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

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Wed Dec 14 17:28:09 EST 2005


> 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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