biomass_allocation.py get_by_id problem

[Elisa Márquez Zavala]

Hi! I tried to use the get_protein_distribution from the ecolime/ecolime/characterization/biomass_allocation.py scrip but I get the next error:

AttributeError: 'generator' object has no attribute 'get_by_id'

from the line

--> 185 protein_mass = model.translation_data.get_by_id(protein).mass

Thank you!

[Elisa Márquez Zavala]

Also, with the rna_to_protein_ratio it says that

~/ME_model/Ecolime/ecolime/characterization/biomass_allocation.py in rna_to_protein_ratio(model, solution)
58 composition['rRNA'] + composition['ncRNA']) /
59 (composition['Protein'] +
---> 60 composition['Unmodeled Protein'])
61 return rna_to_protein
62

ZeroDivisionError: float division by zero

I believe it is because "Protein" is now "protein" and "Unmodeled Protein" doesn't longer exist

[Colton Lloyd]

Hi,

Sorry about that. This module isn't tested as well as it should be. I just pushed some changes in 3bb9e62 that should correct these issues.

Thanks for letting me know about this and let me know if you run into any other issues!

Colton