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..
print "Enter the file containing the amino acid sequence \n";
my $filename = <STDIN>;
unless (open(FILENAME, $filename))
print "File $filename not found. Exiting program \n";
my $length = @AASeq;
my @AAMatrix = ('A','C','D','E','F','G','H','I','K','L','M','N','P','Q
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 $counter=0; #Counter for the initialized matrix
for ($i=0; $i<=19; $i++)
if( $AASeq[$counter]=~ $AAMatrix[$i])
#Calculating frequency of amino acid occurrence
for ($x=0; $x<=19; $x++)
$AAFreq[$x] = $AAOcc[$x]/$length;
#Printing out the final array
print "AMINO ACID \t OCCURRENCE \t FREQUENCY ";
for ($y=0; $y<=19; $y++)
print "$AAMAtrix [$y] \t\t $AAOcc[$y] \t\t $AAFreq[$y] \t\t\n";