If you are sticking to *nix type systems, IPC::Open3 should work. Here is a general example using a shell, but you could open a new IPC::Open3 for each command. Of course, there is a file descriptor, but so does IPC::Run.
#!/usr/bin/perl
use warnings;
use strict;
use IPC::Open3;
use IO::Select;
my $pid = open3(\*WRITE, \*READ,\*ERROR,"/bin/bash");
my $sel = new IO::Select();
$sel->add(\*READ);
$sel->add(\*ERROR);
my($error,$answer)=('','');
while(1){
print "Enter command\n";
chomp(my $query = <STDIN>);
#send query to bash
print WRITE "$query\n";
foreach my $h ($sel->can_read)
{
my $buf = '';
if ($h eq \*ERROR)
{
sysread(ERROR,$buf,4096);
if($buf){print "ERROR-> $buf\n"}
}
else
{
sysread(READ,$buf,4096);
if($buf){print "$query = $buf\n"}
}
}
}
waitpid($pid, 1);
# zombie prevention