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Last active July 19, 2017 06:54
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import cobra.test
from cobra.flux_analysis import pfba
stm = cobra.test.create_test_model("salmonella")
stm_fba = stm.optimize()
stm_pfba = pfba(stm)
pfk_stm = stm.reactions.get_by_id("PFK")
with stm:
print ("STM PFK before KO: ", pfk_stm.lower_bound, "< pfk <", pfk_stm.upper_bound)
print ("""# Absolute predicted flux before PFK KO
1. By FBA : """, stm_fba.fluxes.abs().sum())
print ("2. By pFBA : ", stm_pfba.objective_value)
print ("Diff. betn FBA and pFBA : ", stm_fba.fluxes.abs().sum() -
stm_pfba.objective_value)
stm.reactions.PFK.knock_out()
stm_fba = stm.optimize()
stm_pfba = pfba(stm)
print ("\nSTM PFK after KO: ", pfk_stm.lower_bound, "< pfk <", pfk_stm.upper_bound)
print ("""# Absolute predicted flux after PFK KO
1. By FBA : """, stm_fba.fluxes.abs().sum())
print ("2. By pFBA : ", stm_pfba.objective_value)
print ("Diff. betn FBA and pFBA : ", stm_fba.fluxes.abs().sum() -
stm_pfba.objective_value)
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