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klamt-lab / autopacmen

Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method
Apache License 2.0
12 stars 7 forks source link

get_reactions_kcat_mapping #23

Open FraserAndrews7 opened 1 year ago

FraserAndrews7 commented 1 year ago

Hi @Paulocracy, I would like to say congratulations on this an absolutely fantastic piece of code/paper you published :D

I have however ran into a problem with the kcat_database_combined.json file that is generated from the create_combined_kcat_database.py function. It creates kcat values for the species Salmonella enterica subsp. enterica serovar Typhimurium A0A0F6B484. This entry is not in the cache/ncbi_taxonomy folder. This causes an error later on when I use the function...

get_reactions_kcat_mapping(sbml_path, project_folder, project_name, organism, kcat_database_path, protein_kcat_database_path)

It runs halfway before raising the error 'OSError: [Errno 22] Invalid argument: C:/file_path/cache/ncbi_taxonomy/Salmonella enterica subsp. enterica serovar Typhimurium A0A0F6B484'.

It is possible to solve and allow complete model construction by manually deleting the 'Salmonella enterica subsp. enterica serovar Typhimurium A0A0F6B484' entries in the kcat_database_combined.json file.

Whilst it is possible to work around this, I thought it would be worth raising this for anyone else whom may have this problem.

Keep up the good work :D

Paulocracy commented 1 year ago

Thank you (very late :3) for mentioning this issue and your positive assessment of AutoPACMEN! I will keep this issue open for anyone with a similar problem. Since a solution would need major changes in AutoPACMEN for which I didn't have time yet, your workaround is the best solution for now :-)