[FEATURE REQUEST] `--enzymes-txt` input to `anvi-reaction-network`

[ivagljiva]

This is a request coming from myself and a few students from the EBAME10 workshop.

The need

Some people would like to use anvi-reaction-network and downstream applications like anvi-draw-kegg-pathways and anvi-predict-metabolic-interactions with custom lists of enzyme annotations; e.g., coming from annotations of transcriptomic/proteomic data, or from predictions of the gene content of the last common ancestor (LCA) of a set of related genomes.

We need a way to use these programs without the need to create contigs databases or run anvi-run-kegg-kofams.

The solution

We could reuse the --enzymes-txt file format and parameter from anvi-estimate-metabolism, and plug it into the reaction network classes to bypass the step of loading annotations from contigs databases.

We would also need a file format to store the resulting reaction network in. I believe the easiest would be to use the .json format provided by anvi-get-metabolic-model-file. However, that means we also need a way to load/import reaction networks into anvi'o from those JSON files (essentially the opposite of anvi-get-metabolic-model-file. Then we could add JSON input options to anvi-draw-kegg-pathways and anvi-predict-metabolic-interactions so that people can leverage these reaction networks created from custom enzyme lists.

Beneficiaries

Anybody who doesn't want to jump through a lot of hoops to use reaction networks from custom enzyme lists.

[meren]

Great idea!! I'll happily look into this :)