[Bioperl-l] Bio::DB::GFF and Gadfly GFFs question

Venky Nandagopal venky at myrealbox.com
Wed Jun 11 15:39:19 EDT 2003

I've been using the D.mel GFFs processed using the process_gadfly.pl script 
and accessing the mysql database with Bio::DB::GFF.

I'm trying to figure out how to get the attributes for a gene that I 
retrieve from the database, for example:

my $db = Bio::DB::GFF(
				blah blah

my $cg = "CG2328";
my $gene = $db->segment( -class => 'Gene', -name => $cg );

now this lets me get the gene, its sequence etc as a 

What I want is to access the attributes of the gene... for example the gene 
line for CG2328 in the GFF looks like this:

2R      gadfly  gene    5038224 5041412 .       +       .       Gene CG2328 
; Note "Symbol eve" ; Note "FlyBase FBgn0000606"

I want to be able to read the "Note" attributes. It is possible to *find* 
features by attribute, but I cant find a way to read the attributes from 
the $gene above.

Can anyone help me with this?


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