In [1]:

import logging

In [2]:

logging.basicConfig(level="DEBUG")

In [3]:

from cobra.io import load_model

DEBUG:optlang.util:Gurobi python bindings not available.
DEBUG:optlang.util:GLPK python bindings found at /Users/uridavidakavia/PycharmProjects/venv_cobrapy3_7/lib/python3.7/site-packages/swiglpk
DEBUG:optlang.util:Mosek python bindings not available.
DEBUG:optlang.util:CPLEX python bindings not available.
DEBUG:optlang.util:OSQP python bindings not available.
DEBUG:optlang.util:COINOR_CBC python bindings not available.
DEBUG:optlang.util:Scipy linprog function found at /Users/uridavidakavia/PycharmProjects/venv_cobrapy3_7/lib/python3.7/site-packages/scipy/optimize/__init__.py

In [4]:

from cobra.flux_analysis import single_gene_deletion

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model = load_model("textbook")

INFO:cobra.core.model:The current solver interface glpk doesn't support setting the optimality tolerance.

Scaling...
 A: min|aij| =  1.000e+00  max|aij| =  1.000e+00  ratio =  1.000e+00
Problem data seem to be well scaled

In [6]:

genes = ['b0008', 'b0114', 'b2276', 'b1779']

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model.solver = "cplex"

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logging.getLogger().setLevel(logging.DEBUG)

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%time single_gene_deletion(model, method="linear room", gene_list=genes, processes=1)

CPU times: user 308 ms, sys: 0 ns, total: 308 ms
Wall time: 307 ms

Out[9]:

	growth	status
ids
(b1779)	5.034815e+00	optimal
(b2276)	5.475871e+00	optimal
(b0114)	1.224159e+00	optimal
(b0008)	3.028591e-15	optimal

In [10]:

model.solver = "gurobi"

In [11]:

%time single_gene_deletion(model, method="linear room", gene_list=genes, processes=1)

CPU times: user 271 ms, sys: 0 ns, total: 271 ms
Wall time: 265 ms

Out[11]:

	growth	status
ids
(b1779)	5.034815	optimal
(b2276)	5.475871	optimal
(b0114)	1.224159	optimal
(b0008)	0.000000	optimal

In [12]:

model.solver = "glpk"

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model.solver.configuration.timeout = 20

In [14]:

%time single_gene_deletion(model, method="linear room", gene_list=genes, processes=1)

DEBUG:optlang.glpk_interface:Status undefined. GLPK status code returned by glp_simplex was 1

CPU times: user 205 ms, sys: 4.99 ms, total: 210 ms
Wall time: 203 ms

Out[14]:

	growth	status
ids
(b1779)	5.034815e+00	optimal
(b2276)	5.475871e+00	optimal
(b0114)	1.224159e+00	optimal
(b0008)	-5.857507e-17	optimal

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