[Bioperl-l] load_seqdatabase didn't load the taxon ids
jason.stajich at duke.edu
Wed Dec 14 18:55:11 EST 2005
Well let's try to think this through together Angshu - how do you
think the loading mechanism should be guessing what the species is
for a FASTA file.... (Hint: it doesn't)
On Dec 14, 2005, at 5:42 PM, Angshu Kar wrote:
> 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:
>>> After running the load_seqdatabase.pl I see that it hasn't loaded
>>> 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
>> It is advisable to pre-load the NCBI taxonomy database (use
>> scripts/load_taxonomy.pl in the biosql-schema package, the details
>> 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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