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

Dave Messina David.Messina at sbc.su.se
Thu Aug 26 05:18:25 EDT 2010

So, just to finish the thought:


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 


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.


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