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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 tempfile
import argparse
from macsylib.config import Config, MacsyDefaults
from macsylib.model import ModelBank, Model
from macsylib.profile import ProfileFactory
from macsylib.gene import GeneBank, CoreGene, ModelGene, Exchangeable
from macsylib.registries import ModelRegistry, scan_models_dir
from macsylib.definition_parser import DefinitionParser
from macsylib.error import MacsylibError, ModelInconsistencyError
from tests import MacsyTest
class TestModelParser(MacsyTest):
def setUp(self):
defaults = MacsyDefaults()
self.args = argparse.Namespace()
self.args.sequence_db = self.find_data("base", "test_1.fasta")
self.args.db_type = 'gembase'
self.args.models_dir = self.find_data('models')
self.tmp_dir = tempfile.TemporaryDirectory(prefix='test_msl_DefParser_')
self.args.res_search_dir = self.tmp_dir.name
self.cfg = Config(defaults, self.args)
self.model_bank = ModelBank()
self.gene_bank = GeneBank()
self.profile_factory = ProfileFactory(self.cfg)
self.model_registry = ModelRegistry()
models_location = scan_models_dir(self.args.models_dir)
for ml in models_location:
self.model_registry.add(ml)
self.parser = DefinitionParser(self.cfg, self.model_bank, self.gene_bank,
self.model_registry, self.profile_factory)
def tearDown(self):
self.tmp_dir.cleanup()
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