# generate shapekey from armature (or other) deformation
# deformation should not change the vertex order

import bpy

obj = bpy.context.selected_objects[0]

# use to_mesh to get deformed mesh data
# https://blender.stackexchange.com/questions/34789/how-to-get-vertex-coordinates-after-modifier-in-python
temp_data = obj.to_mesh(bpy.context.scene, True, 'PREVIEW')
verts = temp_data.vertices

# generate shapekey with shape_key_add and set the coordinates
# https://blender.stackexchange.com/questions/111661/creating-shape-keys-using-python
sk = obj.shape_key_add('Deform')
sk.interpolation = 'KEY_LINEAR'
for i in range(len(verts)):
    sk.data[i].co = verts[i].co