I have an array of post ids which I'm passing to query_posts using 'post__in'.
My question is how can I use the order from my array rather than ordering by 'date' etc?
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You would need to build your own query and pass it to query_posts i.e.
if your array of post ids is:
array (10,21,1) // corresponding to post ids.
then you can query this way:
select * from wp_posts where `ID` in (10, 21, 2) order by field(ID,10,21,2)
This will give you a result set in the order of your post ids array.