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If you would like to check what write_by_handle and read_by_handle, then I'd suggest you to check the following links:
In bindings.cpp both write_by_handle and read_by_handle are defined under the "environment" of the Boost Python module. If you check gattlib.cpp, you will see that write_by_handle and read_by_handle end up using the gatt_write_char and gatt_read_char methods. These methods can be found in gatt.c.
If you read these files, you should be able to understand how these commands work and what they "handle". In case you need more help with this library I'd suggest you to contact the library's creator in https://bitbucket.org/OscarAcena/pygattlib/issues?status=new&status=open since he'll be able to provide you more detailed information about how the library works.
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In one sentence you can say that a handle is the "access adress" for an attribute, so you get the value from it
You can find more information here: