For the moment, the geometry system of QGIS does not handle z-values but z-coordinates can be read by parsing the binary format of the geometry (see Why is it not possible to extract the z value of a ...
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 ...
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