[Biopython] Bio.SeqIO.index() - gzip support and/or index stored on disk?

Peter biopython at maubp.freeserve.co.uk
Fri Jun 4 08:42:22 UTC 2010


On Fri, Jun 4, 2010 at 9:10 AM, Renato Alves <rjalves at igc.gulbenkian.pt> wrote:
> Hi Peter and all,
>
> Considering the fact that the first addition 'is' a potential problem,
> while the second is more of an optimization, I would put my vote on the
> first. In addition, an sqlite or similar solution would also allow one
> to use the indexing feature on short run applications where
> recalculating the index every time is a costly (sometimes too much)
> operation.
>
> Obviously the second would be of great use if put together with the
> first, but I'm a little bit biased on that since I was part of the group
> that raised the gzip question in the mailing list some time ago.
>
> Regards,
> Renato

Hi Renato,

Unfortunately I was inconsistent about which order I used in my email
(gzip vs on disk indexes) so I'm not sure which you are talking about.
Are you saying supporting on disk indexes would be your priority (even
though you did ask look at gzip support in the past)?

Peter



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