usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
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]
# Get the genome object from the workspace.
wsClient = Workspace(url=args.wsURL, token=args.token)
try:
# The get() method returns an array of tuples where the first element is
# the object's metadata (which is valid json) and the second element is
# the object's data (which is not valid json).
object = wsClient.get({ 'objects': [ args.genomeref ] })
genome = json.loads(object[0][1])
except WorkspaceServerError as e:
sys.stderr.write('Failed to get genome using reference %s\n' %(args.genomeref))
exit(1)
# Create a worker for running the algorithm.
worker = ProbAnnotationWorker(genome['id'])
# Run the probabilistic annotation algorithm.
complexesFile = os.path.join(args.templatedir, '..', 'Complexes.tsv')
helper.readComplexesFile(complexesFile, includeLinenum=False)
template['complexes'] = [helper.complexes[key] for key in helper.complexes]
# Add the template reactions.
reactionsFile = os.path.join(args.templatedir, 'Reactions.tsv')
helper.readReactionsFile(reactionsFile, includeLinenum=False)
template['reactions'] = [helper.reactions[key] for key in helper.reactions]
# Add the template compounds (constructed from reagents in reactions).
template['compounds'] = [helper.compounds[key] for key in helper.compounds]
# Add the template comp compounds (constructed from reagents in reactions).
template['compcompounds'] = [
helper.compCompounds[key] for key in helper.compCompounds
]
# Save a local copy for easy reference.
filename = os.path.join(args.templatedir, args.id + '.json')
json.dump(template, open(filename, 'w'), indent=4)
# Save the Model Template typed object to the specified workspace path. An existing typed object
# is overwritten with the updated data.
wsClient = Workspace(args.wsurl)
output = wsClient.create({
'objects': [[args.ref, 'modeltemplate', {}, template]],
'overwrite':
1
})
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:
'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)
else:
print 'WARNING: Compound %s is not defined in the list of compounds' %(cpd['compound'])
# Add compartment the first time it is found.
if cpd['compartmentId'] not in compartments:
compartments[cpd['compartmentId']] = { 'id': cpd['compartmentId'], 'name': 'Compartment'+cpd['compartmentId'], 'hierarchy': 3}
reagent['compartment_ref'] = '~/compartments/id/'+cpd['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)