[Gmod-help] gmod_bulk_load_gff3.pl

[Hilmar Lapp]

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
>

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
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