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 [ ]: