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;
    }
}