def parse_json_file(file):
# returns a tuple: (species,reactions,compartments)
# species: { 'id' : Species(...) }
# reactions: { 'id' : Reaction(...) }
# compartments { 'id' : ('name','outside') }
model = util.parse_json_file(file)
compartments = {}
for compartment in model['compartments']:
compartments[compartment['id']] = (compartment['name'],compartment['outside'])
species = {}
for sp in model['species']:
species[sp['id']] = Species(sp['id'],name=sp['name'],compartment=sp['compartment'])
reactions = {}
for reaction in model['reactions']:
reactants = [copy.deepcopy(species[s]) for s in reaction['reactants']]
products = [copy.deepcopy(species[s]) for s in reaction['products']]
reactions[reaction['id']] = Reaction(reaction['id'],
reactants=reactants,
products=products,
reversible=reaction['reversible'],
subsystem=reaction['subsystem'])
return species,reactions,compartments
def parse_json_file(file):
# returns a tuple: (species,reactions,compartments)
# species: { 'id' : Species(...) }
# reactions: { 'id' : Reaction(...) }
# compartments { 'id' : ('name','outside') }
model = util.parse_json_file(file)
compartments = {}
for compartment in model['compartments']:
compartments[compartment['id']] = (compartment['name'],
compartment['outside'])
species = {}
for sp in model['species']:
species[sp['id']] = Species(sp['id'],
name=sp['name'],
compartment=sp['compartment'])
reactions = {}
for reaction in model['reactions']:
reactants = [copy.deepcopy(species[s]) for s in reaction['reactants']]
products = [copy.deepcopy(species[s]) for s in reaction['products']]
reactions[reaction['id']] = Reaction(reaction['id'],
reactants=reactants,
products=products,
reversible=reaction['reversible'],
subsystem=reaction['subsystem'])
return species, reactions, compartments
def read_json_config_file(filename):
defaults.clear()
defaults.update(util.parse_json_file(filename))
def to_fn(key):
# convert a string to a lambda expression in defaults
if key in defaults:
defaults[key] = eval(defaults[key])
# these two parameters are stored as strings in JSON, but should really be lambdas
to_fn("METABOLITE_LABEL_TRANSFORM")
to_fn("REACTION_LABEL_TRANSFORM")
def read_met_file(filename):
minors = []
json = filename.endswith('.json')
if json:
for minor in util.parse_json_file(filename)['minor_counts']:
if minor['minor']:
minors.append(minor['name'])
else:
with open(filename) as infile:
for line in iter(infile):
_, _, name = line.partition("\t")
if name[0] == '*':
minors.append(name.rstrip()[1:])
return minors
def read_met_file(filename):
minors = []
json = filename.endswith('.json')
if json:
for minor in util.parse_json_file(filename)['minor_counts']:
if minor['minor']:
minors.append(minor['name'])
else:
with open(filename) as infile:
for line in iter(infile):
_,_,name = line.partition("\t")
if name[0] == '*':
minors.append(name.rstrip()[1:])
return minors