my @array1;
my @array2;

my @args = (
	[ \@array1, "foo", "file_1.gz"],
	[ \@array2, "bar", "file_2.gz"]
);

foreach (@args) {
	&file_processing($args->[0], $args->[1], $args->[2]);
}

sub file_processing {
      my ($array_ref, $arg, $file) = @_;
	  my $script = "/export/home/ssesar/Perl/another_script.pl";
      open(FILE, $script . ' ' . $arg . ' ' . $file . ' |') or die ("can't do it: $!\n");

      while (<FILE>) { 
          chomp;
          push @{$array_ref}, $_ unless /^(?:\#|none|unknow)/i;
      }
      close FILE;
  }