topology¶
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class
integron_finder.topology.
Topology
(default, topology_file=None)[source]¶ Class to parse and handle replicons topologies
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__getitem__
(replicon_id)[source]¶ Parameters: replicon_id (str) – The id of the replicon. Returns: the topology for the replicon corresponding to the replicon_id
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__init__
(default, topology_file=None)[source]¶ Parameters: - default (str) – the default topology
- topology_file – the path to the file where topology for replicon are specified
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__weakref__
¶ list of weak references to the object (if defined)
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_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
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