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) 2014-2024  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/>.                          #
#########################################################################

"""
Some macsyfinder helper functions
"""

import os
import os.path
import gzip
import contextlib
from itertools import groupby

from .registries import DefinitionLocation, ModelRegistry
from .error import MacsypyError


[docs]def get_def_to_detect(models: list[tuple[str, tuple[str]]], model_registry: ModelRegistry) -> tuple[list[DefinitionLocation], str, str]: """ :param models: the list of models to detect as returned by config.models. :type models: list of tuple with the following structure: [('model_fqn', ('def1, def2, ...)), ('model_2', ('def1', ...)), ...] :param model_registry: the models registry for this run. :return: the definitions to parse :raise ValueError: if a model name provided in models is not in model_registry. """ root, def_names = models root = root.rstrip(os.path.sep) model_family = DefinitionLocation.root_name(root) model_loc = model_registry[model_family] model_vers = model_loc.version 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, model_family, model_vers
[docs]def get_replicon_names(genome_path, db_type) -> list[str]: if db_type == 'gembase': return _get_gembase_replicon_names(genome_path) elif db_type in ('ordered_replicon', 'unordered'): return [os.path.splitext(os.path.basename(genome_path))[0]] else: raise MacsypyError(f"Invalid genome type: {db_type}")
def _get_gembase_replicon_names(genome_path: str) -> list[str]: """ parse gembase file and get the list of replicon identifiers :param genome_path: The path to a file containing sequence in **gembase** format :return: the list of replicon identifiers """ def grp_replicon(ids: str) -> str: """ 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
[docs]def threads_available() -> int: """ :return: The maximal number of threads available. It's nice with cluster scheduler or linux. On Mac it uses the number of physical cores """ if hasattr(os, "sched_getaffinity"): threads_nb = len(os.sched_getaffinity(0)) else: threads_nb = os.cpu_count() return threads_nb
[docs]def parse_time(user_time: int | str) -> int: """ parse user-friendly time and return it in seconds user time supports units as s h m d for sec min hour day or a combination of them 1h10m50s means 1 hour 10 minutes 50 seconds all terms will be converted in seconds and added :param user_time: :return: seconds :raise: ValueError if user_time is not parseable """ try: user_time = int(user_time) return user_time # user time has no units , it's seconds except ValueError: pass import re parts_converter = {'s': lambda x: x, 'm': lambda x: x * 60, 'h': lambda x: x * 3600, 'd': lambda x: x * 86400 } time_parts = re.findall(r'(\d+)(\D+)', user_time) time = 0 for value, unit in time_parts: unit = unit.strip().lower() try: time += parts_converter[unit](int(value)) except KeyError: raise ValueError("Not valid time format. Units allowed h/m/s.") return time
@contextlib.contextmanager def open_compressed(path: str, mode: str = 'rt') -> str: """ :param path: the path to open :param mode: the opening mode by default read text :yield: the content of the file line by line """ _, ext = os.path.splitext(path) if ext == '.gz': my_open = gzip.open elif ext == '.bz2' or ext == '.zip': msg = f"MacSyFinder does not support '{ext[1:]}' compression (only gzip)." raise ValueError(msg) else: # I assumed it's a fasta not compressed my_open = open with my_open(path, mode) as f: yield f