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"""Test functionalities of gap filling."""
from cobra.core import Metabolite, Model, Reaction
from cobra.flux_analysis.gapfilling import GapFiller, gapfill
def test_gapfilling(salmonella: Model) -> None:
"""Test Gapfilling."""
m = Model()
m.add_metabolites([Metabolite(m_id) for m_id in ["a", "b", "c"]])
exa = Reaction("EX_a")
exa.add_metabolites({m.metabolites.a: 1})
b2c = Reaction("b2c")
b2c.add_metabolites({m.metabolites.b: -1, m.metabolites.c: 1})
dmc = Reaction("DM_c")
dmc.add_metabolites({m.metabolites.c: -1})
m.add_reactions([exa, b2c, dmc])
m.objective = "DM_c"
universal = Model()
a2b = Reaction("a2b")
a2d = Reaction("a2d")
universal.add_reactions([a2b, a2d])
a2b.build_reaction_from_string("a --> b", verbose=False)
a2d.build_reaction_from_string("a --> d", verbose=False)
# # GrowMatch
# result = gapfilling.growMatch(m, universal)[0]
result = gapfill(m, universal)[0]
assert len(result) == 1
assert result[0].id == "a2b"
# # SMILEY
# result = gapfilling.SMILEY(m, "b", universal)[0]
with m:
m.objective = m.add_boundary(m.metabolites.b, type="demand")
result = gapfill(m, universal)[0]
assert len(result) == 1
assert result[0].id == "a2b"
# # 2 rounds of GrowMatch with exchange reactions
# result = gapfilling.growMatch(m, None, ex_rxns=True, iterations=2)
result = gapfill(m, None, exchange_reactions=True, iterations=2)
assert len(result) == 2
assert len(result[0]) == 1
assert len(result[1]) == 1
assert {i[0].id for i in result} == {"EX_b", "EX_c"}
# # Gapfilling solution adds metabolites not present in original model
# test for when demand = T
# a demand reaction must be added to clear new metabolite
universal_noDM = Model()
a2b = Reaction("a2b")
universal_noDM.add_reactions([a2b])
a2b.build_reaction_from_string("a --> b + d", verbose=False)
result = gapfill(
m, universal_noDM, exchange_reactions=False, demand_reactions=True
)[0]
# add reaction a2b and demand reaction to clear met d
assert len(result) == 2
assert "a2b" in [x.id for x in result]
# test for when demand = False
# test for when metabolites are added to the model and
# must be cleared by other reactions in universal model
# (i.e. not necessarily a demand reaction)
universal_withDM = universal_noDM.copy()
d_dm = Reaction("d_dm")
universal_withDM.add_reactions([d_dm])
d_dm.build_reaction_from_string("d -->", verbose=False)
result = gapfill(
m, universal_withDM, exchange_reactions=False, demand_reactions=False
)[0]
assert len(result) == 2
assert "a2b" in [x.id for x in result]
# somewhat bigger model
universal = Model("universal_reactions")
with salmonella as model:
for i in [i.id for i in model.metabolites.f6p_c.reactions]:
reaction = model.reactions.get_by_id(i)
universal.add_reactions([reaction.copy()])
model.remove_reactions([reaction])
gf = GapFiller(
model, universal, penalties={"TKT2": 1e3}, demand_reactions=False
)
solution = gf.fill()
assert "TKT2" not in {r.id for r in solution[0]}
assert gf.validate(solution[0])
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