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

[Jason Stajich]

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)
-jason

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?
>
> Thanks,
> Angshu
>
> 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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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12