[Biopython-dev] Storing Bio.SeqIO.index() offsets in SQLite

[Peter]

On Wed, Jun 9, 2010 at 4:56 PM, Brent Pedersen <bpederse at gmail.com> wrote:
> On Wed, Jun 9, 2010 at 7:55 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> On Wed, Jun 9, 2010 at 9:55 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>>
>> Do you fancy trying this version of screed? It seems much
>> faster on medium sized FASTQ files:-
>>
>> http://github.com/peterjc/screed/tree/sqlite-tweaks
>>
>> I'm still running a few tests myself, but will pass this on to
>> the screed team unless I find some regressions.
>>
>> Peter
>>
>
> not too much difference.
>
> screed
> ------
> create: 666.381
> search: 51.839

Still noticeable, but not quite as much of a speed up as I was
seeing (but different example, different OS, etc). Anyway, I've
sent them a "pull request" and they can merge it if they like.

Peter