def simple_merge_models(S, model_id2c_id2group, model_id2dfs, out_sbml):
doc = libsbml.SBMLDocument(2, 4)
model = doc.createModel()
model.setId('merged_model')
model_id2id2id = defaultdict(dict)
common_ids = set()
c_group2id = {}
new_m_id2i, new_r_id2i, new_efm_id2i, new_boundary_m_ids = {}, {}, {}, []
for model_id, [_, _, df] in model_id2dfs.items():
for index, row in df.iterrows():
c_id, name = row['Id'], row['Name']
if model_id in model_id2c_id2group and c_id in model_id2c_id2group[model_id]:
group = model_id2c_id2group[model_id][c_id]
if group in c_group2id:
new_id = c_group2id[group]
else:
new_id = create_compartment(model, name=name, id_='merged_%s_%s' % (model_id, c_id)).getId()
c_group2id[group] = new_id
common_ids.add(new_id)
else:
new_id = create_compartment(model, name=name, id_='%s_%s' % (model_id, c_id)).getId()
model_id2id2id[model_id][c_id] = new_id
id2id = {}
m_id_group_ids = set(S.m_id2gr_id.values())
for (model_id, m_id), i in ((it, i) for (it, i) in S.m_id2i.items() if it not in m_id_group_ids):
c_id = model_id2dfs[model_id][0].at[m_id, 'Compartment']
c_id = model_id2id2id[model_id][c_id]
name = model_id2dfs[model_id][0].at[m_id, 'Name']
is_boundary = (model_id, m_id) in S.boundary_m_ids
new_id = create_species(model, compartment_id=c_id, name=name, bound=is_boundary,
id_='%s_%s' % (model_id, m_id)).getId()
model_id2id2id[model_id][m_id] = new_id
id2id[(model_id, m_id)] = new_id
new_m_id2i[new_id] = i
if is_boundary:
new_boundary_m_ids.append(new_id)
for it in m_id_group_ids:
model_id, m_ids = next(iter(it))
m_id = next(iter(m_ids))
is_boundary = it in S.boundary_m_ids
new_id = \
create_species(model,
compartment_id=model_id2id2id[model_id][model_id2dfs[model_id][0].at[m_id, 'Compartment']],
name=model_id2dfs[model_id][0].at[m_id, 'Name'], bound=is_boundary,
id_='merged_%s_%s' % (model_id, m_id)).getId()
for model_id, m_ids in it:
model_id2id2id[model_id].update({m_id: new_id for m_id in m_ids})
id2id[it] = new_id
new_m_id2i[new_id] = S.m_id2i[it]
if is_boundary:
new_boundary_m_ids.append(new_id)
common_ids.add(new_id)
for ((model_id, r_id), i) in ((it, i) for (it, i) in S.r_id2i.items() if it not in S.gr_id2r_id2c.keys()):
r_id2st, p_id2st = S.st_matrix.get_inputs_outputs((model_id, r_id))
new_id = create_reaction(model, {id2id[m_id]: st for (m_id, st) in r_id2st.items()},
{id2id[m_id]: st for (m_id, st) in p_id2st.items()},
model_id2dfs[model_id][1].at[r_id, 'Name'], reversible=True,
id_='%s_%s' % (model_id, r_id)).getId()
model_id2id2id[model_id][r_id] = new_id
new_r_id2i[new_id] = i
for gr, it2c in S.gr_id2r_id2c.items():
model_id, r_id = next(iter(it2c.keys()))
r_id2st, p_id2st = S.st_matrix.get_inputs_outputs(gr)
new_id = \
create_reaction(model, {id2id[m_id]: st for (m_id, st) in r_id2st.items()},
{id2id[m_id]: st for (m_id, st) in p_id2st.items()},
model_id2dfs[model_id][1].at[r_id, 'Name'], reversible=True,
id_='merged_%s_%s' % (model_id, r_id)).getId()
for model_id, r_id in it2c.keys():
model_id2id2id[model_id][r_id] = new_id
new_r_id2i[new_id] = S.r_id2i[gr]
common_ids.add(new_id)
for ((model_id, efm_id), i) in ((it, i) for (it, i) in S.efm_id2i.items() if it not in S.gr_id2efm_ids.keys()):
new_id = '%s_%s' % (model_id, efm_id)
new_efm_id2i[new_id] = i
model_id2id2id[model_id][efm_id] = new_id
for gr, efm_ids in S.gr_id2efm_ids.items():
model_id, efm_id = next(efm_ids)
new_id = 'merged_%s_%s' % (model_id, efm_id)
new_efm_id2i[new_id] = S.r_id2i[gr]
for model_id, efm_id in efm_ids:
model_id2id2id[model_id][efm_id] = new_id
libsbml.writeSBMLToFile(doc, out_sbml)
return model_id2id2id, common_ids, System(m_id2i=new_m_id2i, r_id2i=new_r_id2i, efm_id2i=new_efm_id2i, N=S.N, V=S.V,
boundary_m_ids=new_boundary_m_ids)
def check_compartments(model):
if not model.getListOfCompartments():
cell = create_compartment(model, "cell", outside=None)
add_annotation(cell, libsbml.BQB_IS, "GO:0005623", GO_PREFIX)
for sp in model.getListOfSpecies():
sp.setCompartment(cell.getId())