def test_make_subject_match_scorer(self):
"""make_subject_match_scorer should keep ids matching n queries"""
qm1 = make_subject_match_scorer(1)
qm3 = make_subject_match_scorer(3)
qm5 = make_subject_match_scorer(5)
qmes = wrap_qmes(QMEBlast9(self.rec3))
self.assertEqualItems(qm1(qmes),
['ece:Z4181', 'ece:Z4182', 'ece:Z4183'])
self.assertEqualItems(qm3(qmes), ['ece:Z4181', 'ece:Z4183'])
self.assertEqualItems(qm5(qmes), [])
def test_QMEBlast9(self):
"""QMEBlast9 should return expected lines from all iterations"""
self.assertFloatEqual(QMEBlast9(self.rec3), [\
('ece:Z4181','ece:Z4181',3e-47),
('ece:Z4181','ecs:ECs3717',3e-47),
('ece:Z4181','spt:SPA2730', 1e-5),
('ece:Z4181','ecs:ECs3717',3e-54), #WARNING: allows duplicates
('ece:Z4181','cvi:CV2421',2e-8),
('ece:Z4182','ece:Z4182',3e-47),
('ece:Z4182','cvi:CV2422',2e-6),
])
def test_make_shotgun_scorer(self):
"""make_shotgun_scorer should keep ids matching n queries"""
sg1 = make_shotgun_scorer(1)
sg2 = make_shotgun_scorer(2)
sg3 = make_shotgun_scorer(3)
sg4 = make_shotgun_scorer(4)
sg5 = make_shotgun_scorer(5)
qmes = wrap_qmes(QMEBlast9(self.rec3))
self.assertEqualItems(sg1(qmes), keep_everything_scorer(qmes))
self.assertEqualItems(sg2(qmes), \
['ece:Z4181','ece:Z4182','ece:Z4183','cvi:CV2421','ecs:ECs3717'])
self.assertEqualItems(sg3(qmes), \
['ece:Z4181','ece:Z4182','ece:Z4183'])
self.assertEqualItems(sg4(qmes), \
['ece:Z4182'])
self.assertEqualItems(sg5(qmes), [])
def test_keep_everything_scorer(self):
"""keep_everything_scorer should keep all ids found."""
k = keep_everything_scorer(wrap_qmes(QMEBlast9(self.rec2)))
self.assertEqualItems(k, \
['ece:Z4181','ecs:ECs3717','spt:SPA2730','cvi:CV2421','ece:Z4182'])