In [1]:

    

from om import base, settings
from om.util import *

import pandas as pd
import cobra

ome = base.Session()
model = cobra.io.read_sbml_model('/Users/dbuser/Dropbox/om_data/annotation/iJO1366.xml')


    

    




/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandas/io/excel.py:626: UserWarning: Installed openpyxl is not supported at this time. Use >=1.6.1 and <2.0.0.
  .format(openpyxl_compat.start_ver, openpyxl_compat.stop_ver))

In [3]:

    

get_regulation_data(model.reactions.DHAPT, expanded_dataset=True)


    

    
Out[3]:





[{'carbon_source': u'glucose',
  'dataset': 354,
  'electron_acceptor': u'O2',
  'gene': u'ptsI',
  'nitrogen_source': u'NH4Cl',
  'regulator': u'Crp',
  'type': 'transcriptional',
  'value': 0.516896},
 {'carbon_source': u'glycerol',
  'dataset': 348,
  'electron_acceptor': u'O2',
  'gene': u'ptsI',
  'nitrogen_source': u'NH4Cl',
  'regulator': u'Crp',
  'type': 'transcriptional',
  'value': -0.287468},
 {'carbon_source': u'fructose',
  'dataset': 353,
  'electron_acceptor': u'O2',
  'gene': u'ptsH',
  'nitrogen_source': u'NH4Cl',
  'regulator': u'Crp',
  'type': 'transcriptional',
  'value': 0.385571},
 {'carbon_source': u'fructose',
  'dataset': 353,
  'electron_acceptor': u'O2',
  'gene': u'ptsI',
  'nitrogen_source': u'NH4Cl',
  'regulator': u'Crp',
  'type': 'transcriptional',
  'value': 0.434559}]

In [4]:

    

pd.DataFrame(get_regulation_data(model.reactions.SUCDi.id, expanded_dataset=True))


    

    
Out[4]:






  

    

      

      
carbon_source
      
dataset
      
electron_acceptor
      
gene
      
nitrogen_source
      
regulator
      
type
      
value
    
  
  

    

      
0
      
 fructose
      
 353
      
 O2
      
 sdhA
      
 NH4Cl
      
 Crp
      
 transcriptional
      
 3.34091
    
    

      
1
      
 glycerol
      
 348
      
 O2
      
 sdhC
      
 NH4Cl
      
 Crp
      
 transcriptional
      
 4.83934
    
    

      
2
      
 glycerol
      
 348
      
 O2
      
 sdhA
      
 NH4Cl
      
 Crp
      
 transcriptional
      
 4.56710
    
    

      
3
      
 fructose
      
 353
      
 O2
      
 sdhC
      
 NH4Cl
      
 Crp
      
 transcriptional
      
 4.05329
    
    

      
4
      
 glycerol
      
 348
      
 O2
      
 sdhB
      
 NH4Cl
      
 Crp
      
 transcriptional
      
 4.87014
    
    

      
5
      
 glycerol
      
 348
      
 O2
      
 sdhD
      
 NH4Cl
      
 Crp
      
 transcriptional
      
 5.26012
    
    

      
6
      
 fructose
      
 353
      
 O2
      
 sdhB
      
 NH4Cl
      
 Crp
      
 transcriptional
      
 3.70510
    
    

      
7
      
 fructose
      
 353
      
 O2
      
 sdhD
      
 NH4Cl
      
 Crp
      
 transcriptional
      
 3.74934
    
  

In [ ]: