[Bioperl-l] Errors loading RefSeqs

[Holland, Richard]

Hi,

I'm loading the vertebrate mammalian refseqs using load_seqdatabase.pl,
having just downloaded them over the holidays. bioperl-db throws a
wobbly on a few of them, an example follows:

DBD::Oracle::st execute failed: ORA-01438: value larger than specified
precision allows for this column (DBD ERROR: OCIStmtExecute) [for
Statement "INSERT INTO bioentry_reference (ent_oid, ref_oid, rank,
end_pos, start_pos) VALUES (?, ?, ?, ?, ?)" with ParamValues: :p5='1',
:p3=129, :p1='26993', :p4='156', :p2='27237'] at
/usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAda
ptor.pm line 418, <GEN1> line 44098.

-------------------- WARNING ---------------------
MSG: ReferenceAdaptor::add_assoc: unexpected failure of statement
execution: ORA-01438: value larger than specified precision allows for
this column (DBD ERROR: OCIStmtExecute)
        name: INSERT ASSOC [3]
Bio::Seq::RichSeq;Bio::Annotation::Reference
        values: FK[Bio::Seq::RichSeq]:26993,
FK[Bio::Annotation::Reference]:27237, rank:"129", end:"156", start:"1"
---------------------------------------------------

The first error of this kind always refers to rank 100. I'm assuming
that the BioSQL schema (in Oracle anyway) only allows ranks of 1-99 (ie.
two digits), as this error occurs for all ranks of 100+. Is this an
error with the RefSeqs or with bioperl-db, or the Oracle BioSQL schema?

cheers,
Richard

---
Richard Holland
Bioinformatics Database Developer
ITS, Agresearch Invermay x3279



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