#########################################################################
# 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