Example #1
0
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
Example #2
0
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
Example #3
0
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")
Example #4
0
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
Example #5
0
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