[Bioperl-l] Re trieve ID tag in GFF3

Hang hangsyin at gmail.com
Wed Feb 13 22:10:54 EST 2008


Dear All,

I wonder what method I should call to retrieve values of ID tags in GFF3
format. For example, a GFF3 entry in the database is like this:

4	FlyBase	gene	24068	25621	.	+	.      
ID=FBgn0040037;Name=ABC;Ontology_term=...

I'd like to retrieve the scalar value 'FBgn0040037' to compare with another
value. Please complete the code below:

use Bio::DB::SeqFeature::Store;
my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql',
                                         -dsn     => 'dbi:mysql:XXX_gff',
                                         -user    => 'XXX',
                                         -pass    => 'XXX')|| die "Database
open failed";

???



Thanks alot!

Hang
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