def test_find_terminal_gaps_all(self):
aseq = skbio.DNA('-------')
exp = np.asarray([True] * len(aseq))
obs = _find_terminal_gaps(aseq)
npt.assert_array_equal(obs, exp)
def test_find_terminal_gaps_3_prime(self):
aseq = skbio.DNA('A---ACGTAGTCGA-AGCT----')
exp = np.asarray(([False] * (len(aseq) - 4)) + ([True] * 4))
obs = _find_terminal_gaps(aseq)
npt.assert_array_equal(obs, exp)
def test_find_terminal_gaps_both_ends(self):
aseq = skbio.DNA('---ACGTA-----GT-CGA-AGCT----')
exp = np.asarray(([True] * 3) + ([False] * (len(aseq) - 7))
+ ([True] * 4))
obs = _find_terminal_gaps(aseq)
npt.assert_array_equal(obs, exp)
def test_find_terminal_gaps_none(self):
aseq = skbio.DNA('A---ACGTAGTCGA-AGCT----GATCG')
exp = np.asarray([False] * len(aseq))
obs = _find_terminal_gaps(aseq)
npt.assert_array_equal(obs, exp)