[Bioperl-l] Bio::DB::GFF problem

[Matthias Wahl]

Hi all!

I have trouble in using Bio::DB::GFF with the following code:

my $aggregator = Bio::DB::GFF::Aggregator->new(-method    => 'gene_density'
                                               -sub_parts => 'EnsEMBL:gene_density');

my $gff_db = Bio::DB::GFF->new(-adaptor =>'dbi::mysqlopt',
                               -dsn=>'dbi:mysql:Mus_musculus_GFF',
                               -user => 'xxxxx',
			       -pass => 'xxxxx',
			       -aggregator => $aggregator
			       );


Calling

$gff_db->segment(-class=>'Chromosome',
                 -value=>'1');

always returns undef (whatever arguments I use)!
The database has been generated by loading a GFF file of the following 
format:

1	EnsEMBL gene_density    1000001 2000000 0                       Chromosome 1

1       EnsEMBL gene_density    2000001 3000000 0                       Chromosome 1

1       EnsEMBL gene_density    3000001 4000000 1                       Chromosome 1

1       EnsEMBL gene_density    4000001 5000000 12                      Chromosome 1

1       EnsEMBL gene_density    5000001 6000000 4                       Chromosome 1

with load_gff.PLS (columns are tab-seperated, the 9th column consists of 
'Chromosome' and name, seperated by space), both with and without the 
associated sequence file.

Calling

$gff_db->features()

works fine. But I need aggregated features for generating a 
Bio::Graphics xyplot (to plot the gene density for a particular chromosome).

Many thanks,

Matthias

-- 
Matthias Wahl
GSF-National Research Center for Environment and Health
Institute of Developmental Genetics
Ingolstaedter Landstrasse 1
D-85764 Neuherberg
Germany
TEL: ++49 89 3187-4117,-2638
FAX: ++49 89 3187-3099
E-mail: matthias.wahl at gsf.de
WWW: http://www.gsf.de/idg