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MMinte with model created by Carveme #13
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Arianna, That should work to start with widget4 using models created by carveme. As long as the model can be loaded by cobrapy, MMinte should work. I would suggest using the MMinte code in my fork at https://github.com/mmundy42/MMinte where the code was restructured to make it easier to use the functionality of MMinte from your own Python code. |
Thx for your suggestion. I will check that code 👍 |
I did as you suggeted but using your fork of the mminte code I get some errors in the file "interaction_worker.py" in detail when I run calculate_growth_rates in my code I get the following error `--------------------------------------------------------------------------- The above exception was the direct cause of the following exception: AttributeError Traceback (most recent call last) /mnt/data_SSD/anaconda3/lib/python3.6/site-packages/mminte/interaction_analysis.py in calculate_growth_rates(pair_models, medium, n_processes) /mnt/data_SSD/anaconda3/lib/python3.6/multiprocessing/pool.py in get(self, timeout) AttributeError: 'Solution' object has no attribute 'x_dict' I checked all the dependencies versions and it should be ok so I wonder if there is something wrong with the code it self. I tried also with the models you provided but I got the same error. Any suggestions? |
What version of cobrapy do you have in your environment? cobrapy changed the Solution object in 0.14.0. The LegacySolution object has the x_dict attribute. Can you go back to cobrapy version 0.12.x? Otherwise there is some work to be done to update MMinte to work with the latest cobrapy. |
I solved creating a new environment with cobra 0.5.2. Quite old version but it worked. Thank you for your kind answer. Sincerely, |
Good morning!
I am trying to use your scripts (adapting them to python3.6) for my metabolic models created by carveme (https://github.com/cdanielmachado/carveme) instead of ModelSEED so starting from widget4. I was wondering whether it is a problem or your scripts work also with carveme models.
Sincerely,
Arianna Basile
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