[Bioperl-l] postgres 8.3 - load_seqdatabase.pl / swissprot

[Hilmar Lapp]

On Mar 22, 2008, at 4:34 PM, Erik wrote:
> On Sat, March 22, 2008 20:30, Hilmar Lapp wrote:
>
>> SELECT * FROM taxon WHERE ncbi_taxon_id = 326939;
>
> No, I don't seem to have that particular id, although I
> ran the ncbi load script yesterday just before the sprot.

Odd. It's on the NCBI taxonomy browser. Maybe just was added the  
other day?

> Btw, in the meantime I figured out that it was a parsing
> error choking on an unexpected period.

Do you want to report that to the BioPerl category on bugzilla.open- 
bio.org?

>
> You asked for preceding errors, but there were none.
>
> I have now restarted the same uniprot_sprot.dat load with
> --safe, which if I understand you correctly will just skip
> any non-parsable records.

And all records that cause some other database error when inserting.  
Note that if you didn't erase the previously loaded records, you will  
either need to choose a new namespace, or, better, use the --lookup  
and --noupdate flags.

	-hilmar

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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