You need to remove the 'mysql' parameter from connect. Should look something like this:
use DBI;

$dsn="DBI:mysql:database=mysql";
$dbh=DBI->connect($dsn, 'root', 'root', {RaiseError => 1});

ah, you are missing a slash of some kind it seems... you are escaping the first backslash with the second. You probably need to add something like this:
$map_drive =...

Wait What?

You're running a script on *nix, and want that script to map a drive on a windows machine?????

#!/usr/bin/perl

$filename = "/root/file";
$var = `cat $filename | wc -l`;

print "$var";

EDIT: you shouldn't be stomping around a system as root.

#!/usr/bin/perl
system("cat '/something/something/something/darkside.txt'");

just check for the newline characters and replace them...something like:
$linefromfile =~ s/\n//gi; Just remember though, that you will have to manually add your own newline character ("\n")...

aha, maybe you should put the entire thing inside of the while loop ;)

have you tried outputting the value of $thinkingof during each guess? This will help you to at least ensure that the randomness works.

Well, the first step in any perl app when using the dbi interface is to make sure perl knows to use it:
use DBI;
Then, you want to make perl connect to the database using the DBI interface, so,...

Not to distract from your original question (ie: how to run commands from perl) but, if accessing a database is what you want to do, why not simply do so directly from Perl, using say.... The DBI...

Good Call