Source code for indra.databases.biogrid_client

from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str
from future.utils import python_2_unicode_compatible
import os
import json
import logging
import requests
from collections import Counter
from indra.statements import Complex, Agent, Evidence

biogrid_url = ''

logger = logging.getLogger('biogrid')

# For more information see
api_key_file = os.path.dirname(os.path.realpath(__file__)) + '/' + \
api_key_env_name = 'BIOGRID_API_KEY'

# Try to read the API key from a file
    with open(api_key_file, 'rt') as fh:
        api_key =
except IOError:
    logger.error('BioGRID API key could not be found, trying environment '
                 'variable $%s.' % api_key_env_name)
    # Try the environment variable
    if api_key_env_name in os.environ:
        api_key = os.environ.get(api_key_env_name)
        logger.error('No BioGRID API key found in environment variable '
                     '%s.' % api_key_env_name)
        api_key = None

def get_interactors(gene_name):
    res_dict = _send_request([gene_name], include_interactors=True)
    interaction_list = []
    for result in res_dict.values():
        if result['OFFICIAL_SYMBOL_A'] == gene_name and \
           result['OFFICIAL_SYMBOL_B'] == gene_name:
        elif result['OFFICIAL_SYMBOL_A'] == gene_name:
        elif result['OFFICIAL_SYMBOL_B'] == gene_name:
            assert False, "Interaction doesn't contain target gene!"
    interaction_counter = Counter(interaction_list)
    interaction_counter = sorted(interaction_counter.items(),
                                 key=lambda x: x[1], reverse=True)
    return interaction_counter

def get_statements(gene_list):
    res_dict = _send_request(gene_list, include_interactors=True)
    statements = []
    for int_id, interaction in res_dict.items():
        agent_a_name = interaction['OFFICIAL_SYMBOL_A']
        agent_b_name = interaction['OFFICIAL_SYMBOL_B']
        agent_a = Agent(agent_a_name, db_refs={'HGNC': agent_a_name})
        agent_b = Agent(agent_b_name, db_refs={'HGNC': agent_b_name})
        ev = Evidence(source_api='biogrid',
        stmt = Complex([agent_a, agent_b], evidence=ev)
    return statements

[docs]def get_publications(gene_names, save_json_name=None): """Return evidence publications for interaction between the given genes. Parameters ---------- gene_names : list[str] A list of gene names (HGNC symbols) to query interactions between. Currently supports exactly two genes only. save_json_name : Optional[str] A file name to save the raw BioGRID web service output in. By default, the raw output is not saved. Return ------ publications : list[Publication] A list of Publication objects that provide evidence for interactions between the given list of genes. """ if len(gene_names) != 2: logger.warning('Other than 2 gene names given.') return [] res_dict = _send_request(gene_names) if not res_dict: return [] if save_json_name is not None: # The json module produces strings, not bytes, so the file should be # opened in text mode with open(save_json_name, 'wt') as fh: json.dump(res_dict, fh, indent=1) publications = _extract_publications(res_dict, gene_names) return publications
@python_2_unicode_compatible class Publication(object): def __init__(self, interaction, interaction_id): self.pmid = "PMID" + str(interaction['PUBMED_ID']) self.modification = interaction['MODIFICATION'] self.experimental_system = interaction['EXPERIMENTAL_SYSTEM'] self.experimental_system_type = interaction['EXPERIMENTAL_SYSTEM_TYPE'] self.throughput = interaction['THROUGHPUT'] self.interaction_id = interaction_id def __str__(self): return "Publication(%s)" % self.pmid def __repr__(self): return str(self) def _extract_publications(res_dict, gene_names): res_filtered = _filter_results(res_dict, gene_names) publications = [] for interaction_id in res_filtered.keys(): pub = Publication(res_filtered[interaction_id], interaction_id) publications.append(pub) return publications def _filter_results(res_dict, gene_names): filtered_dict = {} for interaction_id in res_dict.keys(): interactors = [res_dict[interaction_id]['OFFICIAL_SYMBOL_A'], res_dict[interaction_id]['OFFICIAL_SYMBOL_B']] if set(interactors) == set(gene_names): filtered_dict[interaction_id] = res_dict[interaction_id] return filtered_dict def _send_request(gene_names, include_interactors=False): if api_key is None: logger.error('BioGRID cannot be used without API key') return None params = {'searchNames': 'true', 'geneList': '|'.join(gene_names), 'taxId': '9606', 'format': 'json', 'includeInteractors': include_interactors, 'accesskey': api_key} res = requests.get(biogrid_url, params) res.raise_for_status() # The json module handles the conversion from bytes to unicode internally res_dict = res.json() return res_dict