BOFdat
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Expand applicability of Step1 to a broader range of identifiers
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!
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.
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.