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)
