def _get_react_name_by_kegg_react_id(react_id):
if not react_id.startswith('rn:'):
react_id = 'rn:' + react_id
try:
name, equ = KeggReaction.infos_by_id()[react_id]
return name
except KeyError:
return react_id + ' (can not map kegg id)'
def populate_kegg_reactions_table():
"""
TODO use sqlite3 std lib to use bulk insert
takes too long...
"""
import bioservices
logging.info('Getting all kegg reactions..')
kegg = bioservices.KEGG()
logging.info('Done.')
r = kegg.list('reaction')
reactions = r.strip().split('\n')
logging.info('Begin insertion...')
for react in reactions:
react_id, plus = react.split('\t')
p = plus.split(';')
try:
name, equation = p[0], p[1]
except (ValueError, IndexError):
name, equation = p[0], p[0]
k = KeggReaction()
k.id = react_id
k.name = name
k.organism = equation
k.save()
logging.info('Done.')
