[Bioperl-l] Bio::DB::SeqFeature

Blanchette, Marco MAB at stowers-institute.org
Tue Sep 26 12:40:29 EDT 2006


Dear list,

I have been using the Bio::DB::SeqFeature module to handle the GadFly
4.3 gff annotation. I am very pleased with the resultd, processing the
full fly genome is very fast and the methods of very simple to use,
thanks to the integration of the Bio::SeqFeatureI methods.

However, I am trying to get the value of the ID= field from the 9th
column on the GFF file but  can't seem to find the right methods... 

If I use:

use Bio::DB::SeqFeature::Store;

my $db = Bio::DB::SeqFeature::Store->new(-dsn => 'dbi:mysql:GadFly_43');

for $gene ($db->get_features_by_type('gene')){
	print	">>>>>\n",
			$gene->id, "\n",
			$gene->name, "\n",
			$gene->display_name,	"\n",
			$gene->primary_id, "\n",
			$gene->seq_id, "\n",
			"\n";
}

I don't get the value of the ID= field anywhere (which are the FBgn ids
of the gene in GadFly).

Many thanks

Marco Blanchette, Ph.D.
Assistant Investigator 
Stowers Institute for Medical Research
1000 East 50th St.
Kansas City, MO 64110
Tel:  816-926-4071 
Cell: 816-726-8419 
Fax: 816-926-2018 





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