[Gmod-help] gmod_bulk_load_gff3.pl

[Scott Cain]

Hi Todd,

Yes, that is still the most likely solution for you.  A few months ago,
the BioPerl API changed and Bio::Annotation::SimpleValue objects don't
work the same way that they used to, thus the error you are seeing.
It's not really looking for a method named 'database'; that is an
artifact left over from the API change.

Scott

On Tue, 2008-02-19 at 11:59 -0500, todd.moughamer at syngenta.com wrote:
> I run into the following error when trying to load Chado:
> 
> gmod_bulk_load_gff3.pl --organism yeast  --gfffile
> ~/tmp/saccharomyces_cerevisiae.gff.sorted --dbname chadotest
> Preparing data for inserting into the chadotest database
> (This may take a while ...)
> Can't locate object method "database" via package
> "Bio::Annotation::SimpleValue"
> at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 3061,
> <GEN0> line 1.
> Issuing rollback() for database handle being DESTROY'd without
> explicit disconnect().
> 
> I found reference to this problem online
> (http://www.nabble.com/question-about-gmod_bulk_load_gff3.pl-td15135949.html) with the recommendation of downloading the 'live' version of BioPerl. However, upon browsing the latest code in SVN I do not see inclusion of a "database" method. Is this still the recommended solution to the problem?
> 
> Thanks,
> 
> Todd
> 
> 
> Todd Moughamer 
> 
> Bioinformatics Consultancy & Training Group
> 
> Syngenta Biotechnology, Inc.
> 
> 3054 Cornwallis Road, 1243.E
> 
> Research Triangle Park, NC 27709-2257
> 
> Tel: 919-597-3078
> 
> Email: todd.moughamer at syngenta.com 
> www.syngenta.com
> 
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory