#!/usr/bin/env python
# coding: utf-8

# In[1]:


import cobra


# In[2]:


WT = cobra.io.read_sbml_model("iYali4.1.1.xml") # WT = Wild Type strain of Y. lipolytica

jacaric = cobra.Reaction("XXXX1") # Create the reaction forming jacaric acid
jacaric.name = "jacaric acid formation"
jacaric.lower_bound = 0
jacaric.upper_bound = 1000

jaca = cobra.Metabolite("jaca")
jaca.name = "jacaric acid"
jaca.compartment = "p"

linoleate = WT.metabolites.get_by_id("m1796")

jacaric.add_metabolites({
    linoleate: -1,
    jaca: 1})

exit = cobra.Reaction("XXXX2") # Create the reaction to drain jacaric acid
exit.name = "jacaric acid drain"
exit.lower_bound = 0
exit.upper_bound = 1000
exit.add_metabolites({jaca: -1})

WT.add_reaction(jacaric) # Add the reactions into the model
WT.add_reaction(exit)

cobra.io.write_sbml_model(WT, "Yarrowia lipolytica W29 - Jaca.xml")