[Biopython-dev] Status of SearchIO

[Eric Talevich]

On Fri, Oct 26, 2012 at 6:38 AM, Wibowo Arindrarto
<w.arindrarto at gmail.com>wrote:

> >> Also, I think there are still some issues that need to be dealt
> >
> > >> with before we put SearchIO into master, notably with Bio.BLAST
> > >> module. If not the official deprecation notice, at least the the
> > >> tutorial has to be updated (let Bio.BLAST readers know about the
> > >> plan with SearchIO). I've written a short tutorial here:
> > >> http://bow.web.id/biopython/Tutorial.html. This is still a draft,
> > >> but you can already see that there are some obvious overlaps
> > >> between Bio.BLAST and Bio.SearchIO, which is confusing to new
> > >> readers.
> > >
> > > Personally I wouldn't let this consideration block the inclusion of a
> > > module as useful like that. Of course I need this code, so I'm biased.
> >
> > I'm also OK with merging the code before updating the Tutorial
> > chapter on BLAST (which would probably become a broader
> > chapter on BLAST and other tools using SearchIO). As discussed
> > before, the long term aim would be to remove Bio.BLAST.
>

Bio.Blast does contain some features beyond parsing the output of BLAST...


> > I'll have to read up on the namespace discussion. While I see the
> > > benefit of using PEP8 names, intuitively I don't like bio.seq.search
> > > much. Then again, I started my life in Bio* with BioPerl, and like the
> > > pretty similar module layout BioPython has so far.
> >
> > Yeah - the current naming of SeqIO and AlignIO was directly
> > inspired by BioPerl, and give the working name of SearchIO.
> >
> > Peter
>
> Reaching a unanimous decision on name preference seems difficult :/.
> We now have:
>
> 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)
>
> Any other suggestions? Should we put it to a vote?
>
> regards,
> Bowo
>
>
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.

-Eric