[Bioperl-l] load_seqdatabase didn't load the taxon ids

Angshu Kar angshu96 at gmail.com
Wed Dec 14 17:42:31 EST 2005

Hi Torsten,

Thanks for your help. But I've loaded the taxon tables.
Only thing I'm doing differently is loading my data from a fasta file
instead of the genbank, swissprot format. Does that matter anyhow?


On 12/14/05, Torsten Seemann <torsten.seemann at infotech.monash.edu.au> wrote:
> Angshu,
> > After running the load_seqdatabase.pl I see that it hasn't loaded the
> > bioentry table with the taxon ids from the taxon table!!! Could you please
> > suggest a remedy to this?
> Did you put the taxons in the database first ?
> >From bioperl-cvs/biosql-schema/INSTALL :
> "With bioperl and bioperl-db installed you are ready to load some data.
> It is advisable to pre-load the NCBI taxonomy database (use
> scripts/load_taxonomy.pl in the biosql-schema package, the details are
> in its documentation)."
> Use bioperl-cvs/biosql-schema/scripts/load_ncbi_taxonomy.pl :
> "Usage: load_ncbi_taxonomy.pl" ... (try --help option)
> The BioPerl authors have been very patient answering your questions so
> far, but I think you should read the INSTALL files in biosql-schema and
> bioperl-db first before asking further questions.
> --
> Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
> Victorian Bioinformatics Consortium

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