mgkit.filter.taxon module

New in version 0.1.9.

Taxa filtering functions

mgkit.filter.taxon.filter_by_ancestor(taxon_id, filter_list=None, exclude=False, taxonomy=None)[source]

New in version 0.1.13.

Convenience function for filter_taxon_by_id_list(), as explained in the latter example.

mgkit.filter.taxon.filter_taxon_by_id_list(taxon_id, filter_list=None, exclude=False, func=None)[source]

Filter a taxon_id against a list of taxon ids. Returns True if the conditions of the filter are met.

If func is not None, a function that accepts two values is expected, it should be either a partial is_ancestor which only accepts taxon_id and anc_id or another function that behaves the same way.

Note

if func is None, a simple lambda is used to test identity:

func = lambda t_id, a_id: t_id == a_id
Parameters

  • taxon_id (int) – the taxon id to filter

  • filter_list (iterable) – an iterable with taxon ids

  • exclude (bool) – if the filter is reversed (i.e. included if NOT found)

  • func (func or None) – a function that accepts taxon_id and an anc_id and returns a bool to indicated if anc_id is ancestor of taxon_id. Equivalent to is_ancestor().

Returns

True if the taxon_id is in the filter list (or a descendant of it) False if it’s not found. Exclude equal to True reverse the result.

Found

Exclude

Return Value

Yes

False

True

No

False

False

Yes

True

False

No

True

True

Return type

bool

Example

If using func and assuming that taxonomy is an instance of Taxonomy with data loaded:

>>> import functools
>>> import mgkit.taxon
>>> func = functools.partial(mgkit.taxon.is_ancestor, taxonomy)
>>> filter_taxon_by_id_list(1200582, [838], func=func)
True