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="room", gene_list=genes, processes=1)

WARNING:root:Warning:  No solution found from 6 MIP starts.

CPU times: user 21.4 s, sys: 84.2 ms, total: 21.5 s
Wall time: 3.23 s

Out[9]:

	growth	status
ids
(b1779)	45.0	optimal
(b0008)	0.0	optimal
(b0114)	27.0	optimal
(b2276)	46.0	optimal

In [10]:

model.solver = "gurobi"

In [11]:

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

CPU times: user 1.97 s, sys: 4.23 ms, total: 1.98 s
Wall time: 1.97 s

Out[11]:

	growth	status
ids
(b1779)	45.0	optimal
(b0008)	0.0	optimal
(b0114)	27.0	optimal
(b2276)	46.0	optimal

In [13]:

model.solver = "glpk"

In [14]:

model.solver.configuration.timeout = 20

In [15]:

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

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

CPU times: user 1min 21s, sys: 53.1 ms, total: 1min 21s
Wall time: 1min 21s

Out[15]:

	growth	status
ids
(b1779)	45.0	optimal
(b0008)	0.0	optimal
(b0114)	NaN	time_limit
(b2276)	NaN	time_limit