gistfile1.txt

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

while ($seq_object = $seqio_object->next_seq){

@cds_features = grep { $_->primary_tag eq 'CDS' } $seq_object ->get_SeqFeatures;

%gene_sequences = map {$_->get_tag_values('gene'), $_->spliced_seq->seq } @cds_features;

foreach( keys %gene_sequences ) {
  $gene_sequences{$_} =~ s/A/G/g;
}
}

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