There's the core module Term::ReadLine, and the CPAN module Term::Prompt - see their documentation for examples. Once you've got the string from the user, you can split it to get your @pats. Something like this:

use Term::ReadLine;
my $term = Term::ReadLine->new("prompt");
my $input = $term->readline("Enter search pattern: ")
    or die "no search pattern entered";
my @pats = split ' ', $input;
[download]

Another note: I see you've not checking the return value of your open for errors, which you may want to do:

my $infile = shift;
open(my $in, "<", $infile) or die "Failed to open $infile: $!";
my $outfile = shift;
open(my $out, ">", $outfile) or die "Failed to open $outfile: $!";
[download]

Either that, or add an use autodie; at the top of your script - see autodie.