"""A client for accessing MGI mouse gene data."""
from collections import defaultdict
from typing import List, Union
from indra.util import read_unicode_csv
from indra.resources import get_resource_path
[docs]def get_id_from_name(name: str) -> Union[str, None]:
"""Return an MGI ID from an MGI gene symbol.
Parameters
----------
name :
The MGI gene symbol whose ID will be returned.
Returns
-------
:
The MGI ID (without prefix) or None if not available.
"""
return mgi_name_to_id.get(name)
[docs]def get_name_from_id(mgi_id: str) -> Union[str, None]:
"""Return the MGI gene symbol for a given MGI ID.
Parameters
----------
mgi_id :
The MGI ID (without prefix) whose symbol will be returned.
Returns
-------
:
The MGI symbol for the given ID or None if not available.
"""
if mgi_id and mgi_id.startswith('MGI:'):
mgi_id = mgi_id[4:]
return mgi_id_to_name.get(mgi_id)
[docs]def get_synonyms(mgi_id: str) -> List[str]:
"""Return the synonyms for an MGI ID.
Parameters
----------
mgi_id :
An MGI ID, without prefix.
Returns
-------
:
The list of synonyms corresponding to the MGI ID, or an empty list
if not available.
"""
if mgi_id and mgi_id.startswith('MGI:'):
mgi_id = mgi_id[4:]
return mgi_synonyms.get(mgi_id, [])
[docs]def get_id_from_name_synonym(name_synonym: str) -> Union[None, str, List[str]]:
"""Return an MGI ID from an MGI gene symbol or synonym.
If the given name or synonym is the official symbol of a gene, its
ID is returned. If the input is a synonym, it can correspond to
one or more genes. If there is a single gene whose synonym matches
the input, the ID is returned as a string. If multiple genes share
the given synonym, their IDs are returned in a list. If the input
doesn't match any names or synonyms, None is returned.
Parameters
----------
name_synonym :
The MGI gene symbol or synonym whose ID will be returned.
Returns
-------
:
The MGI ID (without prefix) of a single gene, a list of MGI IDs,
or None.
"""
mgi_id = mgi_name_to_id.get(name_synonym)
if mgi_id:
return mgi_id
mgi_ids = mgi_synonyms_reverse.get(name_synonym)
if mgi_ids:
if len(mgi_ids) == 1:
return mgi_ids[0]
else:
return mgi_ids
return None
def _read_mgi():
fname = get_resource_path('mgi_entries.tsv')
mgi_id_to_name = {}
mgi_name_to_id = {}
mgi_synonyms = {}
mgi_synonyms_reverse = defaultdict(list)
for mgi_id, name, synonyms_str in read_unicode_csv(fname, '\t'):
if name:
mgi_id_to_name[mgi_id] = name
mgi_name_to_id[name] = mgi_id
if synonyms_str:
synonyms = synonyms_str.split('|')
mgi_synonyms[mgi_id] = synonyms
for synonym in synonyms:
mgi_synonyms_reverse[synonym].append(mgi_id)
return mgi_id_to_name, mgi_name_to_id, mgi_synonyms, \
dict(mgi_synonyms_reverse)
mgi_id_to_name, mgi_name_to_id, mgi_synonyms, mgi_synonyms_reverse = _read_mgi()