[Bioperl-l] load_seqdatabase.pl problem

[Hilmar Lapp]

I suspect the database wasn't fresh at the time you loaded the NCBI 
taxonomy. Specifically, the offending species probably was already in 
there through some sequence load.

Alternatively, the EMBL SeqIO parser fails to parse out the NCBI 
taxonID and the species name slightly mismatches with the one in the 
NCBI taxonomy database.

What is the result if you issue the following query:

	select t.* from taxon t, taxon_name tn
	where tn.taxon_id = t.taxon_id
	and tn.name = 'Aspergillus oryzae'
	and tn.name_class = 'scientific name';

-hilmar

On Monday, March 1, 2004, at 04:57  AM, Eric Bazin wrote:

> Hi.
>
> I try to import embl sequence datas in a biosql schema using the perl
> script "load_seqdatabase.pl". Previously I loaded without any problem
> the taxon schema from the NCBI with load_ncbi_taxonomy.pl. Can anybody 
> give
> me a help for this?
>
> This is what I received:
>
> bash#./load_seqdatabase.pl --dbname polymorphix --format embl
> /home/eric/polybase.dat
>
> Could not store AB022832:
> ------------- EXCEPTION  -------------
> MSG: Unique key query in Bio::DB::BioSQL::SpeciesAdaptor returned 3 
> rows
> instead of 1. Query was [name_class="scie
> ntific name",binomial="Aspergillus oryzae"]
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/Ba
> sePersistenceAdaptor.pm:960
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/Bas
> ePersistenceAdaptor.pm:856
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistence
> Adaptor.pm:183
> STACK Bio::DB::Persistent::PersistentObject::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> ect.pm:243
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistence
> Adaptor.pm:170
> [root at thaler biosql]# :BasePersistenceAdaptor::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceA
> daptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObje
> ct.pm:270
> STACK (eval) ./load_seqdatabase.pl:517
> STACK toplevel ./load_seqdatabase.pl:500
>
> --------------------------------------
>
> Thanks a lot
>
> Eric bazin
>
>
>
>
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>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------