Can't open GAATTC: No such file or directory at .//restriction_map_better.pl
        line 15 (#1)
    (S inplace) The implicit opening of a file through use of the <>
    filehandle, either implicitly under the -n or -p command-line
    switches, or explicitly, failed for the indicated reason.  Usually this
    is because you don't have read permission for a file which you named on
    the command line.

$line = "";
@sequence = "";
$int = "";
$length = 0;

$search = $ARGV[0]; # Assign with the input from command line ie THE

while ($line = <>){
        chomp($line);
        @sequence = split /\t/, $line;
        if ($sequence[1] =~ /$search/){
                $int = $`;
                $length = length($int) + 1; # +1 to give loc of found word
        }       
        print $sequence[0] . "\t" . "$length\n";
}