"""
Mapping functions for SNPs - Should be move into an 'iterator' package to
be shared with other modules?
"""
[docs]def map_gene_id(gene_id, gene_map=None):
"""
Returns an iterator for all the values of a dictionary. if gene_id is not
found in the gene_map, an empty iterator is returned.
Arguments:
gene_id (immutable): gene_id or any other dictionary key.
gene_map (dict): a dictionary in the form key->[v1, v2, .. vN]
Returns:
generator: iterator (empty if gene_id is not in gene_map) with the
values
"""
if gene_id not in gene_map:
return
for map_id in gene_map[gene_id]:
yield map_id
[docs]def map_taxon_id_to_rank(taxon_id, rank=None, taxonomy=None,
include_higher=False):
"""
Given a taxon_id, returns an iterator with only the element that correspond
to the requested rank. If the taxon returned by
:class:`mgkit.taxon.Taxonomy.get_ranked_taxon` has a different rank
than requested, the iterator will be empty if `include_higher` is False
and the returned taxon ID if True.
Arguments:
taxon_id (int): taxon ID to be mapped
rank (str): taxon rank used (:data:`mgkit.taxon.TAXON_RANKS`)
include_higher (bool): determines if a rank higher than the one
requested is to be returned
Returns:
generator: iterator with the values or empty
"""
ranked_taxon = taxonomy.get_ranked_taxon(taxon_id, rank=rank)
# in case we don't want to include higher taxa
if (ranked_taxon.rank != rank) and (not include_higher):
return
yield ranked_taxon.taxon_id
[docs]def map_taxon_id_to_ancestor(taxon_id, anc_ids=None, func=None):
"""
Given a taxon_id and a list of ancestors IDs, returns an iterator with the
IDs that are ancestors of taxon_id.
Arguments:
taxon_id (int): taxon ID to be mapped
anc_ids (iterable): taxon IDs to check for ancestry
func: function used to check for ancestry - partial function for
:func:`mgkit.taxon.is_ancestor` that accepts taxon_id and anc_id
Returns:
generator: iterator with the values or empty
.. note::
check :func:`mgkit.filter.taxon.filter_taxon_by_id_list` for examples
on using func
"""
for anc_id in anc_ids:
if func(taxon_id, anc_id):
yield anc_id