def test_fill_ordered_replicon_min_max(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)
db._fill_ordered_min_max(cfg.replicon_topology())
self.assertEqual(len(db._DB), 1)
rep = db[RepliconDB.ordered_replicon_name]
self.assertEqual(rep.topology, cfg.replicon_topology())
self.assertEqual(rep.min, 1)
self.assertEqual(rep.max, 52)
class Test(MacsyTest):
def __init__(self, methodName='runTest'):
super(Test, self).__init__(methodName)
def fake_init(obj, cfg):
obj.cfg = cfg
obj._idx = Indexes(cfg)
obj.sequence_idx = obj._idx.find_my_indexes()
obj.topology_file = cfg.topology_file()
obj._DB = {}
self.fake_init = fake_init
self.real_init = RepliconDB.__init__
def setUp(self):
self.args = argparse.Namespace()
self.args.db_type = 'gembase'
self.args.models_dir = self.find_data('models')
self.args.res_search_dir = tempfile.gettempdir()
self.args.log_level = 30
self.args.out_dir = os.path.join(self.args.res_search_dir,
'test_macsyfinder_repliconDB')
if os.path.exists(self.args.out_dir):
shutil.rmtree(self.args.out_dir)
os.mkdir(self.args.out_dir)
seq_db = self.find_data("base", "test_base.fa")
shutil.copy(seq_db, self.args.out_dir)
self.args.sequence_db = os.path.join(self.args.out_dir,
os.path.basename(seq_db))
self.cfg = Config(MacsyDefaults(), self.args)
self.ESCO030p01_genes = [('000010', 886), ('000020', 291),
('000030', 656), ('000040', 500),
('000050', 407), ('000060', 144),
('000070', 183), ('000080', 121),
('000090', 199), ('000100', 325),
('000110', 425), ('000120', 171),
('000130', 277), ('000140', 133),
('000150', 108), ('000160', 295),
('000170', 273), ('000180', 367),
('000190', 573), ('000200', 343),
('000210', 295), ('000220', 108),
('000230', 117), ('000240', 153),
('000250', 479), ('000260', 706),
('000270', 998), ('000280', 171),
('000290', 108), ('000300', 295),
('000310', 165), ('000320', 243),
('000330', 295), ('000340', 108),
('000350', 1755), ('000360', 248),
('000370', 286), ('000380', 186),
('000390', 83), ('000400', 153),
('000410', 69), ('000420', 295),
('000430', 108), ('000440', 145),
('000450', 59), ('000460', 124),
('000470', 246), ('000480', 325),
('000490', 54), ('000500', 95), ('000510',
83),
('000520', 56), ('000530', 401),
('000540', 320), ('000550', 256),
('000560', 73), ('000570', 144),
('000580', 258), ('000590', 133),
('000600', 140), ('000610', 63),
('000620', 138), ('000630', 68),
('000640', 169), ('000650', 127),
('000660', 295), ('000670', 108),
('000670', 108)]
self.PSAE001c01_genes = [('006940', 803), ('013980', 759),
('017350', 600), ('018920', 776),
('026600', 273), ('031420', 658),
('043580', 416), ('051090', 714),
('055870', 449), ('055880', 447),
('055890', 588), ('055900', 292),
('055910', 262), ('055920', 166),
('055930', 288), ('055940', 194),
('055950', 567), ('055960', 188),
('055970', 247), ('055980', 252),
('055990', 455), ('056000', 450),
('056010', 260), ('056020', 246),
('056030', 70), ('056040', 133),
('056050', 284), ('056060', 585),
('056070', 435), ('056080', 342),
('056090', 252), ('056100', 122),
('056110', 213), ('056120', 400),
('056130', 134), ('056140', 138),
('056150', 397), ('056160', 298),
('056170', 186), ('056180', 445),
('056190', 414), ('056200', 132),
('056210', 674), ('056220', 319),
('056230', 394), ('056240', 207),
('056250', 401), ('056260', 611),
('056270', 257), ('056280', 169),
('056290', 454), ('056300', 141),
('056310', 458), ('056320', 286),
('056330', 514), ('056340', 178),
('056350', 156), ('056360', 85),
('056370', 289), ('056380', 126),
('056390', 290), ('056400', 262),
('056410', 214), ('056420', 630),
('056430', 127), ('056440', 455),
('056440', 455)]
self.NCDB_genes = [('056134', 289), ('056135', 126), ('056136', 290),
('056137', 262), ('056138', 214), ('056139', 630),
('056140', 127), ('056141', 803), ('056141', 803)]
self.idx = Indexes(self.cfg)
self.idx.build()
def tearDown(self):
try:
shutil.rmtree(self.cfg.working_dir())
except:
pass
RepliconDB.__init__ = self.real_init
def test_fill_topology(self):
self.args.topology_file = self.args.sequence_db + ".topo"
db_send = {'ESCO030p01': 'circular', 'PSAE001c01': 'linear'}
with open(self.args.topology_file, 'w') as f:
for k, v in list(db_send.items()):
f.write('{0} : {1}\n'.format(k, v))
cfg = Config(MacsyDefaults(), self.args)
RepliconDB.__init__ = self.fake_init
db = RepliconDB(cfg)
rcv_topo = db._fill_topology()
self.assertDictEqual(db_send, rcv_topo)
def test_fill_ordered_replicon_min_max(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)
db._fill_ordered_min_max(cfg.replicon_topology())
self.assertEqual(len(db._DB), 1)
rep = db[RepliconDB.ordered_replicon_name]
self.assertEqual(rep.topology, cfg.replicon_topology())
self.assertEqual(rep.min, 1)
self.assertEqual(rep.max, 52)
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)
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_with_topology(self):
self.args.topology_file = self.args.sequence_db + ".topo"
with open(self.args.topology_file, 'w') as f:
f.write(
'# topology file\nESCO030p01 : circular\nPSAE001c01 : linear\n'
)
cfg = Config(MacsyDefaults(), self.args)
RepliconDB.__init__ = self.fake_init
db = RepliconDB(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_in(self):
db = RepliconDB(self.cfg)
self.assertIn('ESCO030p01', db)
self.assertIn('PSAE001c01', db)
self.assertIn('NC_xxxxx_xx', db)
self.assertNotIn('toto', db)
def test_getitem(self):
db = RepliconDB(self.cfg)
ESCO030p01 = RepliconInfo(self.cfg.replicon_topology(), 1, 67,
self.ESCO030p01_genes)
PSAE001c01 = RepliconInfo(self.cfg.replicon_topology(), 68, 133,
self.PSAE001c01_genes)
NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)
self.assertEqual(ESCO030p01, db['ESCO030p01'])
self.assertEqual(PSAE001c01, db['PSAE001c01'])
self.assertEqual(NCXX, db['NC_xxxxx_xx'])
self.assertRaises(KeyError, db.__getitem__, 'foo')
def test_get(self):
db = RepliconDB(self.cfg)
ESCO030p01 = RepliconInfo(self.cfg.replicon_topology(), 1, 67,
self.ESCO030p01_genes)
PSAE001c01 = RepliconInfo(self.cfg.replicon_topology(), 68, 133,
self.PSAE001c01_genes)
NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)
self.assertEqual(ESCO030p01, db.get('ESCO030p01'))
self.assertEqual(PSAE001c01, db.get('PSAE001c01'))
self.assertEqual(NCXX, db.get('NC_xxxxx_xx', 'foo'))
self.assertIsNone(db.get('foo'))
self.assertEqual('bar', db.get('foo', 'bar'))
def test_items(self):
db = RepliconDB(self.cfg)
ESCO030p01 = RepliconInfo(self.cfg.replicon_topology(), 1, 67,
self.ESCO030p01_genes)
PSAE001c01 = RepliconInfo(self.cfg.replicon_topology(), 68, 133,
self.PSAE001c01_genes)
NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)
self.assertCountEqual(list(db.items()), [('ESCO030p01', ESCO030p01),
('NC_xxxxx_xx', NCXX),
('PSAE001c01', PSAE001c01)])
def test_iteritems(self):
db = RepliconDB(self.cfg)
ESCO030p01 = RepliconInfo(self.cfg.replicon_topology(), 1, 67,
self.ESCO030p01_genes)
PSAE001c01 = RepliconInfo(self.cfg.replicon_topology(), 68, 133,
self.PSAE001c01_genes)
NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)
iter_items = db.iteritems()
for item in [('ESCO030p01', ESCO030p01), ('PSAE001c01', PSAE001c01),
('NC_xxxxx_xx', NCXX)]:
with self.subTest(item=item):
self.assertEqual(next(iter_items), item)
def test_names(self):
db = RepliconDB(self.cfg)
exp_name = ['ESCO030p01', 'PSAE001c01', 'NC_xxxxx_xx']
self.assertListEqual(db.replicon_names(), exp_name)
def test_replicon_infos(self):
db = RepliconDB(self.cfg)
ESCO030p01 = RepliconInfo(self.cfg.replicon_topology(), 1, 67,
self.ESCO030p01_genes)
PSAE001c01 = RepliconInfo(self.cfg.replicon_topology(), 68, 133,
self.PSAE001c01_genes)
NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)
values = db.replicon_infos()
self.assertCountEqual(values, [ESCO030p01, NCXX, PSAE001c01])
class Test(MacsyTest):
def __init__(self, methodName='runTest'):
super(Test, self).__init__(methodName)
def fake_init(obj, cfg):
obj.cfg = cfg
idx = Indexes(cfg)
obj.sequence_idx = idx.find_my_indexes()
obj.topology_file = cfg.topology_file()
obj._DB = {}
self.fake_init = fake_init
self.real_init = RepliconDB.__init__
def setUp(self):
self.args = argparse.Namespace()
self.args.db_type = 'gembase'
self.args.models_dir = self.find_data('models')
self.args.res_search_dir = tempfile.gettempdir()
self.args.log_level = 30
self.args.out_dir = os.path.join(self.args.res_search_dir,
'test_macsyfinder_repliconDB')
if os.path.exists(self.args.out_dir):
shutil.rmtree(self.args.out_dir)
os.mkdir(self.args.out_dir)
seq_db = self.find_data("base", "test_base.fa")
shutil.copy(seq_db, self.args.out_dir)
self.args.sequence_db = os.path.join(self.args.out_dir,
os.path.basename(seq_db))
self.cfg = Config(MacsyDefaults(), self.args)
self.ESCO030p01_genes = [('000010', '886'), ('000020', '291'),
('000030', '656'), ('000040', '500'),
('000050', '407'), ('000060', '144'),
('000070', '183'), ('000080', '121'),
('000090', '199'), ('000100', '325'),
('000110', '425'), ('000120', '171'),
('000130', '277'), ('000140', '133'),
('000150', '108'), ('000160', '295'),
('000170', '273'), ('000180', '367'),
('000190', '573'), ('000200', '343'),
('000210', '295'), ('000220', '108'),
('000230', '117'), ('000240', '153'),
('000250', '479'), ('000260', '706'),
('000270', '998'), ('000280', '171'),
('000290', '108'), ('000300', '295'),
('000310', '165'), ('000320', '243'),
('000330', '295'), ('000340', '108'),
('000350', '1755'), ('000360', '248'),
('000370', '286'), ('000380', '186'),
('000390', '83'), ('000400', '153'),
('000410', '69'), ('000420', '295'),
('000430', '108'), ('000440', '145'),
('000450', '59'), ('000460', '124'),
('000470', '246'), ('000480', '325'),
('000490', '54'), ('000500', '95'),
('000510', '83'), ('000520', '56'),
('000530', '401'), ('000540', '320'),
('000550', '256'), ('000560', '73'),
('000570', '144'), ('000580', '258'),
('000590', '133'), ('000600', '140'),
('000610', '63'), ('000620', '138'),
('000630', '68'), ('000640', '169'),
('000650', '127'), ('000660', '295'),
('000670', '108'), ('000670', '108')]
self.PSAE001c01_genes = [('006940', '803'), ('013980', '759'),
('017350', '600'), ('018920', '776'),
('026600', '273'), ('031420', '658'),
('043580', '416'), ('051090', '714'),
('055870', '449'), ('055880', '447'),
('055890', '588'), ('055900', '292'),
('055910', '262'), ('055920', '166'),
('055930', '288'), ('055940', '194'),
('055950', '567'), ('055960', '188'),
('055970', '247'), ('055980', '252'),
('055990', '455'), ('056000', '450'),
('056010', '260'), ('056020', '246'),
('056030', '70'), ('056040', '133'),
('056050', '284'), ('056060', '585'),
('056070', '435'), ('056080', '342'),
('056090', '252'), ('056100', '122'),
('056110', '213'), ('056120', '400'),
('056130', '134'), ('056140', '138'),
('056150', '397'), ('056160', '298'),
('056170', '186'), ('056180', '445'),
('056190', '414'), ('056200', '132'),
('056210', '674'), ('056220', '319'),
('056230', '394'), ('056240', '207'),
('056250', '401'), ('056260', '611'),
('056270', '257'), ('056280', '169'),
('056290', '454'), ('056300', '141'),
('056310', '458'), ('056320', '286'),
('056330', '514'), ('056340', '178'),
('056350', '156'), ('056360', '85'),
('056370', '289'), ('056380', '126'),
('056390', '290'), ('056400', '262'),
('056410', '214'), ('056420', '630'),
('056430', '127'), ('056440', '455'),
('056440', '455')]
self.NCDB_genes = [('056134', '289'), ('056135', '126'),
('056136', '290'), ('056137', '262'),
('056138', '214'), ('056139', '630'),
('056140', '127'), ('056141', '803'),
('056141', '803')]
idx = Indexes(self.cfg)
idx._build_my_indexes()
def tearDown(self):
try:
shutil.rmtree(self.cfg.working_dir())
except:
pass
RepliconDB.__init__ = self.real_init
def test_fill_topology(self):
self.args.topology_file = self.args.sequence_db + ".topo"
db_send = {'ESCO030p01': 'circular', 'PSAE001c01': 'linear'}
with open(self.args.topology_file, 'w') as f:
for k, v in list(db_send.items()):
f.write('{0} : {1}\n'.format(k, v))
cfg = Config(MacsyDefaults(), self.args)
RepliconDB.__init__ = self.fake_init
db = RepliconDB(cfg)
rcv_topo = db._fill_topology()
self.assertDictEqual(db_send, rcv_topo)
def test_fill_ordered_replicon_min_max(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_my_indexes()
RepliconDB.__init__ = self.fake_init
db = RepliconDB(cfg)
db._fill_ordered_min_max(cfg.replicon_topology())
self.assertEqual(len(db._DB), 1)
rep = db[RepliconDB.ordered_replicon_name]
self.assertEqual(rep.topology, cfg.replicon_topology())
self.assertEqual(rep.min, 1)
self.assertEqual(rep.max, 52)
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)
def test_fill_gembase_min_max_with_topology(self):
self.args.topology_file = self.args.sequence_db + ".topo"
with open(self.args.topology_file, 'w') as f:
f.write(
'# topology file\nESCO030p01 : circular\nPSAE001c01 : linear\n'
)
cfg = Config(MacsyDefaults(), self.args)
RepliconDB.__init__ = self.fake_init
db = RepliconDB(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_in(self):
db = RepliconDB(self.cfg)
self.assertIn('ESCO030p01', db)
self.assertIn('PSAE001c01', db)
self.assertIn('NC_xxxxx_xx', db)
self.assertNotIn('toto', db)
def test_getitem(self):
db = RepliconDB(self.cfg)
ESCO030p01 = RepliconInfo(self.cfg.replicon_topology(), 1, 67,
self.ESCO030p01_genes)
PSAE001c01 = RepliconInfo(self.cfg.replicon_topology(), 68, 133,
self.PSAE001c01_genes)
NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)
self.assertEqual(ESCO030p01, db['ESCO030p01'])
self.assertEqual(PSAE001c01, db['PSAE001c01'])
self.assertEqual(NCXX, db['NC_xxxxx_xx'])
self.assertRaises(KeyError, db.__getitem__, 'foo')
def test_get(self):
db = RepliconDB(self.cfg)
ESCO030p01 = RepliconInfo(self.cfg.replicon_topology(), 1, 67,
self.ESCO030p01_genes)
PSAE001c01 = RepliconInfo(self.cfg.replicon_topology(), 68, 133,
self.PSAE001c01_genes)
NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)
self.assertEqual(ESCO030p01, db.get('ESCO030p01'))
self.assertEqual(PSAE001c01, db.get('PSAE001c01'))
self.assertEqual(NCXX, db.get('NC_xxxxx_xx', 'foo'))
self.assertIsNone(db.get('foo'))
self.assertEqual('bar', db.get('foo', 'bar'))
def test_items(self):
db = RepliconDB(self.cfg)
ESCO030p01 = RepliconInfo(self.cfg.replicon_topology(), 1, 67,
self.ESCO030p01_genes)
PSAE001c01 = RepliconInfo(self.cfg.replicon_topology(), 68, 133,
self.PSAE001c01_genes)
NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)
self.assertCountEqual(list(db.items()), [('ESCO030p01', ESCO030p01),
('NC_xxxxx_xx', NCXX),
('PSAE001c01', PSAE001c01)])
def test_iteritems(self):
db = RepliconDB(self.cfg)
ESCO030p01 = RepliconInfo(self.cfg.replicon_topology(), 1, 67,
self.ESCO030p01_genes)
PSAE001c01 = RepliconInfo(self.cfg.replicon_topology(), 68, 133,
self.PSAE001c01_genes)
NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)
self.assertCountEqual(iter(db.items()), [('ESCO030p01', ESCO030p01),
('NC_xxxxx_xx', NCXX),
('PSAE001c01', PSAE001c01)])
def test_replicon_infos(self):
db = RepliconDB(self.cfg)
ESCO030p01 = RepliconInfo(self.cfg.replicon_topology(), 1, 67,
self.ESCO030p01_genes)
PSAE001c01 = RepliconInfo(self.cfg.replicon_topology(), 68, 133,
self.PSAE001c01_genes)
NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)
values = db.replicon_infos()
self.assertCountEqual(values, [ESCO030p01, NCXX, PSAE001c01])
