#!/usr/bin/perl-w
use warnings;
use diagnostics;

print "Enter the file containing the amino acid sequence \n";
my $filename = <STDIN>;
chomp $filename;

unless (open(FILENAME, $filename))
	{
		print "File $filename not found. Exiting program \n";
		exit;
	}

my @AASeq=<FILENAME>;
my $length = @AASeq;
close FILENAME;

my @AAMatrix = ('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y');
my @AAOcc = (0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0);
my @AAFreq = (0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0);
my $i=0;
my $counter=0; #Counter for the initialized matrix


while ($counter<=$length)
{
	for ($i=0; $i<=19; $i++)
	{
		
		if( $AASeq[$counter]=~ $AAMatrix[$i])
		{
			++$AAOcc[$counter];
			next;
		}
		
	}
	++$counter;
}


#Calculating frequency of amino acid occurrence
my $x=0;

for ($x=0; $x<=19; $x++)
{
	$AAFreq[$x] = $AAOcc[$x]/$length;
}

#Printing out the final array

print "AMINO ACID \t OCCURRENCE \t FREQUENCY ";
my $y=0;
for ($y=0; $y<=19; $y++)
{
	print  "$AAMAtrix [$y] \t\t $AAOcc[$y] \t\t $AAFreq[$y] \t\t\n";
}