[Bioperl-l] Extracting sequences from GFF3

David Breimann david.breimann at gmail.com
Sat Sep 18 06:45:13 EDT 2010


As you know, GFF3 files can contain FASTA sequences after the features.

How do I extract a specific FASTA sequence given it's ID?

I tried:

use Bio::Tools::GFF;
use Data::Dumper;

my $gffio = Bio::Tools::GFF->new(
    -file =>
        "/path/to/file.gff",
    -gff_version => 3
);

print Dumper $gffio->get_seqs();

but $gffio->get_seqs() seems to return nothing, although the GFF3 has
sequences and is also valid.

By the way, I am able to parse the features themselves (using
$gffio->next_feature()).


Thanks,

Dave


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