[BioSQL-l] help with load_seqdatabase.pl

[Hilmar Lapp]

On Thursday, July 31, 2003, at 02:27  AM, Ulat, Victor (IRRI) wrote:

> Hi,
>
> I am trying to load a genbank formatted sequence to biosql(win2k, perl 
> 5.6,
> mysql 4.x, bioperl 1.2.2 and the recent bioperl-db)using
> load_seqdatabase.pl, I am using the following arguments:
>
> "C:\BioSQL>perl load_seqdatabase.pl -host localhost -dbname testdb 
> -driver
> mysql -namespace genbank -format genbank NC_000913.gbk"
>
> This message appears: "Loading NC_000913.gbk ..." followed by "Can't 
> call
> method "rollback" on an undefined value at load_seqdatabase.pl line 
> 451,
> <GEN0> line 163306"

The only sensible reason for this as far as I can tell from the code 
can be that runtime-loading the persistence adaptor for sequences 
failed. I've just committed a fix that should deal better with this 
situation, a patch is enclosed if you don't want to update from cvs.

First, to make sure the obvious,

	- you have either installed bioperl-db using the same perl that you 
use to run the script, or you have included the path to bioperl-db in 
PERL5LIB
	- ditto for bioperl (it seems you did do that)

If you convinced yourself that that's the case, run the script again 
with --debug added as an option (i.e., before the input filename) and 
email the output (you need to redirect that to a file). You may do so 
even without applying the patch, as the patch doesn't address what's 
going wrong in the first place, it just makes it die more verbosely.

	-hilmar


>
> Many thanks in advance,
>
> Victor
>
>
> _______________________________________________
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> BioSQL-l at open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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