#/usr/bin/perl -w

use strict;

my %sortOrder;

# replace "file1" with the filename of the first file
my $currentOrder=0;

open(FILE1,"<file1") or die "Can't open 'file1', error $!";
while(<FILE1>) {
    chomp;
    # associate the current word with its place in the sort order
    $sortOrder{$_}=$currentOrder++;     
}

close(FILE1);