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I'm writing a script to find out how many functions were recognized after applying a FLIRT signature library, I'm using idapython I would like to know if I can apply the signatures by the script.

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You can apply FLIRT signatures using plan_to_apply_idasgn function from ida_funcs module.

From the official API documentation:

def plan_to_apply_idasgn(*args) ‑> int

Add a signature file to the list of planned signature files.
plan_to_apply_idasgn(fname) -> int
fname: file name. should not contain directory part. (C++: const char *)
return: 0 if failed, otherwise number of planned (and applied) signatures

If you have an older version of IDA (before 7.4), you can use idc.ApplySig function (see link and link).

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