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

[Hilmar Lapp]

Hi Erik,

I suspect that's a seperate Bio::Species issue. If you query your  
BioSQL database for the existence of the taxon:

SELECT * FROM taxon WHERE ncbi_taxon_id = 326939;

do you get a result? If not, then for some reason the taxon wasn't  
yet included in the NCBI taxonomy that you loaded.

If yes, then somehow BioPerl didn't properly parse out the taxonID  
from the record. There should have been another message preceding the  
error below, could you post that too? Otherwise, can you rerun with -- 
printerror as command line argument?

Note also that you can always specify --safe to go past any loading  
error. In fact that's what I recommend doing unless you want to debug  
why a particular record doesn't load.

BTW I would recommend that you restore the CASTs that were removed in  
Pg 8.3; otherwise you may hit random issues in Bioperl-db whenever a  
parameter value for a string-type column happens to be a number.  
(taxon.ncbi_taxon_id is of type integer)

See http://people.planetpostgresql.org/peter/index.php?/archives/18- 
Readding-implicit-casts-in-PostgreSQL-8.3.html

as per Greg's email.

	-hilmar

On Mar 21, 2008, at 5:43 PM, Erik wrote:
> Hi,
>
> PostgreSQL 8.3.1
> DBD::Pg 2.3.0
> perl 5.8.8
>
> (The following error may have to do with the 8.3 problems
> that I reported yesterday (bug 2472) - I don't know)
>
>  I ran biosql-schema/scripts/load_ncbi_taxonomy.pl without
> problem.
>
> Then I ran scripts/biosql/load_seqdatabase.pl as:
>
> perl scripts/biosql/load_seqdatabase.pl \
>   -driver Pg \
>   -dbuser xxxxxxx \
>   -dbname bioseqdb \
>   -namespace swissprot \
>   -format swiss \
>    /DATA/ms/ftp.ebi.ac.uk/pub/databases/uniprot/current_release/ 
> knowledgebase/complete/uniprot_sprot.dat
>
> It took two hours to load 26504 records (7%) of
> uniprot_sprot.dat (is it expected to be so slow?), then
> failed with:
>
> Could not store Q2UXW0:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Species) failed to insert or to
> be found by unique key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/Root/Root.pm:357
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::Persistent::PersistentObject::create
> /home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/DB/Persistent/ 
> PersistentObject.pm:244
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:169
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store
> /home/aardvark/bin/perl/lib/site_perl/5.8.8/Bio/DB/Persistent/ 
> PersistentObject.pm:271
> STACK: scripts/biosql/load_seqdatabase.pl:630
> -----------------------------------------------------------
>
>
> I don't know if this is directly related to the 8.3
> casting problems I reported yesterday (bug 2472), or a
> separate Bio::Species issue
>
>
> regards,
>
> Erik Rijkers
>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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