[Biopython-dev] Status of SearchIO

[Peter Cock]

On Fri, Oct 26, 2012 at 11:25 AM, Kai Blin
<kai.blin at biotech.uni-tuebingen.de> 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.

> 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