[Gmod-help] Bulk load problem with GFF file

[Scott Cain]

Hi Jake,

The most likely problem is that your version of BioPerl isn't
sufficiently new.  Unfortunately, the most recent release (1.5.2) is
too old to work with the Chado loading tools; the Bio::Annotation API
has changed.  You need to get a svn checkout of bioperl-live or a
nightly build from:

  http://www.bioperl.org/DIST/nightly_builds/

Scott


On Wed, Nov 19, 2008 at 12:47 PM, Jake Emerson
<jakeemerson at spatial.maine.edu> wrote:
> I'm working with Dr. Mary Dolan from Jackson Laboratory in Maine. We have
> built a Chado database and loaded all of the BioPerl modules. In following
> the instructions to load a GFF file
> (http://gmod.org/wiki/Load_GFF_Into_Chado) I ran into a snag. I first tried
> loading the example yeast features on that page, which Mary used as the
> example for building our mouse GFF file, and got the following error:
>
> gene at genosis:~/gmod-1.0/yeast_data$ gmod_bulk_load_gff3.pl --organism yeast
> --gfffile saccharomyces_cerevisiae.gff.sorted
> Preparing data for inserting into the genosis_chado database
> (This may take a while ...)
> Operation "ne": no method found,
>     left argument in overloaded package Bio::Annotation::SimpleValue,
>     right argument has no overloaded magic at
> /usr/local/bin/gmod_bulk_load_gff3.pl line 811, <GEN0> line 1.
>
> Is there just something malformed in our GFF file, or have I misused the
> bulk load script?
>
> Thanks for your help!
> Jake
>
> Jake Emerson
> Spatial Information Science and Engineering
> University of Maine
> 127 Boardman Hall
> Orono, ME  04469
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research