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use Bio::CUA; # perl module

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

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

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

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;

------------- WARNING Bio::CUA::CUB::Calculator -------------
MSG: CAI values for codons were not provided for this analyzer, so can
+ not calculate CAI for sequences
...
MSG: No default base composition for seq  '', so no GC-corrected ENC

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