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"""Unit test the MetaboliteSummary class."""
import pytest
from cobra.flux_analysis import flux_variability_analysis, pfba
from cobra.summary import MetaboliteSummary
def test_metabolite_summary_interface(model, opt_solver):
"""Test that a summary can be created successfully."""
model.solver = opt_solver
metabolite = model.metabolites.get_by_id("q8_c")
MetaboliteSummary(
metabolite=metabolite,
model=model,
)
MetaboliteSummary(
metabolite=metabolite,
model=model,
solution=pfba(model),
)
MetaboliteSummary(
metabolite=metabolite,
model=model,
fva=0.95,
)
MetaboliteSummary(
metabolite=metabolite,
model=model,
fva=flux_variability_analysis(
model, reaction_list=["CYTBD", "NADH16", "SUCDi"]
),
)
def test_metabolite_summary_to_frame(model, opt_solver):
"""Test that the summary's method ``to_frame`` can be called."""
model.solver = opt_solver
summary = model.metabolites.get_by_id("atp_c").summary()
summary.to_frame()
@pytest.mark.parametrize(
"kwargs",
[
{},
{"names": True},
{"float_format": ".1f"},
{"threshold": 1e-2},
{"column_width": 20},
],
)
def test_metabolite_summary_to_string(model, opt_solver, kwargs):
"""Test that the summary's method ``to_string`` can be called."""
model.solver = opt_solver
summary = model.metabolites.get_by_id("atp_c").summary()
summary.to_string(**kwargs)
@pytest.mark.parametrize(
"kwargs", [{}, {"names": True}, {"float_format": ".1f"}, {"threshold": 1e-2}]
)
def test_metabolite_summary_to_html(model, opt_solver, kwargs):
"""Test that the summary's method ``to_html`` can be called."""
model.solver = opt_solver
summary = model.metabolites.get_by_id("atp_c").summary()
summary.to_html(**kwargs)
def test_q8_producing_summary(model, opt_solver):
"""Test that the production summary of q8 is accurate."""
model.solver = opt_solver
summary = model.metabolites.get_by_id("q8_c").summary()
assert summary.producing_flux.at["CYTBD", "percent"] == 1
assert summary.producing_flux.at["CYTBD", "flux"] == pytest.approx(43.6, abs=1e-2)
def test_q8_consuming_summary(model, opt_solver):
"""Test that the consumption summary of q8 is accurate."""
model.solver = opt_solver
summary = model.metabolites.get_by_id("q8_c").summary()
assert summary.consuming_flux.at["NADH16", "percent"] == pytest.approx(
0.8838, abs=1e-4
)
assert summary.consuming_flux.at["NADH16", "flux"] == pytest.approx(
-38.54, abs=1e-2
)
assert summary.consuming_flux.at["SUCDi", "percent"] == pytest.approx(
0.1162, abs=1e-4
)
assert summary.consuming_flux.at["SUCDi", "flux"] == pytest.approx(-5.06, abs=1e-2)
def test_fdp_production_with_fva(model, opt_solver):
"""Test that the production summary of fdp is within expected bounds."""
model.solver = opt_solver
summary = model.metabolites.get_by_id("fdp_c").summary(fva=0.99)
assert summary.producing_flux.at["PFK", "percent"] == 1
assert summary.producing_flux.at["PFK", "flux"] == pytest.approx(7.48, abs=1e-2)
assert summary.producing_flux.at["PFK", "minimum"] == pytest.approx(6.17, abs=1e-2)
assert summary.producing_flux.at["PFK", "maximum"] == pytest.approx(9.26, abs=1e-2)
@pytest.mark.parametrize("metabolite_id", ["q8_c", "fdp_c", "atp_c"])
def test_metabolite_summary_flux_in_context(model, opt_solver, metabolite_id: str):
"""Test that the metabolite summary inside and outside of a context are equal."""
model.solver = opt_solver
with model:
context_summary = model.metabolites.get_by_id(metabolite_id).summary()
outside_summary = model.metabolites.get_by_id(metabolite_id).summary()
assert context_summary.to_frame()["flux"].values == pytest.approx(
outside_summary.to_frame()["flux"].values, abs=model.tolerance
)
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