def test_fill_gembase_min_max_with_topology(self): self.cfg.options['topology_file'] = self.cfg.sequence_db + ".topo" with open(self.cfg.topology_file , 'w') as f: f.write('# topology file\nESCO030p01 : circular\nPSAE001c01 : linear\n') RepliconDB.__init__ = self.fake_init db = RepliconDB(self.cfg) topo_dict = db._fill_topology() db._fill_gembase_min_max(topo_dict, 'circular') self.assertEqual(len(db._DB), 3) self.assertEqual(set(db._DB.keys()), set(['ESCO030p01', 'PSAE001c01', 'NC_xxxxx_xx'])) ESCO030p01 = db['ESCO030p01'] self.assertEqual(ESCO030p01.topology, 'circular') self.assertEqual(ESCO030p01.min, 1) self.assertEqual(ESCO030p01.max, 67) self.assertEqual(ESCO030p01.genes, self.ESCO030p01_genes) PSAE001c01 = db['PSAE001c01'] self.assertEqual(PSAE001c01.topology, 'linear') self.assertEqual(PSAE001c01.min, 68) self.assertEqual(PSAE001c01.max, 133) self.assertEqual(PSAE001c01.genes, self.PSAE001c01_genes) DBNC = db['NC_xxxxx_xx'] self.assertEqual(DBNC.topology, 'circular') self.assertEqual(DBNC.min, 134) self.assertEqual(DBNC.max, 141) self.assertEqual(DBNC.genes, self.NCDB_genes)
def test_fill_gembase_min_max_default_topology(self): RepliconDB.__init__ = self.fake_init db = RepliconDB(self.cfg) db._fill_gembase_min_max({}, self.cfg.replicon_topology) self.assertEqual(len(db._DB), 2) PRRU001c01 = db['ESCO030p01'] self.assertEqual(PRRU001c01.topology, 'circular') self.assertEqual(PRRU001c01.min, 1) self.assertEqual(PRRU001c01.max, 67) PSAE001c01 = db['PSAE001c01'] self.assertEqual(PSAE001c01.topology, 'circular') self.assertEqual(PSAE001c01.min, 68) self.assertEqual(PSAE001c01.max, 133)
def test_fill_gembase_min_max_default_topology(self): RepliconDB.__init__ = self.fake_init db = RepliconDB(self.cfg) db._fill_gembase_min_max({}, self.cfg.replicon_topology) self.assertEqual(len(db._DB), 2) PRRU001c01 = db['ESCO030p01'] self.assertEqual(PRRU001c01.topology, 'circular') self.assertEqual(PRRU001c01.min, 1) self.assertEqual(PRRU001c01.max, 67) PSAE001c01 = db['PSAE001c01'] self.assertEqual(PSAE001c01.topology, 'circular') self.assertEqual(PSAE001c01.min, 68) self.assertEqual(PSAE001c01.max, 133)
def test_fill_gembase_min_max_with_topology(self): self.cfg.options['topology_file'] = self.cfg.sequence_db + ".topo" with open(self.cfg.topology_file, 'w') as f: f.write('ESCO030p01 : circular\nPSAE001c01 : linear\n') RepliconDB.__init__ = self.fake_init db = RepliconDB(self.cfg) topo_dict = db._fill_topology() db._fill_gembase_min_max(topo_dict, 'circular') self.assertEqual(len(db._DB), 2) ESCO030p01 = db['ESCO030p01'] self.assertEqual(ESCO030p01.topology, 'circular') self.assertEqual(ESCO030p01.min, 1) self.assertEqual(ESCO030p01.max, 67) PSAE001c01 = db['PSAE001c01'] self.assertEqual(PSAE001c01.topology, 'linear') self.assertEqual(PSAE001c01.min, 68) self.assertEqual(PSAE001c01.max, 133)
def test_fill_gembase_min_max_with_topology(self): self.cfg.options['topology_file'] = self.cfg.sequence_db + ".topo" with open(self.cfg.topology_file , 'w') as f: f.write('ESCO030p01 : circular\nPSAE001c01 : linear\n') RepliconDB.__init__ = self.fake_init db = RepliconDB(self.cfg) topo_dict = db._fill_topology() db._fill_gembase_min_max(topo_dict, 'circular') self.assertEqual(len(db._DB), 2) ESCO030p01 = db['ESCO030p01'] self.assertEqual(ESCO030p01.topology, 'circular') self.assertEqual(ESCO030p01.min, 1) self.assertEqual(ESCO030p01.max, 67) PSAE001c01 = db['PSAE001c01'] self.assertEqual(PSAE001c01.topology, 'linear') self.assertEqual(PSAE001c01.min, 68) self.assertEqual(PSAE001c01.max, 133)
def test_fill_gembase_min_max_oredered_replicon(self): seq_ori = self.find_data("base", "ordered_replicon_base.fasta") shutil.copy(seq_ori, self.args.out_dir) self.args.sequence_db = os.path.join(self.args.out_dir, os.path.basename(seq_ori)) cfg = Config(MacsyDefaults(), self.args) idx = Indexes(cfg) idx.build() RepliconDB.__init__ = self.fake_init db = RepliconDB(cfg) with self.assertRaises(MacsypyError) as ctx: with self.catch_log() as log: db._fill_gembase_min_max({}, self.cfg.replicon_topology()) self.assertEqual( str(ctx.exception), f"Error during sequence-db '{self.args.sequence_db}' parsing. " f"Are you sure db-type is 'gembase'?")
def test_fill_gembase_min_max_default_topology(self): RepliconDB.__init__ = self.fake_init db = RepliconDB(self.cfg) db._fill_gembase_min_max({}, self.cfg.replicon_topology) self.assertEqual(len(db._DB), 3) self.assertEqual(set(db._DB.keys()), set(['ESCO030p01', 'PSAE001c01', 'NC_xxxxx_xx'])) PRRU001c01 = db['ESCO030p01'] self.assertEqual(PRRU001c01.topology, 'circular') self.assertEqual(PRRU001c01.min, 1) self.assertEqual(PRRU001c01.max, 67) self.assertEqual(PRRU001c01.genes, self.ESCO030p01_genes) PSAE001c01 = db['PSAE001c01'] self.assertEqual(PSAE001c01.topology, 'circular') self.assertEqual(PSAE001c01.min, 68) self.assertEqual(PSAE001c01.max, 133) self.assertEqual(PSAE001c01.genes, self.PSAE001c01_genes) DBNC = db['NC_xxxxx_xx'] self.assertEqual(DBNC.topology, 'circular') self.assertEqual(DBNC.min, 134) self.assertEqual(DBNC.max, 141) self.assertEqual(DBNC.genes, self.NCDB_genes)