[Bioperl-l] Re: Loading gff files into a MySQL database

Lincoln Stein lstein at cshl.edu
Wed Aug 18 15:45:23 EDT 2004

Hi Esther,

It sounds as though the version of bp_bulk_load_gff.pl that you are 
using is out of synch with the bioperl libraries.  Make sure that the 
Perl include path that you are using (as set with PERL5LIB 
environment variable) is pointing to the library files in 


On Wednesday 18 August 2004 10:08 am, Esther Kabore wrote:
> Hello,
> I have troubles when trying to load some gff files into my MySQL
> database via bp_bulk_load_gff or bp_fast_load_gff. Here is my
> command line:
> /db/gcgadmin/bioperl-1.4/scripts_temp/bp_bulk_load_gff.pl -d human
> XXI/NC_000021.gff
> And here is the error message I get back:
> Can't locate object method "split_group" via package "Bio::DB::GFF"
> at /db/gcgadmin/bioperl-1.4/scripts_temp/bp_bulk_load_gff.pl line
> 256, <> line 2
> Thank you for any help.
> Sincerely yours,
> Esther.

Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

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