[Bioperl-l] Errors loading RefSeqs

Hilmar Lapp hlapp at gmx.net
Sun Jan 4 16:46:31 EST 2004

This is a problem with the Oracle version of biosql. Sorry you had to  
be the first one to be hit by this. The rank as you suspected correctly  
is a NUMBER(2). Do the following in sqlplus (or any other sql-shell  
you're using for Oracle) to relax the restriction.

	SQL> ALTER TABLE sg_bioentry_ref_assoc MODIFY (rank NUMBER(4));

You'll need to issue this command as the schema owner, and be aware  
that it will implicitly commit an open transaction if there is any (b/c  
it is a DDL statement).

Of course, there are lots of GUI-based tools that will let you do the  

I'll fix this in the repository.


On Sunday, January 4, 2004, at 12:13  PM, Holland, Richard wrote:

> 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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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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