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bebop / poly

A Go package for engineering organisms.
https://pkg.go.dev/github.com/bebop/poly
MIT License
659 stars 68 forks source link

Proposal - New external package - rebased #426

Open TimothyStiles opened 7 months ago

TimothyStiles commented 7 months ago

Describe the desired feature/enhancement

For a while we've had this really great parser for NEB's enzyme cut site database rebase.

Is your feature request related to a problem?

It can be difficult looking up these enzymes and inputting their data manually for simulating digests. Right now we have a couple of common ones available but it'd be better to have have a more expansive solution.

Describe the solution you'd like

I want to be able to access rebase programmatically for arbitrary enzymes. We haven't manually added rebase because of possible git repo size ballooning.

The ways I could see this being done are:

  1. Including a "download" function in poly that downloads the database for the user into their project to be handled manually.
  2. Create a minimal go package that are just predefined enzyme structs based on rebase. We could have a GH action to auto-update the package on a new rebase release and maybe force push an overwriting update so we don't end up making a huge git repo over time.
carreter commented 7 months ago

I'm personally a fan of 2, as it means that binaries don't need to access the internet to use the database but our repo stays small.

Maybe we make it so that the external repo is for dumping all of the external DBs we might want our users to have access to that aren't a part of core functionality? Something like: bebop/poly-data?

github-actions[bot] commented 5 months ago

This issue has had no activity in the past 2 months. Marking as stale.