[Bioperl-l] getting DNA sequence for exon features from GFF

[Dave Messina]

So, just to finish the thought:

Kanmani,

Apologies for my sloppy and uninformed answer. The following is only slightly less sloppy and uninformed, but may actually answer your question.

I think you need to call 

   $gffio->get_seqs()

probably as

  my @seq_objects = $gffio->get_seqs();


and then loop through those something like:

	foreach my $seq_object (@seq_objects) {
		my $seq = $seq_object->seq();
    
		foreach my $feat ($seq->get_SeqFeatures) {
			# do your feature processing here
		}
	}



Note that I haven't tested the above code.


Dave