my @sorted = sort {
    my ($chr_a, $num_a) = $a =~ m/^([a-z]+)(\d+)/;
    my ($chr_b, $num_b) = $b =~ m/^([a-z]+)(\d+)/;
    $chr_a cmp $chr_b || $num_a <=> $num_b
} @array;

my @sorted = map {
    $_->[2]
} sort {
    $a->[0] cmp $b->[0] || $a->[1] cmp $b->[1]
} map {
    my ($chr, $num) =~ m/^([a-z]+)(\d+)/; [$chr, $num, $_]
} @array;