[Biopython-dev] Status of SearchIO

[Peter Cock]

On Fri, Oct 26, 2012 at 11:43 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
>Peter wrote:
>> 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
>
> No objection from me for the commit :).
>
> But I have some concerns for the SearchIO naming. I like Bio.seqsearch
> best at the moment. Bio.seq.search is good, but I understand that
> Bio.SearchIO will eventually contain app wrappers and code for remote
> searches as well. Putting it three levels-deep doesn't feel nice to
> me. As comparisons, submodules with similar features (Bio.Phylo, and
> possibly Bio.AlignIO, if in the future it will be merged with
> alignment app wrappers and the alignment object model) are available
> under Bio.

I think we'd get used to the nested namespace pretty quickly, and
this really only affect the import line anyway, e.g. something like
this isn't so bad as long as we document this:

from Bio.seq.search.apps import BlatCommandLine

If the namespace nesting bothers you, then you might not like
my thoughts for how to combine Bio.Align and Bio.AlignIO
(since we can't use Bio.align due to the folder name clash on
case incentive platforms): I was wondering about using
Bio.seq.align for this, which again is a bit nested but would
make it a system module to Bio.seq.search (aka SearchIO)
and Bio.seq.record (which could include the former SeqIO
code as well as the SeqRecord class).

Peter