[Biopython] Biopython Enhancement Proposal (BEP): Alphabets

[T.A. Wemyss]

Dear all,

BioPython is now looking for someone new to take over the project in the 
email below. If anyone is interested, please do let Michiel or me know. 
It's a great opportunity to be involved in the future of BioPython!

All the best,
Thomas

On 2018-08-04 03:04, Michiel de Hoon wrote:
> Dear all,
> 
> While sequence objects in Biopython have an associated alphabet, the
> purpose of alphabets in Biopython is currently not well-defined.
> I can imagine these three interpretations of their purpose:
> 
> 	* To define how the sequence data is stored internally in a Seq
> object (i.e. what kind of objects are in seq.data);
> 	* To define conceptually what the Seq object contains (e.g. this is a
> protein, or this is DNA, or this is DNA with or without methylation);
> 	* To define how a Seq object should be presented to the user (e.g. as
> a single-letter string, a three-letter string, or something else).
> 
> (and there may be others that I have overlooked).
> 
> To justify having alphabets as a part of Biopython, their purpose
> should be clearly defined.
> 
> Because of the complexity of alphabets and their use in Biopython, we
> felt that it may be a good idea to have a PEP (Python Enhancement
> Proposal)-like discussion to define the purpose of alphabets and their
> technical implementation in Biopython. This would mean that somebody
> who is in favor of having alphabets in Biopython would work out a
> proposal with all the details to allow developers and users to think
> through the implications.
> 
> Here you can find a description of PEPs and what should go in them:
> https://www.python.org/dev/peps/pep-0001/ [1]
> 
> Not all of it is applicable to Biopython, but it may serve as a
> general guideline.
> 
> The Alphabet BEP (Biopython Enhancement Proposal) could be hosted on
> the Biopython website so that everybody can follow the discussion.
> 
> Since alphabets have been under discussion for more than 10 years, we
> are thinking to put a time limit to the proposal (e.g., until January
> 1st, 2020), meaning that if no agreement on the proposal is reached by
> then, alphabets would be removed from Biopython. This would give
> people who are in favor of alphabets to make their case, while
> guaranteeing that a conclusion will be reached (either a well-defined
> and usable alphabet, or no alphabet) within the next ~1.5 years.
> 
> Any volunteers? Seq objects and therefore their alphabets are a key
> feature of Biopython, and working through a BEP can give you the
> opportunity to help design a major part of Biopython.
> 
> Best,
> -Michiel
> 
> 
> 
> Links:
> ------
> [1] https://www.python.org/dev/peps/pep-0001/
> 
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython