Source code for integron_finder.config

# -*- 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: """ 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): """The absolute path to the phage-integrase model file""" 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