# -*- coding: utf-8 -*-
####################################################################################
# Integron_Finder - Integron Finder aims at detecting integrons in DNA sequences #
# by finding particular features of the integron: #
# - the attC sites #
# - the integrase #
# - and when possible attI site and promoters. #
# #
# Authors: Jean Cury, Bertrand Neron, Eduardo PC Rocha #
# Copyright (c) 2015 - 2018 Institut Pasteur, Paris and CNRS. #
# See the COPYRIGHT file for details #
# #
# integron_finder 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. #
# #
# integron_finder 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 this program (COPYING file). #
# If not, see <http://www.gnu.org/licenses/>. #
####################################################################################
import os
from . import utils
from . import __INTEGRON_DATA__
[docs]class Config(object):
"""
Config object hold values issue from command lines
"""
[docs] def __init__(self, args):
self._model_len = None # model_len cache, because it's computation is "heavy" (open file)
self._args = args
if __INTEGRON_DATA__ == '$' + 'INTEGRONDATA':
self._prefix_data = os.path.normpath(os.path.join(os.path.join(os.path.dirname(__file__)), '..', 'data'))
else:
self._prefix_data = os.path.join(__INTEGRON_DATA__, 'data')
def __getattr__(self, item):
try:
attr = getattr(self._args, item)
return attr
except AttributeError:
raise AttributeError("config object has no attribute '{}'".format(item))
@property
def replicon_path(self):
"""The absolute path to the replicon"""
return os.path.abspath(self._args.replicon)
@property
def input_dir(self):
"""The absolute path to the directory where is located the replicon"""
in_dir, sequence_file = os.path.split(self.replicon_path)
return in_dir
@property
def outdir(self):
"""The absolute path where to write the results directory"""
return os.path.abspath(self._args.outdir)
@property
def result_dir(self):
"""The absolute path to results directory"""
file_name = utils.get_name_from_path(self.replicon_path)
result_dir = os.path.join(self.outdir, "Results_Integron_Finder_" + file_name)
return result_dir
[docs] def tmp_dir(self, replicon_id):
"""The absolute path of the tmp results dir."""
return os.path.join(self.result_dir, 'tmp_{}'.format(replicon_id))
@property
def default_topology(self):
"""The default topology
available values are: 'circ' for circular or 'lin' for linear."""
try:
if self._args.circular:
return 'circ'
elif self._args.linear:
return 'lin'
else:
return None
except AttributeError:
return None
@property
def model_dir(self):
"""The absolute path to the directory containing the models"""
return os.path.join(self._prefix_data, "Models")
@property
def model_integrase(self):
"""The absolute path to the integrase model file"""
return os.path.join(self.model_dir, "integron_integrase.hmm")
@property
def model_phage_int(self):
return os.path.join(self.model_dir, "phage-int.hmm")
@property
def model_attc_path(self):
"""The absolute path to the attC model file"""
try:
self._args.attc_model
except AttributeError:
raise RuntimeError("'model_attc' is not define.")
if len(self._args.attc_model.split(os.sep)) > 1: # contain path
model_attc = self._args.attc_model
else:
model_attc = os.path.join(self.model_dir, self._args.attc_model)
return model_attc
@property
def model_attc_name(self):
"""The name of the attc model"""
try:
self._args.attc_model
except AttributeError:
raise RuntimeError("'model_attc' is not define.")
return utils.get_name_from_path(self.model_attc_path)
@property
def model_len(self):
"""
:return: The length of the attc model (corresponding to CLEN field).
:raises: IOError if model_attc_path does match an existing file
RuntimeError if the file doe not content CLEN field.
"""
try:
self._args.attc_model
except AttributeError:
raise RuntimeError("'model_attc' is not define.")
if self._model_len is None:
model_len = utils.model_len(self.model_attc_path)
self._model_len = model_len
return model_len
else:
return self._model_len
@property
def func_annot_path(self):
"""
The canonical absolute path to the directory containing
file needed for the functional annotation.
It does not take in account the argument passed via the command line.
"""
return os.path.join(self._prefix_data, "Functional_annotation")
@property
def log_level(self):
"""
:return: the level to apply to loggers. 0 <= level <=50
:rtype: int
"""
level = utils.log_level(self._args.verbose, self._args.quiet)
return level
