Source code for macsypy.utils

#########################################################################
# MacSyFinder - Detection of macromolecular systems in protein dataset  #
#               using systems modelling and similarity search.          #
# Authors: Sophie Abby, Bertrand Neron                                  #
# Copyright (c) 2014-2021  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/>.                          #
#########################################################################


from itertools import groupby

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. """ root, def_names = models model_family = DefinitionLocation.root_name(root) model_loc = model_registry[model_family] if 'all' in [d.lower() for d in def_names]: if root == model_loc.name: root = None def_to_detect = model_loc.get_all_definitions(root_def_name=root) else: def_to_detect = [model_loc.get_definition(f'{root}/{one_def}') for one_def in def_names] return def_to_detect
[docs]def get_replicon_names(genome_path): """ parse gembase file and the list of replicon identifiers :param str genome_path: The path to a file containing sequence in **gembase** format :return: the list of replicon identifiers :rtype: list of str """ def grp_replicon(ids): """ in gembase the identifier of fasta sequence follows the following schema: <replicon-name>_<seq-name> with eventually '_' inside the <replicon_name> but not in the <seq-name>. so grp_replicon allow to group sequences belonging to the same replicon. """ return "_".join(ids.split('_')[: -1]) seq_ids = [] with open(genome_path, 'r') as fh: for line in fh: if line.startswith('>'): seq_ids.append(line.split()[0][1:]) replicons = [rep_name for rep_name, _ in groupby(seq_ids, key=grp_replicon)] return replicons