[Gmod-help] gmod_bulk_load_gff3.pl

[Scott Cain]

Hi Hilmar,

Hah!  I was getting ready to write a response where I basically said I
didn't think that was what was going on, and I would have justified it
with some hand waving, since I didn't have the actual error message, so
I was just guessing and hopefully, updating bioperl will fix the problem
(and that still is a possibility).

However, I do have the actual error message, so I went and looked the
offending line, and it is in a method called 'handle_dbxref', so it
looks like your diagnosis is spot on.  Now I need to figure out if this
is still happening with bioperl-live and figure out why.  I've got a
Bio::SeqFeature::Annotated->annotation->get_Annotations('Dbxref'), which
I think should return a list of DBLink features.  I guess I'll go see.

Thanks for pointing that out!
Scott

On Tue, 2008-02-19 at 13:55 -0500, Hilmar Lapp wrote:
> Well, B::A::SimpleValue never had a method called database(). It is  
> B::A::DBLink that has that (and always had).
> 
> So my first diagnosis from afar would be that something is returning  
> or creating a B::A::SimpleValue when it was expected to return or  
> create a B::A::DBLink.
> 
> 	-hilmar
> 
> On Feb 19, 2008, at 1:07 PM, Scott Cain wrote:
> 
> > 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
> >
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory