Source code for integron_finder.topology

# -*- 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 - 2024  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 .prot_db import GembaseDB, RepliconType


[docs] class Topology: """Class to parse and handle replicons topologies"""
[docs] def __init__(self, seq_nb, cmd_topo, gembase=False, topology_file=None): """ :param str default: the default topology :param topology_file: the path to the file where topology for replicon are specified """ self._seq_nb_in_file = seq_nb self._cmd_line_opt = self._parse_topology(cmd_topo) if cmd_topo else cmd_topo self._gembase = gembase self._topology_file = dict() 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_file[seq_id] = self._parse_topology(topology)
[docs] def _gembase_replicon_default_topo(self, seqid): """ :param seqid: the id of the replicon :type seqid: str :return: The default topology corresponding to the repliocon seqid in gembase format. :rtype: str 'circ' | 'lin' """ r_type = GembaseDB.get_replicon_type(seq_id=seqid) if r_type in (RepliconType.CHROMOSOME, RepliconType.PLASMID): topo = 'circ' elif r_type in (RepliconType.DRAFT, RepliconType.PHAGE, RepliconType.OTHER): topo = 'lin' return topo
[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 """ topo = 'circ' if self._seq_nb_in_file == 1 else 'lin' if self._gembase: topo = self._gembase_replicon_default_topo(replicon_id) if self._cmd_line_opt: topo = self._cmd_line_opt if replicon_id in self._topology_file: topo = self._topology_file[replicon_id] return topo