[BioSQL-l] load_seqdatabase.pl error due to bad DBSOURCE parsing

[Hilmar Lapp]

This is in reality a Uniprot entry. The Genbank parser apparently  
doesn't succeed in picking apart accession and namespace prefix  
(dbname).

If at all possible I'd recommend loading Uniprot in Uniprot  
(swissprot) format. Would that work for you?

	-hilmar

On May 23, 2006, at 12:02 PM, Gerben Menschaert wrote:

> Hello all,
>
> I'm trying to load genbank accession number Q99ML8 as a genpept  
> file with
> the load_seqdatabase.pl script. It fails on the DB_SOURCE part:
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed,  
> values were
> ("","UniGene:Mm.388865","0","") FKs ()
> ORA-01400: cannot insert NULL into  
> ("TEST_BIOSQL"."SG_DBXREF"."DBNAME") (DBD
> ERROR: error possibly near <*> indicator at char 57 in 'INSERT INTO  
> dbxref
> (dbname, accession, version) VALUES (:<*>p1, :p2, :p3)')
> ---------------------------------------------------
>
> The DBSOURCE block from the genpept file looks like this:
>
> DBSOURCE    swissprot: locus UCN2_MOUSE, accession Q99ML8;
>             class: standard.
>             created: May 10, 2002.
>             sequence updated: Jun 1, 2001.
>             annotation updated: May 16, 2006.
>             xrefs: AF331517.1, AAK16157.1
>             xrefs (non-sequence databases): UniGene:Mm.388865,
>             Ensembl:ENSMUSG00000049699, MGI:2176375, GO:0005576, GO: 
> 0001664,
>             GO:0006171, GO:0007586, GO:0006950
>
> How is this parsed? Could anybody point me into the good direction?
>
> Regards,
> Gerben
>
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>

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