use Bio::CUA; # perl module

##</code><code>##

use Bio::CUA::CUB::Calculator;
use Bio::CUA::SeqIO;

##</code><code>##

my $io = Bio::CUA::SeqIO->new($cds);

##</code><code>##

my $io = Bio::CUA::SeqIO->new(-file => 'cds.dat'); 

##</code><code>##

my $tai_val  = sprintf "%10s: %.7f\n", $seq->id, $tai;
my $CAI_val  = sprintf "%10s: %.7f\n", $seq->id, $CAI;
my $encp_val = sprintf "%10s: %.7f\n", $seq->id, $encp;

##</code><code>##

------------- WARNING Bio::CUA::CUB::Calculator -------------
MSG: CAI values for codons were not provided for this analyzer, so can not calculate CAI for sequences

-------------------------------------------------------------

...

------------- WARNING Bio::CUA::CUB::Calculator -------------
MSG: No default base composition for seq  '', so no GC-corrected ENC

-------------------------------------------------------------