'compartmentId']
reagent['coefficient'] = cpd['stoich']
reagent[
'isCofactor'] = 0 # @todo Is this set separately from value in compound?
rxn['reagents'].append(reagent)
del rxn['equation'] # Remove after converting to reagent format
biochem['reactions'].append(rxn)
# Create the compartment list from the dictionary assembled above.
biochem['compartments'] = list()
for id in compartments:
biochem['compartments'].append(compartments[id])
# Add the aliases from all of the aliases files.
print(('Reading aliases from %s ...' % (args.aliasdir)))
compoundAliases, reactionAliases = helper.readAliasFiles(args.aliasdir)
biochem['compound_aliases'] = compoundAliases
biochem['reaction_aliases'] = reactionAliases
# Save the Biochemistry typed object to the specified workspace path. An existing typed object
# is overwritten with the updated data.
print(('Saving typed object to %s ...' % (args.ref)))
wsClient = Workspace(args.wsurl)
output = wsClient.create({
'objects': [[args.ref, 'biochemistry', {}, biochem]],
'overwrite':
1
})
# json.dump(biochem, open('master.json', 'w'), indent=4)
exit(0)
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Get the token from the config file if one is not provided.
if args.token is None:
authdata = _read_inifile()
args.token = authdata['token']
# Workaround for extraneous delimiter tacked on the end of references.
if args.genomeref[-2:] == '||':
args.genomeref = args.genomeref[:-2]
if args.templateref[-2:] == '||':
args.templateref = args.templateref[:-2]
# Get the genome object from the workspace (for the features).
wsClient = Workspace(url=args.wsURL, token=args.token)
genome = getObject(wsClient, args.genomeref, args.token)
# Get the template object from the workspace (for the complexes and roles).
template = getObject(wsClient, args.templateref, args.token)
# Build a dictionary to look up roles in the template by ID.
roles = dict()
for index in range(len(template['roles'])):
roles[template['roles'][index]['id']] = index
# Create a dictionary to map a complex to a list of roles as defined in the template.
complexesToRoles = dict()
for index in range(len(template['complexes'])):
complexId = template['complexes'][index]['id']
if len(template['complexes'][index]['complexroles']) > 0:
