gistfile1.txt

use Bio::SeqIO;

$in_file = Bio::SeqIO->new(-file => 'test1.txt',
				-format => 'EMBL');

$out_file = Bio::SeqIO->new(-file => '>test_final.txt', 
				-format => 'EMBL' );

while ($file = $in_file->next_seq){
	for $feature ($file -> get_SeqFeatures) {
		if ($feature -> primary_tag eq "CDS") {
		$feature->spliced_seq->seq;
		$feature =~ s/A/G/g;
		}
	}
	$out_file -> write_seq($in_file);
}