error when trying to update biomass

[Christiansj83]

---

TypeError Traceback (most recent call last)
in ()
----> 1 update.update_biomass(d,model_so)

~/.local/lib/python3.6/site-packages/BOFdat-0.1.7-py3.6.egg/BOFdat/util/update.py in update_biomass(dict_of_coefficients, model)
115 :return: none
116 """
--> 117 biomass = _get_biomass_objective_function(model)
118 find_in_biomass(biomass, dict_of_coefficients)
119

~/.local/lib/python3.6/site-packages/BOFdat-0.1.7-py3.6.egg/BOFdat/util/update.py in _get_biomass_objective_function(model)
62 def _get_biomass_objective_function(model):
63 from cobra.util.solver import linear_reaction_coefficients
---> 64 return linear_reaction_coefficients(model).keys()[0]
65
66 #------------------------------#

TypeError: 'dict_keys' object does not support indexing

[EBosi]

Hi, I cannot push anything right now, I'm writing how to solve it hoping that someone can commit a fixed code.
The method dict.keys() in python 3 doesn't return a list. You should use list(dict) to get a list of keys, in that it works for both python 2 and 3

[jclachance]

Hi Christian,

Are you still struggling with this issue?

Thank you,

JC

[Christiansj83]

Hi JC I think it ended with me updating the Biomass reaction manually... And further I ended up using Python 2 instead of 3. Christian

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________________________________ From: Jean-Christophe Lachance <[email protected]> Sent: Friday, April 12, 2019 2:02 AM To: jclachance/BOFdat Cc: Christiansj83; Author Subject: Re: [jclachance/BOFdat] error when trying to update biomass (#31) Hi Christian, Are you still struggling with this issue? Thank you, JC — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#31 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ApDBhEjHcvdcuDm2m4eBBRIHcMFen2aXks5vf80AgaJpZM4YFc7K>.