def dump_model(bigg_id):
session = Session()
# find the model
model_db = (session
.query(Model)
.filter(Model.bigg_id == bigg_id)
.first())
if model_db is None:
session.commit()
session.close()
raise Exception('Could not find model %s' % bigg_id)
model = cobra.core.Model(bigg_id)
# COBRApy uses the description as the ID sometimes. See
# https://github.com/opencobra/cobrapy/pull/152
model.description = bigg_id
# genes
logging.debug('Dumping genes')
gene_names = (session
.query(Gene.bigg_id, Gene.name)
.join(ModelGene)
.filter(ModelGene.model_id == model_db.id)
.order_by(Gene.bigg_id)
)
for gene_id, gene_name in gene_names:
gene = cobra.core.Gene(gene_id)
gene.name = gene_name
model.genes.append(gene)
# reactions
logging.debug('Dumping reactions')
reactions_db = (session
.query(Reaction, ModelReaction, Synonym)
.join(ModelReaction)
.join(OldIDSynonym, OldIDSynonym.ome_id == ModelReaction.id)
.join(Synonym, Synonym.id == OldIDSynonym.synonym_id)
.filter(ModelReaction.model_id == model_db.id)
.order_by(Reaction.bigg_id)
)
# make dictionaries and cast results
result_dicts = []
for r_db, mr_db, synonym_db in reactions_db:
d = {}
d['bigg_id'] = r_db.bigg_id
d['name'] = r_db.name
d['gene_reaction_rule'] = mr_db.gene_reaction_rule
d['lower_bound'] = float(mr_db.lower_bound)
d['upper_bound'] = float(mr_db.upper_bound)
d['objective_coefficient'] = float(mr_db.objective_coefficient)
d['original_bigg_id'] = synonym_db.synonym
result_dicts.append(d)
def filter_duplicates(result_dicts):
"""Find the reactions with multiple ModelReactions and increment names."""
tups_by_bigg_id = defaultdict(list)
# for each ModelReaction
for d in result_dicts:
# add to duplicates
tups_by_bigg_id[d['bigg_id']].append(d)
# duplicates have multiple ModelReactions
duplicates = {k: v for k, v in tups_by_bigg_id.iteritems() if len(v) > 1}
for bigg_id, dup_dicts in duplicates.iteritems():
# add -copy1, copy2, etc. to the bigg ids for the duplicates
last = bigg_id
for d in dup_dicts:
last = increment_id(last, 'copy')
d['bigg_id'] = last
return result_dicts
# fix duplicates
result_filtered = filter_duplicates(result_dicts)
reactions = []
for result_dict in result_filtered:
r = cobra.core.Reaction(result_dict['bigg_id'])
r.name = result_dict['name']
r.gene_reaction_rule = result_dict['gene_reaction_rule']
r.lower_bound = result_dict['lower_bound']
r.upper_bound = result_dict['upper_bound']
r.objective_coefficient = result_dict['objective_coefficient']
r.notes = {'original_bigg_id': result_dict['original_bigg_id']}
reactions.append(r)
model.add_reactions(reactions)
# metabolites
logging.debug('Dumping metabolites')
metabolites_db = \
(session
.query(Component.bigg_id, Compartment.bigg_id, Component.name)
.join(CompartmentalizedComponent)
.join(Compartment)
.join(ModelCompartmentalizedComponent)
.filter(ModelCompartmentalizedComponent.model_id == model_db.id)
.order_by(Component.bigg_id)
)
metabolites = []
compartments = set()
for component_id, compartment_id, component_name in metabolites_db:
if component_id is not None and compartment_id is not None:
m = cobra.core.Metabolite(
id=component_id + '_' + compartment_id,
compartment=compartment_id)
m.name = component_name
compartments.add(compartment_id)
metabolites.append(m)
model.add_metabolites(metabolites)
# compartments
compartment_db = (session.query(Compartment)
.filter(Compartment.bigg_id.in_(compartments)))
model.compartments = {i.bigg_id: i.name for i in compartment_db}
# reaction matrix
logging.debug('Dumping reaction matrix')
matrix_db = (session
.query(ReactionMatrix.stoichiometry, Reaction.bigg_id,
Component.bigg_id, Compartment.bigg_id)
# component, compartment
.join(CompartmentalizedComponent)
.join(Component)
.join(Compartment)
# reaction
.join(Reaction)
.join(ModelReaction)
.filter(ModelReaction.model_id == model_db.id)
.distinct()) # make sure we don't duplicate
# load metabolites
for stoich, reaction_id, component_id, compartment_id in matrix_db:
try:
m = model.metabolites.get_by_id(component_id + '_' + compartment_id)
except KeyError:
logging.warn('Metabolite not found %s in compartment %s for reaction %s' % \
(component_id, compartment_id, reaction_id))
continue
# add to reactions
if reaction_id in model.reactions:
# check again that we don't duplicate
r = model.reactions.get_by_id(reaction_id)
if m not in r.metabolites:
r.add_metabolites({m: float(stoich)})
else:
# try incremented ids
while True:
reaction_id = increment_id(reaction_id, 'copy')
try:
# check again that we don't duplicate
r = model.reactions.get_by_id(reaction_id)
if m not in r.metabolites:
r.add_metabolites({m: float(stoich)})
except KeyError:
break
session.commit()
session.close()
return model
