#!/usr/bin/perl
use strict;
use warnings;

my ($rna,$rnalen,$posi, $pos, $base, $dibase,$percent);
my (%bases, %occur, %count); my($max_position, $sum, $tot) = 0;
my @dinucleotide = qw(A C G T);#change the number of bases

my $file = $ARGV[0] or die "Please provide the input file\n";
my $column = $ARGV[1];
open (X, $file) || die "Check the input $file\n";
while (<X>) {
#    chomp $_;
    if ($_=~/^#/) { next; }
    if ($_=~/^\s+/) { next; }
    if ($_=~/^CLUSTAL/) { next; }
    if ($_=~/\*/) { next; }
    my @temp = split (/\s+/, $_);
    $rna = $temp[$column];
    $rna = uc $rna;
    $rnalen = length($rna);
    my @nucleotides = split (//,$rna);
    $tot++;    
    foreach my $key(@dinucleotide) {
	$bases{$key}=1;
	$sum++;    
    }
    $max_position = $rnalen if($rnalen > $max_position);
    for (my $position=0;$position<=$rnalen-1;$position++) {
	$dibase = substr($rna, $position, 1); #change the splitting number
	foreach my $dinucleotide(@dinucleotide)	{
	    if ($dibase eq $dinucleotide){
		$posi = $position+1;		
		$occur{$posi,$dibase}++;
#		print "$posi\t$dibase\n";		
	    }
	}
    }
}
for($pos=1;$pos<=$max_position;$pos++) {
    print "$pos\t";
    foreach $base(sort keys %bases) {
	print "$base\t";			
	if(exists $occur{$pos,$base}) {	
	    my $percent = sprintf ("%0.1f", (($occur{$pos,$base})/$tot)*100);
#	    print "$occur{$pos,$base}\t";
	    print "$percent\t";
	}
	else {
	    print "0\t";
	}
    }
    print "\n";
}
close (X);