#########################################################################
# MacSyFinder - Detection of macromolecular systems in protein dataset #
# using systems modelling and similarity search. #
# Authors: Sophie Abby, Bertrand Neron #
# Copyright (c) 2014-2020 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 contextlib
import os
import sys
from .registries import DefinitionLocation
[docs]def get_def_to_detect(models, model_registry):
"""
:param models: the list of models to detect as returned by config.models.
:type models: list of tuple with the following structure:
[('model_1', ('def1, def2, ...)), ('model_2', ('def1', ...)), ...]
:param model_registry: the models registry for this run.
:type model_registry: :class:`macsypy.registries.ModelRegistry` object.
:return: the definitions to parse
:rtype: list of :class:`macsypy.registries.DefinitionLocation` objects
:raise ValueError: if a model name provided in models is not in model_registry.
"""
def_to_detect = []
for group_of_model in models:
root, def_name = group_of_model
model_family = DefinitionLocation.root_name(root)
model_loc = model_registry[model_family]
if 'all' in [d.lower() for d in def_name]:
if root == model_loc.name:
root = None
def_loc = model_loc.get_all_definitions(root_def_name=root)
def_to_detect += def_loc
else:
def_to_detect += [model_loc.get_definition(f'{root}/{one_def}') for one_def in def_name]
return def_to_detect