[Bioperl-l] Multiple gene segment problem

Marco Blanchette mblanche at berkeley.edu
Fri Mar 10 20:05:22 EST 2006

Dear all--

One more unusual behavior from the latest GadFly gff3 database loaded into
mySQL... I had been following Lincoln Stein advice as to how populate a
Bio::DB::GFF mySQL database with GadFly. Everything seemed to work nicely
but somehow, while calling for gene segment based on CG ids, I hit a CG with
more than one assignment as in


use strict;
use Bio::DB::GFF;

my $agg1 = Bio::DB::GFF::Aggregator->new(    -method => 'pre_mRNA',
                                            -sub_parts    =>
my $dmdb = Bio::DB::GFF->new( -adaptor => 'dbi::mysql',
                      -dsn => 'dbi:mysql:database=dmel_421;host=riolab.net',
                      -user => 'guest',
                      -aggregators=> [$agg1],

my @hits = ('CG2086', 'CG17894', 'CG32912');

for my $gene (@hits){
    my $tg = $dmdb->segment(-name => $gene);
    print "$gene is ", $tg->length,  " nt long\n";

When I tried to get the segment for gene CG32912, I get the following:

------------- EXCEPTION  -------------
MSG: multiple segment exception
STACK Bio::DB::GFF::_multiple_return_args
STACK Bio::DB::GFF::segment /Library/Perl/5.8.6/Bio/DB/GFF.pm:938
STACK toplevel test.pl:19


Any clue??? Any fix???

Marco Blanchette, Ph.D.

mblanche at uclink.berkeley.edu

Donald C. Rio's lab
Department of Molecular and Cell Biology
16 Barker Hall
University of California
Berkeley, CA 94720-3204

Tel: (510) 642-1084
Cell: (510) 847-0996
Fax: (510) 642-6062

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