use Tie::File::AnyData::Bio::Fasta;

tie my @fastaArray, 'Tie::File::AnyData::Bio::Fasta' or die $!;

# Substitute the 10th sequence:
$fastaArray[9] = $newsequence;

# Get 10 random sequences:
use List::Util qw/shuffle/;
my @out = (shuffle @fastaArray)[0..9];