1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
|
"""Test functionalities of Flux Variability Analysis."""
import os
from typing import Callable, List
import numpy as np
import pandas as pd
import pytest
from cobra import Model
from cobra.exceptions import Infeasible
from cobra.flux_analysis.variability import (
find_blocked_reactions,
find_essential_genes,
find_essential_reactions,
flux_variability_analysis,
)
# FVA
def test_flux_variability_benchmark(
large_model: Model, benchmark: Callable, all_solvers: List[str]
) -> None:
"""Benchmark FVA."""
large_model.solver = all_solvers
benchmark(
flux_variability_analysis,
large_model,
reaction_list=large_model.reactions[1::100],
processes=1,
)
def test_pfba_flux_variability(
model: Model,
pfba_fva_results: pd.DataFrame,
fva_results: pd.DataFrame,
all_solvers: List[str],
) -> None:
"""Test FVA using pFBA."""
model.solver = all_solvers
with pytest.warns(UserWarning):
flux_variability_analysis(
model,
pfba_factor=0.1,
reaction_list=model.reactions[1::3],
processes=1,
)
fva_out = flux_variability_analysis(
model, pfba_factor=1.1, reaction_list=model.reactions, processes=1
)
fva_out.sort_index(inplace=True)
assert np.allclose(fva_out, pfba_fva_results)
abs_fva_out = fva_out.dropna().abs()
abs_fva_results = fva_results.dropna().abs()
comparison = np.isclose(abs_fva_out, abs_fva_results) | (
abs_fva_out < abs_fva_results
)
assert comparison["minimum"].all()
assert comparison["maximum"].all()
def test_loopless_pfba_fva(model: Model) -> None:
"""Test loopless FVA using pFBA."""
loop_reactions = [model.reactions.get_by_id(rid) for rid in ("FRD7", "SUCDi")]
fva_loopless = flux_variability_analysis(
model,
pfba_factor=1.1,
reaction_list=loop_reactions,
loopless=True,
processes=1,
)
assert np.allclose(fva_loopless["maximum"], fva_loopless["minimum"])
def test_flux_variability(
model: Model, fva_results: pd.DataFrame, all_solvers: List[str]
) -> None:
"""Test FVA."""
model.solver = all_solvers
fva_out = flux_variability_analysis(
model, reaction_list=model.reactions, processes=1
)
fva_out.sort_index(inplace=True)
assert np.allclose(fva_out, fva_results)
@pytest.mark.skipif("SKIP_MP" in os.environ, reason="unsafe for parallel execution")
def test_parallel_flux_variability(
model: Model, fva_results: pd.DataFrame, all_solvers: List[str]
) -> None:
"""Test parallel FVA."""
model.solver = all_solvers
fva_out = flux_variability_analysis(model, processes=2)
fva_out.sort_index(inplace=True)
assert np.allclose(fva_out, fva_results)
# Loopless FVA
def test_flux_variability_loopless_benchmark(
model: Model, benchmark: Callable, all_solvers: List[str]
) -> None:
"""Benchmark loopless FVA."""
model.solver = all_solvers
benchmark(
flux_variability_analysis,
model,
loopless=True,
reaction_list=model.reactions[1::50],
)
def test_flux_variability_loopless(model: Model, all_solvers: List[str]) -> None:
"""Test loopless FVA."""
model.solver = all_solvers
loop_reactions = [model.reactions.get_by_id(rid) for rid in ("FRD7", "SUCDi")]
fva_normal = flux_variability_analysis(model, reaction_list=loop_reactions)
fva_loopless = flux_variability_analysis(
model, reaction_list=loop_reactions, loopless=True
)
assert not np.allclose(fva_normal["maximum"], fva_normal["minimum"])
assert np.allclose(fva_loopless["maximum"], fva_loopless["minimum"])
# Internals (essentiality, blocked reactions)
def test_fva_data_frame(model: Model) -> None:
"""Test DataFrame obtained from FVA."""
df = flux_variability_analysis(model)
assert np.all([df.columns.values == ["minimum", "maximum"]])
def test_fva_infeasible(model: Model) -> None:
"""Test FVA infeasibility."""
infeasible_model = model.copy()
infeasible_model.reactions.get_by_id("EX_glc__D_e").lower_bound = 0
# ensure that an infeasible model does not run FVA
with pytest.raises(Infeasible):
flux_variability_analysis(infeasible_model)
def test_fva_minimization(model: Model) -> None:
"""Test minimization using FVA."""
model.objective = model.reactions.EX_glc__D_e
model.objective_direction = "min"
solution = flux_variability_analysis(model, fraction_of_optimum=0.95)
assert solution.at["EX_glc__D_e", "minimum"] == -10.0
assert solution.at["EX_glc__D_e", "maximum"] == -9.5
def test_find_blocked_reactions_solver_none(model: Model) -> None:
"""Test find_blocked_reactions() [no specific solver]."""
result = find_blocked_reactions(model, model.reactions[40:46])
assert result == ["FRUpts2"]
def test_essential_genes(model: Model) -> None:
"""Test find_essential_genes()."""
essential_genes = {
"b2779",
"b1779",
"b0720",
"b2416",
"b2926",
"b1136",
"b2415",
}
observed_essential_genes = {g.id for g in find_essential_genes(model)}
assert observed_essential_genes == essential_genes
def test_essential_reactions(model: Model) -> None:
"""Test find_blocked_reactions()."""
essential_reactions = {
"GLNS",
"Biomass_Ecoli_core",
"PIt2r",
"GAPD",
"ACONTb",
"EX_nh4_e",
"ENO",
"EX_h_e",
"EX_glc__D_e",
"ICDHyr",
"CS",
"NH4t",
"GLCpts",
"PGM",
"EX_pi_e",
"PGK",
"RPI",
"ACONTa",
}
observed_essential_reactions = {r.id for r in find_essential_reactions(model)}
assert observed_essential_reactions == essential_reactions
def test_find_blocked_reactions(model: Model, all_solvers: List[str]) -> None:
"""Test find_blocked_reactions()."""
model.solver = all_solvers
result = find_blocked_reactions(model, model.reactions[40:46])
assert result == ["FRUpts2"]
result = find_blocked_reactions(model, model.reactions[42:48])
assert set(result) == {"FUMt2_2", "FRUpts2"}
result = find_blocked_reactions(model, model.reactions[30:50], open_exchanges=True)
assert result == []
|
