[Biopython-dev] Status of SearchIO

[Peter Cock]

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 don't like Bio.SearchIO much because a) it doesn't tell you clearly
> what the module is about; and b) I think it it is a mistake to have
> Bio.SeqIO separate from Bio.Seq, and Bio.AlignIO separate from
> Bio.Align, because in both cases the two modules conceptually deal
> with the same thing. We don't have Bio.Cluster and Bio.ClusterIO,
> Bio.Entrez and Bio.EntrezIO, Bio.Motif and Bio.MotifIO; why should
> Bio.Seq and Bio.Align be different?

After all, not everyone was exposed to BioPerl before Biopython ;)

Peter