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

Marco Blanchette mblanche at berkeley.edu
Fri Mar 3 14:52:11 EST 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:
#!/usr/bin/perl


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

______________________________
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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