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')
