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#########################################################################
# MacSyLib - Python library to detect macromolecular systems #
# in prokaryotes protein dataset using systems modelling #
# and similarity search. #
# #
# Authors: Sophie Abby, Bertrand Neron #
# Copyright (c) 2014-2025 Institut Pasteur (Paris) and CNRS. #
# See the COPYRIGHT file for details #
# #
# This file is part of MacSyLib package. #
# #
# MacSyLib 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. #
# #
# MacSyLib 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 MacSyLib (COPYING). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
import os
import shutil
import tempfile
import argparse
from macsylib.config import Config, MacsyDefaults
from macsylib.database import RepliconDB, Indexes, RepliconInfo
from tests import MacsyTest
class TestRepliconDB(MacsyTest):
def __init__(self, methodName = 'runTest'):
super().__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 = {}
obj._ordered_replicon_name = os.path.splitext(os.path.basename(cfg.sequence_db()))[0]
self.fake_init = fake_init
self.real_init = RepliconDB.__init__
def setUp(self):
self._tmp_dir = tempfile.TemporaryDirectory(prefix='test_msl_RepliconDB_')
self.args = argparse.Namespace()
self.args.db_type = 'gembase'
self.args.models_dir = self.find_data('models')
self.args.res_search_dir = self._tmp_dir.name
self.args.log_level = 30
self.args.out_dir = os.path.join(self.args.res_search_dir,
'test_macsylib_repliconDB')
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):
self._tmp_dir.cleanup()
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[db.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_guess_if_really_gembase(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_gembase_min_max({}, self.cfg.replicon_topology())
self.assertFalse(db.guess_if_really_gembase())
seq_ori = self.find_data("base", "gembase.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_gembase_min_max({}, self.cfg.replicon_topology())
self.assertTrue(db.guess_if_really_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])
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