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open(HAND,"mysql -u $user -p$pass $db < $file | 2>&1") 
      or return "failed: $!";

my $user = <STDIN>;
chomp $user;
...
     # if $user = "fred; rm -rf *;" then your script will
     # try very very hard to remove everything in its    
     # working directory.

#!/usr/bin/perl -wT 
# the -T flag turns on taint checking
...

open (HAND, "mysql -u $user") or die "error $!";
     # only good values of $user get to here