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modernatx / seqlike

Unified biological sequence manipulation in Python
https://modernatx.github.io/seqlike
Apache License 2.0
207 stars 21 forks source link

Simplify .aa() interface, return original SeqRecord attributes #26

Closed ndousis closed 2 years ago

ndousis commented 2 years ago

Removed **kwargs from SeqLike aa, and hard-coded arguments in the call to self.translate so as to return original attributes like id and name. This is the behavior I would expect from aa().

I left the interface to SeqLike translate as is to maintain flexibility.

Closes #25

ericmjl commented 2 years ago

@ndousis I think I get the direction of the sentiment, but I think your implementation may need to be changed as it hard-codes behaviour that, in my own experience, should be left flexible, and the hard-coded behaviour is opposite to BioPython's behaviour. I am going to propose a few ideas in the PR as comments. Please hang tight!

ericmjl commented 2 years ago

@ndousis, I think there is an issue with the CI, which will take a bit of time for me to get right tomorrow. Hope you don't mind the delay here.

ndousis commented 2 years ago

@ndousis, I think there is an issue with the CI, which will take a bit of time for me to get right tomorrow. Hope you don't mind the delay here.

No rush