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