Search HGNC when you can't remember the official gene symbol.

search_hgnc.py

from http_get import http_get # uses https://gist.github.com/dmyersturnbull/fade1a5901beeb1003680f8267454640
from typing import Mapping, Union, Iterable
import json

searchable_fields = {'alias_name', 'alias_symbol', 'ccds_id', 'ena', 'ensemble_gene_id',
                    'entrez_id', 'hgnc_id', 'locus_group', 'locus_type', 'mgd_id',
                    'name', 'prev_name', 'prev_symbol', 'refseq_accession', 'rgd_id',
                    'status', 'symbol', 'ucsc_id', 'uniprot_ids', 'vega_id'}


def search_hgnc(fields: Union[Mapping[str, str], str]) -> Iterable[str]:
    """Searches HGNC and returns a list of HGNC symbol IDs.
    fields is either:
        A) A map of field names (contained in searchable_fields) to their values
        B) A string for the name field; i.e. search_hgnc('abc') === search_hgnc({'name': 'abc'})
    """
    if isinstance(fields, str):
        fields = {'name': fields}
    for key in fields.keys():
        if key not in searchable_fields:
            raise ValueError("'{}' is not a searchable field".format(key))
    query = 'http://rest.genenames.org/search/' + '+AND+'.join([key + ':' + value for key, value in fields.items()])
    text = http_get(query, {'Accept': 'application/json'})
    results = json.loads(text)
    return [x['symbol'] for x in results['response']['docs']]