topology

class integron_finder.topology.Topology(seq_nb, cmd_topo, gembase=False, topology_file=None)[source]

Class to parse and handle replicons topologies

__getitem__(replicon_id)[source]
Parameters

replicon_id (str) – The id of the replicon.

Returns

the topology for the replicon corresponding to the replicon_id

__init__(seq_nb, cmd_topo, gembase=False, topology_file=None)[source]
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)

_gembase_replicon_default_topo(seqid)[source]
Parameters

seqid (str) – the id of the replicon

Returns

The default topology corresponding to the repliocon seqid in gembase format.

Return type

str ‘circ’ | ‘lin’

_parse(topology_file)[source]

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)[source]

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