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lobolab / mergem

mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models
https://lobolab.umbc.edu/mergem/
GNU General Public License v3.0
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Enable only mapping of IDs #1

Closed sulheim closed 10 months ago

sulheim commented 1 year ago

Hey, this looks great! The mapping you do here seems very thorough, but would it be possible to map the namespace of one model to a different namespace without actually merging models?

dnlobo commented 1 year ago

Thanks. That's a great idea. We'll implement it in a future release.

PratikPathade commented 1 year ago

hey, I am using mergem for merging two models. i am giving the input file in mat format but some fields are absent in the output format which is also in mat format. I need all the fields which are there in my input file. what can I do?

dnlobo commented 1 year ago

A merged model only contains reactions, metabolites, and objective functions. If needed, you could copy back any other field to the merged model after it has been created with the tool. Please let us know if you are missing anything in particular that you could not copy back.

dnlobo commented 10 months ago

@sulheim, this functionality is now implemented. To translate models, you can use the new function (translate) we have added to the mergem package, an option in the command line (-t), and you can also translate models in Fluxer. Hopefully this is useful.