Expand applicability of Step1 to a broader range of identifiers

jclachance / BOFdat

Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data

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Expand applicability of Step1 to a broader range of identifiers #36

Open greenetarget opened 4 years ago

greenetarget commented 4 years ago

I downloaded a xml- model constructed by others, the file is using SEED ID for metabolite and when I ran DNA/RNA/protein_coefficients, it gives: AttributeError: DictList has no attribute or entry atp_c AttributeError: 'dict' object has no attribute 'iteritems'

Any suggestion?... Thank you!

jclachance commented 4 years ago

Yes, BOFdat is implemented for BiGG identifiers. The SEED identifiers in your model will therefore not be recognized.

It was previously suggested to add a conversion feature so that other identifiers could be used, which would indeed greatly improve the applicability of the package. I am changing the name of that issue to refer specifically to this issue.

hariszaf commented 1 year ago

Hi @jclachance . It seems that you had merged @EBosi PR in the main branch but the conversion_table is not there.. I thought of letting you know as it 's a bit weird to me. As changes came through years, I have a revised version of his script if you d be interested.