Вы просто передаете дескриптор открытого файла numpy.savetxt()
:
In [1]: import numpy as np
In [2]: a = np.zeros((3,3))
In [3]: b = np.ones((5,6))
In [4]: with open('mix.txt', 'w') as f:
...: np.savetxt(f, a, fmt='%g')
...: f.write('my comment followed by a new array:\n')
...: np.savetxt(f, b, fmt='%g')
...:
In [5]: !more mix.txt
0 0 0
0 0 0
0 0 0
my comment followed by a new array:
1 1 1 1 1 1
1 1 1 1 1 1
1 1 1 1 1 1
1 1 1 1 1 1
1 1 1 1 1 1