Chickens run in and out of doorways and often may be seen peering out from roosts on the second floor of houses.
The chickens, not allowed in the houses, are kept in pens outside. 
mnli hypothesis: The chickens, not allowed in the houses, are kept in pens outside.  premise: Chickens run in and out of doorways and often may be seen peering out from roosts on the second floor of houses.