topology

class integron_finder.topology.Topology(default, topology_file=None)

Class to parse and handle replicons topologies

__getitem__(replicon_id)

Parameters:replicon_id (str) – The id of the replicon. Returns:the topology for the replicon corresponding to the replicon_id

__init__(default, topology_file=None)

Parameters:

• default (str) – the default topology
• topology_file – the path to the file where topology for replicon are specified

__weakref__

list of weak references to the object (if defined)

_parse(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’

Parameters:topology_file (str) – The path to the topology file

_parse_topology(topo)

Parse a field topology in topology file the authorized values are circular, linear or circ, lin, or in uppercase

Parameters:topo – the field corresponding to topology in topology file Returns:the topology in “normed” format ‘circ’ or ‘lin’ Return type:str