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

Gerben Menschaert Gerben.Menschaert at UGent.be
Tue May 23 12:02:12 EDT 2006

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?


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