There seem to be no compilation errors, but once the filename is input, the screen just... does nothing. I have to restart the terminal to get anything done. What am I doing wrong? I'm writing a program to compare an input string against a list, and calculating occurrence and frequency of that particular element. I have the code, it's a little messy, and I would appreciate ALL the help you have. Also, why is , 'S' showing up as a highlighted + sign? Updated the while loop but the values don't seem to be incrementing, the output shows 0, 0, 0 and 1, 2 for the first column instead of showing A, C, D.. 


#!/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";
}

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In reply to Code won't proceed after input. by newbie1991

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