use PerlIO::gzip;

open my $in_fh  => "<:gzip", 'input.gz' or die "ack: $!";
open my $out_fh => ">:gzip", 'output.gz' or die "ack: $!";

while(<$in_fh>) {
  do_stuff($_) if /matches some condition/;
  print {$out_fh} $_;
}