In [1]:

import logging

In [2]:

logging.basicConfig(level="DEBUG")

In [3]:

from cobra.test import create_test_model

DEBUG:optlang.util:Gurobi python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/gurobipy
DEBUG:optlang.util:GLPK python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/swiglpk
DEBUG:optlang.util:Mosek python bindings not available.
DEBUG:optlang.util:CPLEX python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/cplex
DEBUG:optlang.util:Scipy solver not available
DEBUG:pip._internal.utils.misc:lzma module is not available
DEBUG:pip._internal.vcs:Registered VCS backend: git
DEBUG:pip._internal.vcs:Registered VCS backend: hg
DEBUG:pip._internal.vcs:Registered VCS backend: svn
DEBUG:pip._internal.vcs:Registered VCS backend: bzr

In [4]:

from cobra.flux_analysis import single_gene_deletion

In [5]:

model = create_test_model("textbook")

In [6]:

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

In [7]:

model.solver = "cplex"

In [8]:

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

In [9]:

%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"

In [13]:

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

In [ ]: