The disadvantages of using backticks are plenty. In your case, you are starting 4600 external processes, which will take quite a lot of time and resources.

Using something like Compress::Zlib or IO::Compress::Gzip also let's you handle compressed text files similar to plaintext files, without using temporary (uncompressed) files.

 use PerlIO::gzip;
  open FOO, "<:gzip", "file.gz" or die $!;
  print while <FOO>; # And it will be uncompressed...

  binmode FOO, ":gzip(none)" # Starts reading deflate stream from here
+ on
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There aren't really enough ratings to make an informed choice... Opinions would be appreciated :-)

Pick one from 2012/2011 and try it out, it shouldn't take more than half an hour to find a module with an interface you like, that works for your files

IO::Uncompress::Bunzip2 looks ok to me

IPC::System::Simple capturex also looks useful

See also How does one choose among modules?

I knew there must be something on choosing modules somewhere in the monastery. Couldn't find it easily though. Thanks.

##Open file - special case for gzip
    if ($input_file =~ /\.gz$/) {
        open(IN, "gunzip -c $input_file |") || die "can't open pipe to
+ $input_file";
    }
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If your data is line-oriented (or otherwise processed in chunks), I'd just open a pipe to an external process:

# read
open my $in, '-|', 'gzip', '-dc', $filename;
while (<$in>) {
    print $_;
}
close $in;

# write
open my $out, '|-', 'gzip', '-c', $filename;
print $out "blah";
close $out;
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Whoops, that writing doesn't quite work (it prints the compressed data to STDOUT), and I'm not sure how to fix that without invoking the shell.

With the shell, it goes something like this:

open my $out, '| gzip -c > ' . $filename;
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