Polyclonal dependency

[jgallowa07]

We have a pretty weak dependency on polyclonal - we could remove this by simply adding our own alphabets, and mutation parser. Although, I wonder if these could be part of binarymap 🤔 @jbloom

[jbloom]

binarymap already defines alphabets: https://github.com/jbloomlab/binarymap/blob/main/binarymap/binarymap.py#L33-L64

Can you let me know more precisely what mutation parser you are using from polyclonal by pointing me to specific function / method?

[jgallowa07]

RE alphabets - amazing!

I was referring to the mut parser in polyclonal utils https://github.com/jbloomlab/polyclonal/blob/3e51bee35993f6e425c779171a0202d2f5008dfb/polyclonal/utils.py#L18

That we use here, in multidms ->

multidms/multidms/data.py

Line 235 in 5a667ff

self._mutparser = MutationParser(alphabet, letter_suffixed_sites)

[jbloom]

@jgallowa07, sorry for taking so long to reply to this. I think this is a reasonable idea, but will not have time to do it myself for a while.

If you want, you should feel free to open a pull request adding this feature to binarymap (or multidms) as well.

[jgallowa07]

Great, yes will do. I'll keep this open as a reminder to do that when I get a chance - but it's pretty low priority AFAICT.