def test_seq_to_symbol_factory(self): """checks factory function for conversion works""" motifs = ['AA', 'AT', 'TT'] seq_to_symbols = SeqToSymbols(motifs) self.assertEqual(seq_to_symbols('AATGGTTA'), numpy.array([1,1,0,0,0,1,0,0])) self.assertEqual(seq_to_symbols('AAGATT'), numpy.array([1,0, 0, 1, 1, 0], numpy.uint8))
def test_seq_to_symbol(self): """both py and pyx seq_to_symbol versions correctly convert a sequence""" motifs = ['AA', 'AT', 'TT'] symbols = _seq_to_symbols('AATGGTTA', motifs, 2) self.assertEqual(symbols, numpy.array([1,1,0,0,0,1,0,0])) symbols = seq_to_symbols('AAGATT', motifs, 2, numpy.zeros(6, numpy.uint8)) self.assertEqual(symbols, numpy.array([1,0,0,1,1,0]))