def test_all_metrics_weird_input(self):
"""all_metrics: should work when ref or prediction empty or no seqs"""
ref = Pairs([(3, 10)])
pred = Pairs()
seqs = ['UACGUAGCUAGCUAGCUACG']
obs = all_metrics(ref, pred, seqs=[seqs], min_dist=4)
exp = {'SENSITIVITY':0, 'SELECTIVITY':0,\
'AC':0, 'CC':0, 'MCC':0}
for k in exp:
self.assertFloatEqual(obs[k], exp[k])
ref = Pairs()
pred = Pairs()
seqs = ['UACGUAGCUAGCUAGCUACG']
obs = all_metrics(ref, pred, seqs=[seqs], min_dist=4)
exp = {'SENSITIVITY':1, 'SELECTIVITY':1,\
'AC':1, 'CC':1, 'MCC':1}
for k in exp:
self.assertFloatEqual(obs[k], exp[k])
ref = Pairs([(3, 10)])
pred = Pairs([(1, 12)])
seqs = ['UACGUAGCUAGCUAGCUACG']
self.assertRaises(ValueError, all_metrics, ref, pred, seqs="",\
min_dist=4)
def test_all_metrics_weird_input(self):
"""all_metrics: should work when ref or prediction empty or no seqs"""
ref = Pairs([(3,10)])
pred = Pairs()
seqs = ['UACGUAGCUAGCUAGCUACG']
obs = all_metrics(ref, pred, seqs=[seqs], min_dist=4)
exp = {'SENSITIVITY':0, 'SELECTIVITY':0,\
'AC':0, 'CC':0, 'MCC':0}
for k in exp:
self.assertFloatEqual(obs[k], exp[k])
ref = Pairs()
pred = Pairs()
seqs = ['UACGUAGCUAGCUAGCUACG']
obs = all_metrics(ref, pred, seqs=[seqs], min_dist=4)
exp = {'SENSITIVITY':1, 'SELECTIVITY':1,\
'AC':1, 'CC':1, 'MCC':1}
for k in exp:
self.assertFloatEqual(obs[k], exp[k])
ref = Pairs([(3,10)])
pred = Pairs([(1,12)])
seqs = ['UACGUAGCUAGCUAGCUACG']
self.assertRaises(ValueError, all_metrics, ref, pred, seqs="",\
min_dist=4)
def test_all_metrics(self):
"""all_metrics: check against compare_ct.pm"""
exp = {'SENSITIVITY':0.4, 'SELECTIVITY':0.5, 'AC':0.45,\
'CC':0.42906394, 'MCC':0.42906394}
obs = all_metrics(self.true, self.predicted, seqs=self.seq, min_dist=4)
self.assertEqualItems(obs.keys(), exp.keys())
for k in exp:
self.assertFloatEqual(obs[k], exp[k])
def test_all_metrics(self):
"""all_metrics: check against compare_ct.pm"""
exp = {'SENSITIVITY':0.4, 'SELECTIVITY':0.5, 'AC':0.45,\
'CC':0.42906394, 'MCC':0.42906394}
obs = all_metrics(self.true, self.predicted, seqs=self.seq, min_dist=4)
self.assertEqualItems(obs.keys(), exp.keys())
for k in exp:
self.assertFloatEqual(obs[k], exp[k])
def test_all_metrics_pseudo(self):
"""all_metrics: pseudoknot in ref, check against compare_ct.pm"""
ref = Pairs([(0, 8), (1, 7), (4, 10)])
pred = Pairs([(0, 8), (3, 6), (4, 10)])
seq = 'GACUGUGUCAU'
exp = {'SENSITIVITY':0.6666667, 'SELECTIVITY':0.6666667,\
'AC':0.6666667, 'CC':0.57575758, 'MCC':0.57575758}
obs = all_metrics(ref, pred, seqs=[seq], min_dist=4)
self.assertEqualItems(obs.keys(), exp.keys())
for k in exp:
self.assertFloatEqual(obs[k], exp[k])
def test_all_metrics_pseudo(self):
"""all_metrics: pseudoknot in ref, check against compare_ct.pm"""
ref = Pairs([(0,8),(1,7),(4,10)])
pred = Pairs([(0,8),(3,6),(4,10)])
seq = 'GACUGUGUCAU'
exp = {'SENSITIVITY':0.6666667, 'SELECTIVITY':0.6666667,\
'AC':0.6666667, 'CC':0.57575758, 'MCC':0.57575758}
obs = all_metrics(ref, pred, seqs=[seq], min_dist=4)
self.assertEqualItems(obs.keys(), exp.keys())
for k in exp:
self.assertFloatEqual(obs[k], exp[k])
