[BioSQL-l] BioSQL/SwissProt

[Hilmar Lapp]

It sounds like you're using an old release of bioperl-db; 0.1 is very 
old and doesn't support the current version of biosql. Download 
bioperl-db from cvs and let me know if that doesn't solve the problem. 
If you check at the top of the load_seqdatabase.pl file, there should 
be a CVS Id tag that has a date stamp of no earlier than January this 
year (later is fine).

	-hilmar

On Friday, July 9, 2004, at 09:14  AM, Hegedus, Tamas . wrote:

> Dear All,
> Dear Hilmar,
>
> I try to load SwissProt newest release or rel.43 into the BioSQL 
> schema (I have the newest version from all perl package (BioPerl, 
> BioDB)).
> (Note: I am not familiar with perl; but I could not do it with 
> BioPython, so I wanted to try it with perl)
>
> I try to use the load_seqdatabase.pl:
> perl /home/src/bioperl/bioperl-db-0.1/scripts/load_seqdatabase.pl 
> --driver mysql --format swiss /home/src/uniprot/uniprot_sprot.dat
>
> - If I specified more command line arguments than two (like 
> --namespace --dbuser, too) the script wanted to open one of the 
> options as a sequence file.
> - So I set the user name, password, dbname in the load_seqdatabase.pl, 
> run the script,
> and I received the following errors (I think for all the entries 
> parsed from the dat_file)
>
> DBD::mysql::st execute failed: Unknown column 'display_id' in 'field 
> list' at /usr/lib/perl5/site_perl/5.8.0/Bio/DB/SQL/SeqAdaptor.pm line 
> 427, <GEN0> line 37864.
> Could not store P46952 because of DBD::mysql::st execute failed: 
> Unknown column 'display_id' in 'field list' at 
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/SQL/SeqAdaptor.pm line 427, 
> <GEN0> line 37864.
>
> Thanks for your help and suggestions,
> Tamas
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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