Use a Hash!

#!/usr/bin/perl
use strict;
use warnings;

my $guidefile = './guide';
my $flatfile = './flat';
my $delimiter = qr{\s*\|\s*};

my (%guide,@flat);

open GUIDE,'<',$guidefile or die "E: open($guidefile): $!";

{my $i = 0;
    while(<GUIDE>){ chomp; $guide{$_}=$i++ }
}

close GUIDE;

open FLAT,'<',$flatfile or die "E: open($flatfile): $!";

while( <FLAT> ){
    chomp;
    push @flat,[split /$delimiter/];
}

close FLAT;

foreach( sort { ($guide{ $b->[0] }||0) <=> ($guide{ $a->[0] }||0)  } @
+flat ){

    print join("\t",
        exists($guide{$_->[0]}) ? $guide{$_->[0]} : '-',
        @$_),"\n";

}
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