"""Test functionalities of reaction and gene deletions."""
import math
from typing import Callable, List
import numpy as np
import pandas as pd
import pytest
from cobra import Model, Solution
from cobra.flux_analysis.deletion import (
double_gene_deletion,
double_reaction_deletion,
single_gene_deletion,
single_reaction_deletion,
)
from cobra.flux_analysis.room import add_room
# Single gene deletion FBA
[docs]def test_single_gene_deletion_fba_benchmark(
model: Model, benchmark: Callable, all_solvers: List[str]
) -> None:
"""Benchmark single gene deletion using FBA."""
model.solver = all_solvers
benchmark(single_gene_deletion, model)
[docs]def test_single_gene_deletion_fba(model: Model, all_solvers: List[str]) -> None:
"""Test single gene deletion using FBA."""
# expected knockouts for textbook model
model.solver = all_solvers
growth_dict = {
"b0008": 0.87,
"b0114": 0.80,
"b0116": 0.78,
"b2276": 0.21,
"b1779": 0.00,
}
result = single_gene_deletion(
model=model, gene_list=list(growth_dict), method="fba", processes=1
)
for gene, value in growth_dict.items():
assert np.isclose(result.knockout[gene].growth, value, atol=1e-02)
# Singe gene deletion MOMA
[docs]def test_single_gene_deletion_moma_benchmark(
model: Model, benchmark: Callable, qp_solvers: List[str]
) -> None:
"""Benchmark single gene deletion using MOMA."""
model.solver = qp_solvers
genes = ["b0008", "b0114", "b2276", "b1779"]
benchmark(
single_gene_deletion,
model=model,
gene_list=genes,
method="moma",
processes=1,
)
[docs]def test_single_gene_deletion_moma(model: Model, qp_solvers: List[str]) -> None:
"""Test single gene deletion using MOMA."""
model.solver = qp_solvers
# expected knockouts for textbook model
growth_dict = {
"b0008": 0.87,
"b0114": 0.71,
"b0116": 0.56,
"b2276": 0.11,
"b1779": 0.00,
}
result = single_gene_deletion(
model=model, gene_list=list(growth_dict), method="moma", processes=1
)
for gene, value in growth_dict.items():
assert np.isclose(result.knockout[gene].growth, value, atol=1e-02)
[docs]def test_single_gene_deletion_moma_reference(
model: Model, qp_solvers: List[str]
) -> None:
"""Test single gene deletion using MOMA (reference solution)."""
model.solver = qp_solvers
# expected knockouts for textbook model
growth_dict = {
"b0008": 0.87,
"b0114": 0.71,
"b0116": 0.56,
"b2276": 0.11,
"b1779": 0.00,
}
sol = model.optimize()
result = single_gene_deletion(
model=model,
gene_list=list(growth_dict),
method="moma",
solution=sol,
processes=1,
)
for gene, value in growth_dict.items():
assert np.isclose(result.knockout[gene].growth, value, atol=1e-02)
# Single gene deletion linear MOMA
[docs]def test_single_gene_deletion_linear_moma_benchmark(
model: Model, benchmark: Callable, all_solvers: List[str]
) -> None:
"""Benchmark single gene deletion using linear MOMA."""
model.solver = all_solvers
genes = ["b0008", "b0114", "b2276", "b1779"]
benchmark(
single_gene_deletion,
model=model,
gene_list=genes,
method="linear moma",
processes=1,
)
[docs]def test_single_gene_deletion_linear_moma(model: Model, all_solvers: List[str]) -> None:
"""Test single gene deletion using linear MOMA (reference solution)."""
model.solver = all_solvers
# expected knockouts for textbook model
growth_dict = {
"b0008": 0.87,
"b0114": 0.76,
"b0116": 0.65,
"b2276": 0.08,
"b1779": 0.00,
}
sol = model.optimize()
result = single_gene_deletion(
model=model,
gene_list=list(growth_dict),
method="linear moma",
solution=sol,
processes=1,
)
for gene, value in growth_dict.items():
assert np.isclose(result.knockout[gene].growth, value, atol=1e-02)
# Single gene deletion ROOM
[docs]def test_single_gene_deletion_room_benchmark(
model: Model, benchmark: Callable, all_solvers: List[str]
) -> None:
"""Benchmark single gene deletion using ROOM."""
if all_solvers == "glpk":
pytest.skip("GLPK is too slow to run ROOM.")
model.solver = all_solvers
genes = ["b0008", "b0114", "b2276", "b1779"]
benchmark(
single_gene_deletion,
model=model,
gene_list=genes,
method="room",
processes=1,
)
# Single gene deletion linear ROOM
[docs]def test_single_gene_deletion_linear_room_benchmark(
model: Model, benchmark: Callable, all_solvers: List[str]
) -> None:
"""Benchmark single gene deletion using linear ROOM."""
model.solver = all_solvers
genes = ["b0008", "b0114", "b2276", "b1779"]
benchmark(
single_gene_deletion,
model=model,
gene_list=genes,
method="linear room",
processes=1,
)
# Single reaction deletion
[docs]def test_single_reaction_deletion_benchmark(
model: Model, benchmark: Callable, all_solvers: List[str]
) -> None:
"""Benchmark single reaction deletion."""
model.solver = all_solvers
benchmark(single_reaction_deletion, model=model, processes=1)
[docs]def test_single_reaction_deletion(model: Model, all_solvers) -> None:
"""Test single reaction deletion."""
model.solver = all_solvers
expected_results = {
"FBA": 0.70404,
"FBP": 0.87392,
"CS": 0,
"FUM": 0.81430,
"GAPD": 0,
"GLUDy": 0.85139,
}
result = single_reaction_deletion(
model=model, reaction_list=list(expected_results), processes=1
)
for reaction, value in expected_results.items():
assert np.isclose(result.knockout[reaction].growth, value, atol=1e-05)
# Single reaction deletion ROOM
[docs]def test_single_reaction_deletion_room(
room_model: Model, room_solution: Solution, all_solvers: List[str]
) -> None:
"""Test single reaction deletion using ROOM."""
room_model.solver = all_solvers
expected = pd.Series(
{
"v1": 10.0,
"v2": 5.0,
"v3": 0.0,
"v4": 5.0,
"v5": 5.0,
"v6": 0.0,
"b1": 10.0,
"b2": 5.0,
"b3": 5.0,
},
index=["v1", "v2", "v3", "v4", "v5", "v6", "b1", "b2", "b3"],
)
with room_model:
room_model.reactions.v6.knock_out()
add_room(room_model, solution=room_solution, delta=0.0, epsilon=0.0)
room_sol = room_model.optimize()
assert np.allclose(room_sol.fluxes, expected)
# Single reaction deletion linear ROOM
[docs]def test_single_reaction_deletion_linear_room(
room_model: Model, room_solution: Solution, all_solvers: List[str]
) -> None:
"""Test single reaction deletion using linear ROOM."""
room_model.solver = all_solvers
expected = pd.Series(
{
"v1": 10.0,
"v2": 5.0,
"v3": 0.0,
"v4": 5.0,
"v5": 5.0,
"v6": 0.0,
"b1": 10.0,
"b2": 5.0,
"b3": 5.0,
},
index=["v1", "v2", "v3", "v4", "v5", "v6", "b1", "b2", "b3"],
)
with room_model:
room_model.reactions.v6.knock_out()
add_room(
room_model,
solution=room_solution,
delta=0.0,
epsilon=0.0,
linear=True,
)
linear_room_sol = room_model.optimize()
assert np.allclose(linear_room_sol.fluxes, expected)
# Double gene deletion
[docs]def test_double_gene_deletion_benchmark(
large_model: Model, benchmark: Callable
) -> None:
"""Benchmark double gene deletion."""
genes = [
"b0726",
"b4025",
"b0724",
"b0720",
"b2935",
"b2935",
"b1276",
"b1241",
]
benchmark(double_gene_deletion, large_model, gene_list1=genes, processes=1)
[docs]def test_double_gene_deletion(model: Model) -> None:
"""Test double gene deletion."""
genes = [
"b0726",
"b4025",
"b0724",
"b0720",
"b2935",
"b2935",
"b1276",
"b1241",
]
growth_dict = {
"b0720": {
"b0720": 0.0,
"b0724": 0.0,
"b0726": 0.0,
"b1241": 0.0,
"b1276": 0.0,
"b2935": 0.0,
"b4025": 0.0,
},
"b0724": {
"b0720": 0.0,
"b0724": 0.814,
"b0726": 0.814,
"b1241": 0.814,
"b1276": 0.814,
"b2935": 0.814,
"b4025": 0.739,
},
"b0726": {
"b0720": 0.0,
"b0724": 0.814,
"b0726": 0.858,
"b1241": 0.858,
"b1276": 0.858,
"b2935": 0.858,
"b4025": 0.857,
},
"b1241": {
"b0720": 0.0,
"b0724": 0.814,
"b0726": 0.858,
"b1241": 0.874,
"b1276": 0.874,
"b2935": 0.874,
"b4025": 0.863,
},
"b1276": {
"b0720": 0.0,
"b0724": 0.814,
"b0726": 0.858,
"b1241": 0.874,
"b1276": 0.874,
"b2935": 0.874,
"b4025": 0.863,
},
"b2935": {
"b0720": 0.0,
"b0724": 0.814,
"b0726": 0.858,
"b1241": 0.874,
"b1276": 0.874,
"b2935": 0.874,
"b4025": 0.863,
},
"b4025": {
"b0720": 0.0,
"b0724": 0.739,
"b0726": 0.857,
"b1241": 0.863,
"b1276": 0.863,
"b2935": 0.863,
"b4025": 0.863,
},
}
solution = double_gene_deletion(model, gene_list1=genes, processes=3)
solution_one_process = double_gene_deletion(model, gene_list1=genes, processes=1)
for rxn_a, sub in growth_dict.items():
for rxn_b, growth in sub.items():
sol = solution.knockout[{rxn_a, rxn_b}]
sol_one = solution_one_process.knockout[{rxn_a, rxn_b}]
assert np.isclose(sol.growth, growth, atol=1e-3)
assert np.isclose(sol_one.growth, growth, atol=1e-3)
[docs]def test_double_gene_knockout_bug(large_model: Model) -> None:
"""Test that the bug reported in #1102 is fixed."""
genes = ["b0118", "b1276"]
expected = (
pd.DataFrame(
data={
"ids": [
{"b0118"},
{"b1276"},
{"b1276", "b0118"},
],
"growth": [0.98, 0.98, 0.0],
"status": ["optimal"] * 3,
}
)
.sort_values("ids")
.reset_index()
)
result = (
double_gene_deletion(large_model, genes, processes=1)
.sort_values("ids")
.reset_index()
)
assert result["growth"].values == pytest.approx(expected["growth"].values, abs=0.01)
assert (result["status"] == expected["status"]).all()
# Double reaction deletion
[docs]def test_double_reaction_deletion_benchmark(
large_model: Model, benchmark: Callable
) -> None:
"""Benchmark double reaction deletion."""
reactions = large_model.reactions[1::100]
benchmark(double_reaction_deletion, large_model, reaction_list1=reactions)
[docs]def test_double_reaction_deletion(model: Model) -> None:
"""Test double reaction deletion."""
reactions = ["FBA", "ATPS4r", "ENO", "FRUpts2"]
growth_dict = {
"FBA": {"ATPS4r": 0.135, "ENO": float("nan"), "FRUpts2": 0.704},
"ATPS4r": {"ENO": float("nan"), "FRUpts2": 0.374},
"ENO": {"FRUpts2": 0.0},
}
solution = double_reaction_deletion(model, reaction_list1=reactions, processes=3)
solution_one_process = double_reaction_deletion(
model, reaction_list1=reactions, processes=1
)
for (rxn_a, sub) in growth_dict.items():
for rxn_b, growth in sub.items():
sol = solution.knockout[{rxn_a, rxn_b}]
sol_one = solution_one_process.knockout[{rxn_a, rxn_b}]
if math.isnan(growth):
assert math.isnan(sol.growth)
assert math.isnan(sol_one.growth)
else:
assert np.isclose(sol.growth, growth, atol=1e-3)
assert np.isclose(sol_one.growth, growth, atol=1e-3)
[docs]def test_deletion_accessor(small_model: Model) -> None:
"""Test the DataFrame accessor."""
single = single_reaction_deletion(small_model, small_model.reactions[0:10])
double = double_reaction_deletion(small_model, small_model.reactions[0:10])
rxn1 = small_model.reactions[0]
rxn2 = small_model.reactions[1]
with pytest.raises(ValueError):
single.knockout[1]
with pytest.raises(ValueError):
single.knockout[{"a": 1}]
assert single.knockout[rxn1].ids.iloc[0] == {rxn1.id}
assert double.knockout[{rxn1, rxn2}].ids.iloc[0] == {rxn1.id, rxn2.id}
assert all(single.knockout[rxn1.id] == single.knockout[rxn1])
assert all(double.knockout[{rxn1.id, rxn2.id}] == double.knockout[{rxn1, rxn2}])
assert single.knockout[rxn1, rxn2].shape == (2, 3)
assert double.knockout[rxn1, rxn2].shape == (2, 3)
assert double.knockout[{rxn1, rxn2}].shape == (1, 3)
assert double.knockout[{rxn1}, {rxn2}].shape == (2, 3)