use Storable;

open IN, "input.fa";
my %id2off;
while (<IN>) {
    next unless /^>/;
    chomp;
    $id2off{substr($_, 1)} = tell(IN); # file pointer points to start
                                       # of next line
}

store \%id2off, 'input.idx';

##</code><code>##

use Storable;
$id2off = retrieve 'input.idx';
open IN, 'input.fa';
while (<>) {
    chomp;
    next unless exists $id2off->{$_};
    print ">$_\n";
    seek(IN, $id2off->{$_}, 0); # move file pointer to start of sequence
    while (<IN>) {              # print until we reach next sequence
        last if /^>/;
        print;
    }
}