After that, it's like a GIS: you use the modules 1) to open, save the shapefiles and carry out the treatments with other modules like numpy or scipy, if you want. you can use shapely for manipulation ...
from [Python Script examples for geoprocessing shapefiles without using arcpy](http://gis.stackexchange.com/questions/64146/python-script-examples-for-geoprocessing ...
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