This just prints out what is found in file that is declared in the predefined list, although I suspect (but don't know) you want more than this, e.g. to compare the two orderings and organise the result of that in some way.

my @baselist = qw ( alpha beta etc ); # or from wherever
my %baselist = ();
$baselist{ $baselist[$_] } = $_  for ( 0..$#baselist );

# find baselist in the order it appears in input
my %rank = ();
my $rank = 0;
while(<>)
    chomp;
    defined( $baselist( $_ ) ) or next;
    if ( defined( $rank{ $_ } ) {
        warn "duplicate entry at line $.\n";
    }
    else {
        $rank{ $_ } = ++$rank;
    }
}

# print order actually found
print "$_\n"
  for sort { $rank{$a} <=> $rank{$b} } keys %rank;
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