[Biopython-dev] Status of SearchIO

[Wibowo Arindrarto]

>> 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.

Ah, ok then :). There are other things I'm still working on at the
moment (BLAST plain text writer, details about migrating from
Bio.Blast), but I consider these to be less urgent than the tutorial.
If everyone is ok for merging, then I'm good too :). I suppose we are
going to use the 'beta' new feature warning here, right?

> > 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