[Biopython-dev] Bio.SeqIO.index extension, Bio.SeqIO.index_many

[Peter]

On Tue, Dec 7, 2010 at 3:40 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Tue, Dec 7, 2010 at 10:11 AM, Peter wrote:
>> On Tue, Dec 7, 2010 at 1:59 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>> > My only suggestion would be the naming: index_file makes it a little
>> > clearer about the intentions, instead of index_many (the best
>> > naming would be 'index' for this functionality and 'index_memory' for
>> > the in-memory indexing, but the ship has probably sailed on that).
>>
>> Yes, we've already used "index" for the in-memory index, and
>> its API doesn't lend itself to being extended in this way. So too
>> late now.
>>
>> What do you think of index_files (plural) rather than index_file?
>
> How about index_db or index_sqlite? The fact that it uses a SQLite
> database for storage seems significant enough to be noted in the name.
>
> Thanks for adding this feature, it will be very useful!
>
> -Eric

I'd actually wondered about index_sqlite as a name myself. However,
does it really matter to the user that it is implemented in SQLite3?
Also we might one day want to make the backend an option (e.g.
SQLite3 or the OBDA BDB index format still used by other Bio*
projects).

Thanks for the positive comments guys :)

Peter