def test_create_position_map_some_gaps(self): obs = _create_position_map(self.msa1, 's2') exp = np.array([0, 1, 3]) npt.assert_array_equal(obs, exp) obs = _create_position_map(self.msa1, 's3') exp = np.array([1, 3]) npt.assert_array_equal(obs, exp)
def test_create_position_map_all_gaps(self): seqs = [ skbio.DNA('ACGT', metadata=dict(id='s1')), skbio.DNA('AG-T', metadata=dict(id='s2')), skbio.DNA('----', metadata=dict(id='s3'))] msa = skbio.TabularMSA(seqs, minter='id') obs = _create_position_map(msa, 's3') exp = np.array([]) npt.assert_array_equal(obs, exp)
def test_create_position_map_no_gaps(self): obs = _create_position_map(self.msa1, 's1') exp = np.array([0, 1, 2, 3]) npt.assert_array_equal(obs, exp)
def test_create_position_map_error(self): with self.assertRaisesRegex(KeyError, 'Reference sequence s4 is not'): _create_position_map(self.msa1, 's4')