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#########################################################################
# 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 <https://www.gnu.org/licenses/>. #
#########################################################################
import tempfile
import argparse
from macsypy.model import ModelBank
from macsypy.model import Model
from macsypy.config import Config, MacsyDefaults
from tests import MacsyTest
class Test(MacsyTest):
def setUp(self):
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.res_search_dir = tempfile.gettempdir()
args.log_level = 30
self.cfg = Config(MacsyDefaults(), args)
self.system_bank = ModelBank()
def tearDown(self):
ModelBank._model_bank = {}
def test_add_get_model(self):
model_name = 'foo'
self.assertRaises(KeyError, self.system_bank.__getitem__, model_name)
system_foo = Model(model_name, 10)
self.system_bank.add_model(system_foo)
self.assertTrue(isinstance(system_foo, Model))
self.assertEqual(system_foo, self.system_bank[model_name])
with self.assertRaises(KeyError) as ctx:
self.system_bank.add_model(system_foo)
self.assertEqual(str(ctx.exception),
'"a model named {0} is already registered in the models\' bank"'.format(model_name))
def test_contains(self):
system_in = Model("foo", 10)
self.system_bank.add_model(system_in)
self.assertIn(system_in, self.system_bank)
system_out = Model("bar", 10)
self.assertNotIn(system_out, self.system_bank)
def test_iter(self):
systems = [Model('foo', 10), Model('bar', 10)]
for s in systems:
self.system_bank.add_model(s)
i = 0
for s in self.system_bank:
self.assertIn(s, systems)
i += 1
self.assertEqual(i, len(systems))
def test_get_uniq_object(self):
system_foo = Model("foo", 10)
self.system_bank.add_model(system_foo)
system_1 = self.system_bank[system_foo.name]
system_2 = self.system_bank[system_foo.name]
self.assertEqual(system_1, system_2)
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