#!/usr/bin/perl
use Getopt::Long;
use Math::BigFloat;
use Math::BigInt;

my $codon_fname="codons.txt";
my $n_amer_fname="codon_pair.txt";
my $codon_usage_fname="";
my $mfactor=100;
my $codon_usage_per=100;


GetOptions(
	"c=s"	=>	\$codon_usage_fname,


) or die ("Error in command line arguments\n");

open(CODON,'<',$codon_fname)||die "No $codon_fname file available\n";

my %codon_counts;
while (my $line=<CODON>){
	chomp $line;
	$codon_counts{$line}= 0 ;
}
close CODON;

open(NAMER,'<',$n_amer_fname)||die "No $n_amer_fname file available\n";


my @namer;
while (my $line=<NAMER>){
	chomp $line;
	push @namer, $line;
}
close NAMER;

my %cd_lookup;

open(CLT,'<',$codon_usage_fname)||die "Cannot find codon score lookup table file $codon_usage_fname\n";
while(my $line=<CLT>){
	chomp $line;
	my @array=split(/\t/,$line);
	$cd_lookup{$array[0]}=$array[1];
}
close CLT;

use bignum;
my $x,$y,$z,$a,$b,$c;
#Math::BigFloat->accuracy(40);
#$x=Math::BigInt->new($x);
#$y=Math::BigInt->new($y);
#$z=Math::BigInt->new($z);
#$a=Math::BigFloat->new($a);
#$b=Math::BigFloat->new($b);
#$c=Math::BigFloat->new($c);




for(my $i=0;$i<@namer;++$i){
	my @choose_numerator_array;
	my %cchash=%codon_counts;
	my $count=0;
	for(my $j=0;$j<length($namer[$i])-2;++$j){
		++$cchash{substr($namer[$i],$j,3)};
		++$count;
	}
	foreach my $codon(%cchash){
		if($cchash{$codon}){
			$x=$cchash{$codon};
			$y=$cd_lookup{$codon}*$mfactor;
			$z=binomial($y,$x);
			push @choose_numerator_array,$z->copy();
		}
	}
	$b=$choose_numerator_array[0];
	for(my $j=1;$j<scalar(@choose_numerator_array);++$j){
		$a=$choose_numerator_array[$j];
		$b=$b*$a;
	}
	$y=$codon_usage_per*$mfactor;
	$a=&binomial($y,$count);
	$c=$b/$a;
	print $namer[$i],"\t",$c,"\n";
}
			
sub binomial {
    use bigint;
    my ($r, $n, $k) = (1, @_);
    for (1 .. $k) { $r *= $n--; $r /= $_ }
    $r;
}