[Biopython-dev] Status of SearchIO

[Peter Cock]

On Fri, Oct 26, 2012 at 5:14 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Fri, Oct 26, 2012 at 4:58 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>>> 1. Bio.seq.search (in line with the namespace change)
>>> 2. Bio.seqsearch (top-level module, separate from Bio.seq. This used
>>>    to be Bio.SeqSearch, now adjusted for PEP8 compliance)
>>> 3. Bio.search (same reasoning + explanation like Bio.seqsearch).
>>> 4. Bio.SearchIO / Bio.searchio
>>> 5. Bio.psearch (p for pairwise)
>>
>>> If it's down to a vote, I would vote to merge this branch as
>>> Bio.SearchIO, and perhaps lowercase it to Bio.searchio or
>>> biopy.searchio in the Py3 lowercase branch.
>>>
>>> Rationale: We already follow BioPerl with SeqIO and AlignIO, and it
>>> seems to help users. It's also Google-friendly.
>>
>> I would vote for Bio.seq.search.
>
> And would you support moving other existing Bio.SeqXXX
> modules under Bio.seq.* as for example outlined here?:
> http://lists.open-bio.org/pipermail/biopython-dev/2012-October/009999.html
> If so then I think we should go with that plan.

I have started exploring that idea on this new branch,
https://github.com/peterjc/biopython/tree/bioseq

Does anyone object to me applying the first commit to the master
branch (defining the previously discussed new warning for 'beta' code)?
https://github.com/peterjc/biopython/commit/97485d5dcf2620f7664ae46a7897c1203847538d

Note that introducing Bio.seq now (and any relocations under this)
can (I believe) still be combined with the lower-case modules under
Python 3 idea as well. This just requires the public classes and
functions defined under Bio.Seq.* remains mirrored under Bio.Seq.*
(this means assorted Seq objects and some functions like translate).

Peter