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

[Blanchette, Marco]

One more Bio::DB::SeqFeature oddities...

I am trying to fetch the genes underlying a given location in the genome.
The MySql database was populated whit the most recent Drosophila gff3
annotation using bp_seqfeature_load.pl using the fast mode (-f). Somehow,
there is something I don¹t get with the features Ogene¹.

For example, I can get 10 mRNAs from the fourth chromosome using:

use Bio::DB::SeqFeature::Store;
our $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
                                           -dsn => 'dbi:mysql:dmel_5_15');

map{print $_->name, "\n"} (map{$_->get_SeqFeatures('mRNA')}
                           $db->get_features_by_location(-seq_id =>
'4'))[1..10];

Results:
CG11231-RA
CG33797-RA
CG11077-RA
JYalpha-RB
RpS3A-RA
RpS3A-RB
RpS3A-RD
CG32006-RA
CG31997-RA
CG2219-RA

However, if I try to fetch the Ogene¹ features, I get an empty array as in

map{print $_->name, "\n"} (map{$_->get_SeqFeatures('gene')}
                              $db->get_features_by_location(-seq_id =>
'4'))[1..10];

>>NOTHING

And I get the same whether I use OGene¹ or OGENE¹.

Any idea what¹s going on here?

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