#!/usr/bin/perl

#############################################################file:
#	take the sequence file and count nucleotide frequency at
#	each position
#
#<Christina Chen Feb 17, 2004>
###########################################################
if($#ARGV != 1){die ("perl count_freq.pl INFILE OUTFILE\n");}

open(IN,"$ARGV[0]")||die("cannot open $ARGV[0]\n");

while($line=<IN>)
{
	chomp($line);
	push @data, $line;
}
close(IN);

for($i=0;$i<$#data+1;$i++)
{
	for($j=0;$j<length($data[0]);$j++)
	{
		$temp=substr($data[$i],$j,1);
		if($temp eq 'a')
		{
			$count[$j][0]++;
		}
		elsif($temp eq 't')
		{
			$count[$j][1]++;
		}
		elsif($temp eq 'c')
		{
			$count[$j][2]++;
		}
		else
		{
			$count[$j][3]++;
		}
	}
}

#print
open(OUT, ">>$ARGV[1]") || die("cannot open $ARGV[1]\n");
print OUT "\tA\tT\tC\tG\n";

for($i=0;$i<length($data[0]);$i++)
{
	print OUT "$i\t";
	foreach $element (@{$count[$i]}) {
		print OUT $element."\t";
	}
	print OUT "\n";
}