Calculating intersection between points and polygon in shapefile

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I want accomplish the following using command line python tools only (shapely + fiona)

I was wondering if there was a straightforward way for me to do the following:

1. Read in a shapefile (all counties in the UK)
   
2. Read in a csv with a list of lat / lon (this I know how to do)
   
3. Spit out a csv with the same list of points and the polygon id fromthe shapefile, indicating that the point lies within the polygon (i.e.in the county)
   

Ive got this to work by manually constructing polygons from a csvexport of the shapefile, but I'm afraid that Im not going to deal verywell with holes in counties, or edge cases. A standard out-of-the-boxsolution would be great.



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