[Bioperl-l] Help with Bio::DB::GFF
fgarret at ub.edu
Tue Sep 12 09:30:27 EDT 2006
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.
# 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');
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,
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