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"""Test functionalities of ROOM."""
from typing import List
import pytest
from cobra import Model
from cobra.flux_analysis.room import add_room
@pytest.mark.parametrize(
"linear, delta, eps",
[(True, 0.03, 1e-3), (False, 0.03, 1e-3), (True, 0.1, 1e-2), (False, 0.1, 1e-2)],
)
def test_room_sanity(
model: Model, all_solvers: List[str], linear: bool, delta: float, eps: float
) -> None:
"""Test optimization criterion and optimality for ROOM."""
model.solver = all_solvers
sol = model.optimize()
with model:
model.reactions.PYK.knock_out()
knock_sol = model.optimize()
with model:
# let it calculate its own reference solution (pFBA)
add_room(model, linear=linear, delta=delta, epsilon=eps)
model.reactions.PYK.knock_out()
room_sol = model.optimize()
with model:
# use the more distant FBA reference
add_room(model, solution=sol, linear=linear, delta=delta, epsilon=eps)
model.reactions.PYK.knock_out()
room_sol_ref = model.optimize()
# The
flux_change = (sol.fluxes - knock_sol.fluxes).abs()
flux_change_room = (sol.fluxes - room_sol.fluxes).abs()
flux_change_room_ref = (sol.fluxes - room_sol_ref.fluxes).abs()
rxn_count_naive = (flux_change > delta * sol.fluxes.abs() + eps + 1e-6).sum()
rxn_count_room = (flux_change_room > delta * sol.fluxes.abs() + eps + 1e-6).sum()
rxn_count_room_ref = (
flux_change_room_ref > delta * sol.fluxes.abs() + eps + 1e-6
).sum()
# Expect the ROOM solution to have less changed reactions then a pFBA or FBA
assert rxn_count_room <= rxn_count_naive
assert rxn_count_room_ref <= rxn_count_naive
|
