_ho) c_gene_toto = CoreGene(self.model_location, "toto", self.profile_factory) gene_toto = ModelGene(c_gene_toto, model) c_gene_totote = CoreGene(self.model_location, "totote", self.profile_factory) gene_toto_ho = Exchangeable(c_gene_totote, gene_toto) gene_toto.add_exchangeable(gene_toto_ho) model.add_mandatory_gene(gene_sctn) model.add_mandatory_gene(gene_sctj) model.add_accessory_gene(gene_gspd) model.add_accessory_gene(gene_abc) model.add_neutral_gene(gene_toto) h_sctj = CoreHit(c_gene_sctj, "hit_sctj", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_sctj_flg = CoreHit(c_gene_sctj_flg, "hit_sctj_flg", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_sctn = CoreHit(c_gene_sctn, "hit_sctn", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_sctn_flg = CoreHit(c_gene_sctn_flg, "hit_sctn_flg", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_gspd = CoreHit(c_gene_gspd, "hit_gspd", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_gspd_an = CoreHit(c_gene_flgB, "hit_gspd_an", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_abc = CoreHit(c_gene_abc, "hit_abc", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_abc_ho = CoreHit(c_gene_tadZ, "hit_abc_ho", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_toto = CoreHit(c_gene_toto, "hit_toto", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_toto_ho = CoreHit(c_gene_totote, "hit_toto_ho", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) model._min_mandatory_genes_required = 2 model._min_genes_required = 1 mh_sctj = ModelHit(h_sctj, gene_sctj, GeneStatus.MANDATORY) mh_sctn = ModelHit(h_sctn, gene_sctn, GeneStatus.MANDATORY) mh_gspd = ModelHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY) l_h_gspd = Loner(h_gspd, gene_gspd, GeneStatus.ACCESSORY) l_ms_abc = LonerMultiSystem(h_abc, gene_abc, GeneStatus.ACCESSORY) mh_toto = ModelHit(h_toto, gene_toto, GeneStatus.NEUTRAL) c1 = Cluster([mh_sctj, mh_sctn, mh_gspd, mh_toto], model, self.hit_weights) # 1 cluster s1 = System(model, [c1], self.cfg.redundancy_penalty()) self.assertSetEqual(set(), s1.get_loners()) c2 = Cluster([mh_sctj, mh_sctn], model, self.hit_weights) c3 = Cluster([mh_gspd, mh_toto], model, self.hit_weights) # 2 clusters of 2 hits each s2 = System(model, [c2, c3], self.cfg.redundancy_penalty()) self.assertTrue(s2.multi_loci) # c2 contains 2 hits # c4 one hit one loner # c5 one hit Loner Multi Systems c4 = Cluster([l_h_gspd], model, self.hit_weights) c5 = Cluster([l_ms_abc], model, self.hit_weights) s3 = System(model, [c2, c4, c5], self.cfg.redundancy_penalty()) self.assertSetEqual({l_h_gspd, l_ms_abc}, s3.get_loners()) def test_get_hits_encoding_multisystem(self): model = Model("foo/T2SS", 10) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model) c_gene_sctn_flg = CoreGene(self.model_location, "sctN_FLG", self.profile_factory) gene_sctn_flg = Exchangeable(c_gene_sctn_flg, gene_sctn) gene_sctn.add_exchangeable(gene_sctn_flg) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) c_gene_sctj_flg = CoreGene(self.model_location, "sctJ_FLG", self.profile_factory) gene_sctj_flg = Exchangeable(c_gene_sctj_flg, gene_sctj) gene_sctj.add_exchangeable(gene_sctj_flg) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model, loner=True) c_gene_flgB = CoreGene(self.model_location, "flgB", self.profile_factory) gene_gspd_an = Exchangeable(c_gene_flgB, gene_gspd, loner=True) gene_gspd.add_exchangeable(gene_gspd_an) c_gene_abc = CoreGene(self.model_location, "abc", self.profile_factory) gene_abc = ModelGene(c_gene_abc, model, loner=True, multi_system=True) c_gene_tadZ = CoreGene(self.model_location, "tadZ", self.profile_factory) gene_abc_ho = Exchangeable(c_gene_tadZ, gene_abc, loner=True, multi_system=True) gene_abc.add_exchangeable(gene_abc_ho) c_gene_toto = CoreGene(self.model_location, "toto", self.profile_factory) gene_toto = ModelGene(c_gene_toto, model) c_gene_totote = CoreGene(self.model_location, "totote", self.profile_factory) gene_toto_ho = Exchangeable(c_gene_totote, gene_toto) gene_toto.add_exchangeable(gene_toto_ho) model.add_mandatory_gene(gene_sctn) model.add_mandatory_gene(gene_sctj) model.add_accessory_gene(gene_gspd) model.add_accessory_gene(gene_abc) model.add_neutral_gene(gene_toto) h_sctj = CoreHit(c_gene_sctj, "hit_sctj", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_sctn = CoreHit(c_gene_sctn, "hit_sctn", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_gspd = CoreHit(c_gene_gspd, "hit_gspd", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_abc = CoreHit(c_gene_abc, "hit_abc", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_abc_ho = CoreHit(c_gene_tadZ, "hit_abc_ho", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_toto = CoreHit(c_gene_toto, "hit_toto", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) model._min_mandatory_genes_required = 2 model._min_genes_required = 1 mh_sctj = ModelHit(h_sctj, gene_sctj, GeneStatus.MANDATORY) mh_sctn = ModelHit(h_sctn, gene_sctn, GeneStatus.MANDATORY) mh_gspd = ModelHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY) l_h_gspd = Loner(h_gspd, gene_gspd, GeneStatus.ACCESSORY) l_ms_abc = Loner(h_abc, gene_abc, GeneStatus.ACCESSORY) ms_tadZ = ModelHit(h_abc_ho, gene_abc_ho, GeneStatus.ACCESSORY) mh_toto = ModelHit(h_toto, gene_toto, GeneStatus.NEUTRAL) c1 = Cluster([mh_sctj, mh_sctn, mh_gspd, mh_toto], model, self.hit_weights) # 1 cluster s1 = System(model, [c1], self.cfg.redundancy_penalty()) self.assertSetEqual(set(), s1.get_hits_encoding_multisystem()) c2 = Cluster([mh_sctj, mh_sctn], model, self.hit_weights) c3 = Cluster([mh_sctj, mh_sctn, ms_tadZ, mh_toto], model, self.hit_weights) c4 = Cluster([l_h_gspd], model, self.hit_weights) c5 = Cluster([l_ms_abc], model, self.hit_weights) # c2 2 regular hits # c3 4 hits with 1 multi_systems (homolog) s2 = System(model, [c2, c3], self.cfg.redundancy_penalty()) self.assertSetEqual({ms_tadZ}, s2.get_hits_encoding_multisystem()) # c2 contains 2 hits # c4 one hit one loner # c5 one hit Loner MultiSystems s3 = System(model, [c2, c4, c5], self.cfg.redundancy_penalty()) self.assertSetEqual({l_ms_abc}, s3.get_hits_encoding_multisystem()) def test_get_multisystems(self): model = Model("foo/T2SS", 10) c_gene_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) gene_sctn = ModelGene(c_gene_sctn, model) c_gene_sctn_flg = CoreGene(self.model_location, "sctN_FLG", self.profile_factory) gene_sctn_flg = Exchangeable(c_gene_sctn_flg, gene_sctn) gene_sctn.add_exchangeable(gene_sctn_flg) c_gene_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) gene_sctj = ModelGene(c_gene_sctj, model) c_gene_sctj_flg = CoreGene(self.model_location, "sctJ_FLG", self.profile_factory) gene_sctj_flg = Exchangeable(c_gene_sctj_flg, gene_sctj) gene_sctj.add_exchangeable(gene_sctj_flg) c_gene_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) gene_gspd = ModelGene(c_gene_gspd, model, loner=True) c_gene_flgB = CoreGene(self.model_location, "flgB", self.profile_factory) gene_gspd_an = Exchangeable(c_gene_flgB, gene_gspd, loner=True) gene_gspd.add_exchangeable(gene_gspd_an) c_gene_abc = CoreGene(self.model_location, "abc", self.profile_factory) gene_abc = ModelGene(c_gene_abc, model, loner=True, multi_system=True) c_gene_tadZ = CoreGene(self.model_location, "tadZ", self.profile_factory) gene_abc_ho = Exchangeable(c_gene_tadZ, gene_abc, loner=True, multi_system=True) gene_abc.add_exchangeable(gene_abc_ho) c_gene_toto = CoreGene(self.model_location, "toto", self.profile_factory) gene_toto = ModelGene(c_gene_toto, model) c_gene_totote = CoreGene(self.model_location, "totote", self.profile_factory) gene_toto_ho = Exchangeable(c_gene_totote, gene_toto) gene_toto.add_exchangeable(gene_toto_ho) model.add_mandatory_gene(gene_sctn) model.add_mandatory_gene(gene_sctj) model.add_accessory_gene(gene_gspd) model.add_accessory_gene(gene_abc) model.add_neutral_gene(gene_toto) h_sctj = CoreHit(c_gene_sctj, "hit_sctj", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_sctn = CoreHit(c_gene_sctn, "hit_sctn", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_gspd = CoreHit(c_gene_gspd, "hit_gspd", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_abc = CoreHit(c_gene_abc, "hit_abc", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_abc_ho = CoreHit(c_gene_tadZ, "hit_abc_ho", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) h_toto = CoreHit(c_gene_toto, "hit_toto", 803, "replicon_id", 1, 1.0, 1.0, 1.0, 1.0, 10, 20) model._min_mandatory_genes_required = 2 model._min_genes_required = 1 mh_sctj = ModelHit(h_sctj, gene_sctj, GeneStatus.MANDATORY) mh_sctn = ModelHit(h_sctn, gene_sctn, GeneStatus.MANDATORY) mh_gspd = ModelHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY) l_h_gspd = Loner(h_gspd, gene_gspd, GeneStatus.ACCESSORY) l_ms_abc = LonerMultiSystem(h_abc, gene_abc, GeneStatus.ACCESSORY) ms_tadZ = MultiSystem(h_abc_ho, gene_abc_ho, GeneStatus.ACCESSORY) mh_toto = ModelHit(h_toto, gene_toto, GeneStatus.NEUTRAL) c1 = Cluster([mh_sctj, mh_sctn, mh_gspd, mh_toto], model, self.hit_weights) # 1 cluster s1 = System(model, [c1], self.cfg.redundancy_penalty()) self.assertSetEqual(set(), s1.get_multisystems()) c2 = Cluster([mh_sctj, mh_sctn], model, self.hit_weights) c3 = Cluster([mh_sctj, mh_sctn, ms_tadZ, mh_toto], model, self.hit_weights) c4 = Cluster([l_h_gspd], model, self.hit_weights) c5 = Cluster([l_ms_abc], model, self.hit_weights) # c2 2 regular hits # c3 4 hits with 1 multi_systems (homolog) s2 = System(model, [c2, c3], self.cfg.redundancy_penalty()) self.assertSetEqual({ms_tadZ}, s2.get_multisystems()) # c2 contains 2 hits # c4 one hit one loner # c5 one hit Loner MultiSystems s3 = System(model, [c2, c4, c5], self.cfg.redundancy_penalty()) self.assertSetEqual({l_ms_abc}, s3.get_multisystems()) def test_fulfilled_function(self): model = Model("foo/T2SS", 11) cg_gspd = CoreGene(self.model_location, "gspD", self.profile_factory) cg_sctc = CoreGene(self.model_location, "sctC", self.profile_factory) cg_sctj = CoreGene(self.model_location, "sctJ", self.profile_factory) cg_sctj_flg = CoreGene(self.model_location, "sctJ_FLG", self.profile_factory) cg_tadz = CoreGene(self.model_location, "tadZ", self.profile_factory) cg_sctn = CoreGene(self.model_location, "sctN", self.profile_factory) mg_gspd = ModelGene(cg_gspd, model) mg_sctc = ModelGene(cg_sctc, model) mg_sctj = ModelGene(cg_sctj, model) mg_sctj_flg = Exchangeable(cg_sctj_flg, mg_sctj) mg_sctj.add_exchangeable(mg_sctj_flg) mg_tadz = ModelGene(cg_tadz, model) mg_sctn = ModelGene(cg_sctn, model) model.add_mandatory_gene(mg_gspd) model.add_mandatory_gene(mg_sctc) model.add_accessory_gene(mg_sctj) model.add_accessory_gene(mg_tadz) model.add_accessory_gene(mg_sctn) # CoreHit(gene, model, hit_id, hit_seq_length, replicon_name, position, i_eval, score, # profile_coverage, sequence_coverage, begin_match, end_match ch_gspd = CoreHit(cg_gspd, "gspD", 10, "replicon_1", 10, 1.0, 10.0, 1.0, 1.0, 10, 20) ch_sctc = CoreHit(cg_sctc, "sctC", 10, "replicon_1", 20, 1.0, 20.0, 1.0, 1.0, 10, 20) ch_sctj = CoreHit(cg_sctj, "sctJ", 10, "replicon_1", 30, 1.0, 20.0, 1.0, 1.0, 10, 20) ch_sctj_flg = CoreHit(cg_sctj_flg, "sctJ_FLG", 10, "replicon_1", 40, 1.0, 50.0, 1.0, 1.0, 10, 20) ch_tadz = CoreHit(cg_tadz, "tadZ", 10, "replicon_1", 50, 1.0, 50.0, 1.0, 1.0, 10, 20) mh_gspd = ModelHit(ch_gspd, mg_gspd, GeneStatus.MANDATORY) mh_sctc = ModelHit(ch_sctc, mg_sctc, GeneStatus.MANDATORY) mh_sctj = ModelHit(ch_sctj, mg_sctj, GeneStatus.ACCESSORY) mh_sctj_flg = ModelHit(ch_sctj_flg, mg_sctj_flg, GeneStatus.ACCESSORY) mh_tadz = ModelHit(ch_tadz, mg_tadz, GeneStatus.ACCESSORY) c1 = Cluster([mh_gspd, mh_sctc], model, self.hit_weights) c2 = Cluster([mh_sctj, mh_tadz], model, self.hit_weights) c3 = Cluster([mh_tadz, mh_sctj_flg], model, self.hit_weights) # One system with 2 regular clusters, No exchangeable s1 = System(model, [c1, c2]) self.assertSetEqual(s1.fulfilled_function(mg_gspd), {mg_gspd.name}) self.assertFalse(s1.fulfilled_function(mg_sctn)) # test with several genes self.assertSetEqual(s1.fulfilled_function(mg_gspd, mg_sctn, mg_tadz), {mg_gspd.name, mg_tadz.name}) # One cluster contains exchangeable s2 = System(model, [c1, c3]) self.assertSetEqual(s2.fulfilled_function(mg_sctj), {mg_sctj.name}) # Test with function as string self.assertSetEqual(s1.fulfilled_function(mg_gspd.name), {mg_gspd.name})