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

[Lincoln Stein]

Hi,

I'm catching up on my bioperl mail after being on vacation for August.  The 
problem is that you need an entry for the whole chromosome because the 
segment() call needs to retrieve it in order to get the length.  Something 
like this will do the trick:

1 EnsEMBL chromosome 1 1502911 . . . Chromosome 1

Lincoln

On Wednesday 13 August 2003 07:02 pm, Matthias Wahl wrote:
> 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

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)