Here is the standard approach:

(1) In file X/CCD/Human.pm (where X is some directory listed in @INC):

package CCD::Human;

use strict;
use warnings;

sub new
{
    my ($class, $in_filename, $out_filename) = @_;

    my %self =
    (
        in  => $in_filename,
        out => $out_filename,
    );

    return bless \%self, $class;
}

sub parse
{
    my ($self) = @_;

    open(my $in,  '<', $self->{in})
        or die "Cannot open file '$self->{in}' for reading: $!";

    open(my $out, '>', $self->{out})
        or die "Cannot open file '$self->{out}' for writing: $!";

    while (<$in>)
    {
        chomp;
        my @fields = split /\t/;
        print $out "$fields[0]    $fields[2]    $fields[6]    $fields[
+5]\n"
            if ($fields[0] =~ /16/ &&
                $fields[6] eq '-'  &&
                $fields[5] =~ /Public/);
    }

    close $in
        or die "Cannot close file '$self->{in}': $!";

    close $out
        or die "Cannot close file '$self->{out}': $!";
}
[download]

(2) Client code would use this class as follows:

use CCD::Human;
...
my $human = CCD::Human->new
            (
                '/home/ki/Downloads/currenthumanccds.txt',
                '/home/ki/output.txt',
            );
...
$human->parse();
[download]

Disclaimers:

1. The above compiles but is otherwise untested.
2. This doesn’t look like a use-case for which a class is either required or appropriate. Simply putting your code into a subroutine within a module would likely be a better approach.

Hope that helps,