#!/usr/bin/perl
use Bio::Tools::SeqStats;
use Bio::SeqIO;
use Data::Dumper;

die "Usage: $0 <FASTA_file>\n" unless @ARGV==1;
my $filename = shift @ARGV;
my $in = Bio::SeqIO->new(-file=>$filename, -format=>'fasta');
my $seqobj = $in->next_seq();
my $monomers = count_monomers($seqobj->seq);
my $codons = count_codons($seqobj->seq);
print Dumper($monomers, $codons);

#****************** sub count_monomers *************************
# Read from fasta, count and print frequency of each nucleotide
# returns as a reference to a hash, sorted and percentaged
#***************************************************************
sub count_monomers{
my %monomers_list = ();
foreach my $base (split//,$seqobj) {
	$monomers_list{$base}++;
	}
my @uniq = keys %monomers_list;
};

#***************** sub count_codons ****************************
# Read from fasta file, count and print frequency of each codon
#****************************************************************
sub count_codons{
my %codons_list = ();
foreach my $codon (split /\d{3}/, $seqobj) {
	 $codons_list{$codon}++;
	}
my @uniq2 = keys %codons_list;
};
exit;