mgkit.mappings.taxon module

Module used to map taxon_id to different levels in the taxonomy.

mgkit.mappings.taxon.map_taxon_by_id_list(taxon_id, map_ids, func)[source]

Maps a taxon_id to a list of taxon IDs, using the function supplied.

Parameters

  • taxon_id (int) – taxon ID to map

  • map_ids (iterable) – list of taxon IDs to which the taxon_id will be mapped.

  • func (func) – function used to map the IDs, accepts two taxon IDs

Results:
generator: generator expression of all IDs in map_ids to which taxon_id

can be mapped.

Example

If mapping a taxon (Prevotella ruminicola) to Prevotella or Clostridium, using as func mgkit.taxon.is_ancestor() and taxonomy is an instance of mgkit.taxon.Taxonomy.

>>> import functools
>>> from mgkit.taxon import is_ancestor
>>> func = functools.partial(is_ancestor, taxonomy)
>>> list(map_taxon_by_id_list(839, [838, 1485], func))
[838]