# -*- 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/>. #
####################################################################################
from collections import defaultdict
[docs]class Topology(object):
"""Class to parse and handle replicons topologies"""
[docs] def __init__(self, default, topology_file=None):
"""
:param str default: the default topology
:param topology_file: the path to the file where topology for replicon are specified
"""
self._default = self._parse_topology(default)
self._topology = defaultdict(lambda: self._default)
if topology_file:
self._parse(topology_file)
[docs] def _parse_topology(self, topo):
"""
Parse a field topology in topology file
the authorized values are circular, linear or circ, lin, or in uppercase
:param topo: the field corresponding to topology in topology file
:return: the topology in "normed" format 'circ' or 'lin'
:rtype: str
"""
topo = topo.lower()
if topo in 'circular':
return 'circ'
elif topo in 'linear':
return 'lin'
else:
raise RuntimeError("'{}' is not allowed for topology".format(topo))
[docs] def _parse(self, topology_file):
"""
Parse a topology file where topology is specified for replicons
on each line a topology is specified for a replicon
the syntax of each line is ::
replicon_id topology
the allowed value for toplogy are 'circ', 'circular', 'lin', 'linear'
:param str topology_file: The path to the topology file
"""
with open(topology_file) as topo_f:
for entry in topo_f:
if entry.startswith('#'):
continue
seq_id, topology = entry.split()
self._topology[seq_id] = self._parse_topology(topology)
[docs] def __getitem__(self, replicon_id):
"""
:param str replicon_id: The id of the replicon.
:returns: the topology for the replicon corresponding to the replicon_id
"""
return self._topology[replicon_id]
