def toLogOddsMatrix(self, symbol_freqs=None):
"""Returns the LogOddsMatrix of a profile as a new Profile/
symbol_freqs: per character array of background frequencies
e.g. [.25,.25,.25,.25] for equal frequencies for each of the
four bases.
See toOddsMatrix for more information.
"""
odds = self.toOddsMatrix(symbol_freqs)
log_odds = safe_log(odds.Data)
return Profile(log_odds, self.Alphabet, self.CharOrder)
def test_safe_log(self):
"""safe_log: should handle pos/neg/zero/empty arrays as expected
"""
#normal valid array
a = array([[4,0,8],[2,16,4]])
self.assertEqual(safe_log(a),array([[2,0,3],[1,4,2]]))
#input integers, output floats
self.assertFloatEqual(safe_log(array([1,2,3])),array([0,1,1.5849625]))
#just zeros
a = array([[0,0],[0,0]])
self.assertEqual(safe_log(a),array([[0,0],[0,0]]))
#negative number
self.assertFloatEqual(safe_log(array([0,3,-4]))[0:2],array([0,1.5849625007]))
self.assertNotEqual(safe_log(array([0,3,-4]))[2],\
safe_log(array([0,3,-4]))[2])
#empty array
self.assertEqual(safe_log(array([])),array([]))
#double empty array
self.assertEqual(safe_log(array([[]])),array([[]]))
