[Bioperl-l] Feature extraction using Bio::DB::GFF

Marco Blanchette mblanche at berkeley.edu
Fri Mar 3 19:52:11 UTC 2006

Dear all--

I have been trying to find a way to rapidly retrieve feature data from genes
to pass to Bio::Graphics using a local version of the drosophila gff
annotation loaded on a PostgreSQL database using the bp_pg_bulk_load_gff.pl
script and the Bio::DB::GFF module.

My goal is to pass to a script a series of gene id and get a graphical
representation of the exon-intron gene structure where I could add
additional tracts of information (custom micro-array probes position,
binding sites for protein etc...).

My current problem is that I can't seems to be able to retrieve the group of
features associated with a given gene.

I've been experimenting with simple script like:

use strict;
use warnings;
use Bio::DB::GFF;

# Open the sequence database
my $db      = Bio::DB::GFF->new( -adaptor    => 'dbi::pg',
                                    -dsn        => 'dbi:Pg:dbname=chr4',
                                    -aggregator => ['processed_transcript'],

my $feats = $db->features(  -types => 'processed_transcript',
                            -merge => 1,
                            -iterator => 1,
while (my $feat = $feats -> next_seq() ){
    print "$feat\n";
    print $feat -> sub_SeqFeature(), "\n";


Without any success.

Any help to get me started would be greatly appreciated.


Marco Blanchette, Ph.D.

mblanche at uclink.berkeley.edu

Donald C. Rio's lab
Department of Molecular and Cell Biology
16 Barker Hall
University of California
Berkeley, CA 94720-3204

Tel: (510) 642-1084
Cell: (510) 847-0996
Fax: (510) 642-6062

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