[Bioperl-l] Help with Bio::DB::GFF

Filipe Garrett fgarret at ub.edu
Tue Sep 12 09:30:27 EDT 2006


Hi all,

I'm trying to access to Flybase Dmel GFF files through the bioperl 
module. I've tried different approaches (below) but none seem to work.


"
use DBI;
use Bio::DB::GFF;

# Open the sequence database
my $db = Bio::DB::GFF->new(-adaptor => 'dbi::mysql',
                            -dsn => 'dbi:mysql:dmel_gff:123.456.78.90',
                            -user => 'user',
                            -pass => 'pass');

$db->initialize(1);
$db->load_gff('dmel-4-r4.2.1.gff');



my @f;
my $segment1 = $db->segment(-name => '4', -start => 200000, -end => 230000);
my @features = $segment1->features('transcript', -automerge=>0);



@f = $db->contained_features(-start => 200000, -stop => 230000);
@f = $db->overlapping_features(-start => 200000, -stop => 230000);


@f = $db->features(-start => 200000, -end => 230000);


my $g = $db->segment(-start => 200000, $end => 230000);

"


What I need is to get all the features in a genome region.
Can anyone help me?

thanks in adv,
FG


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