How long are your strings going to be? If they are going to be huge (e.g., in the gigabytes), you will want to pass around references to the string to your subroutines. E.g.:
my ($data) = @_;
# obtain the count of each nucleotide in the sequence
my $a_count = ($$data =~ tr/Aa//);
my $c_count = ($$data =~ tr/Cc//);
my $g_count = ($$data =~ tr/Gg//);
my $t_count = ($$data =~ tr/Tt//);
return ($a_count, $c_count, $g_count, $t_count);
# Called with:
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