[BioSQL-l] [BioPython] Concerns the update of BioSQL.taxon table
Peter
biopython at maubp.freeserve.co.uk
Tue Mar 25 15:56:16 UTC 2008
On Tue, Mar 25, 2008 at 3:53 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Hi Eric,
>
> Your issue is almost certainly due to switching from Biopython 1.44 to
> 1.45, rather than from a prerelease BioSQL to the recently released
> BioSQL 1.0.0.
>
> For background, you should read Bug 2422 and the BioSQL thread it points to.
> http://bugzilla.open-bio.org/show_bug.cgi?id=2422
>
> Biopython 1.44 never recorded the taxon id (and therefore didn't use
> the taxon/taxon_name tables)
> Biopython 1.45 does record the taxon id, and attempts to fill in
> missing taxon/taxon_name entries
>
> I'm a little unclear on what is going wrong for you. Did you pre-load
> the NCBI taxonomy for example? The script you are talking about, is
> this your own?
>
> Peter
>
P.S. Did you mean to send your original message to the BioSQL list as well Eric?
You need biosql-l at lists.open-bio.org not biosql at lists.open-bio.org
Peter
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