[BioSQL-l] fill taxon_id field in bioentry from Seq object?

Peter biopython at maubp.freeserve.co.uk
Wed Aug 27 16:52:27 UTC 2008


Adam wrote:
> is it possible to add a taxon_id to a Seq object such that when i save it
>to  my BioSQL database, it is stored in the bioentry table?
> ...
> sorry forgot to mention that bit.... I am using BioPerl

I'm afraid I can't help you with BioPerl, sorry.  Hopefully a BioPerl
expect will reply.

All I can suggest is you could try parsing a GenBank file with BioPerl
and see where the taxon id is stored in the Seq object's annotation,
then try and do the same with your data before asking BioPerl to save
it to the BioSQL database.

Peter



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