I haven't tested it, but there is PerlIO::gzip, which could allow you to do something like this:

use PerlIO::gzip;
use Carp;
...

my $iolayer = '';
if($filename =~ /\.gz$/i) {
    $iolayer = ':gzip';
}

open($ifh, '<' . $iolayer, $filename) or croak("$!");

...
# Process data
while((my $line = <$ifh>)) {
    chomp $line;
    if($line =~ /bla/) {
        doBla($line);
    } else {
        doBlub($line);
    }
}
...
close $ifh;
[download]

No pipes, no external program to worry about, just basic IO stuff.