def test_taxa_score(self):
"""score taxa strings in the face of replicates"""
master = {'a':['k__k1','p__p1','c__c1','o__o1','f__f1','g__g1','s__s1'],
'b':['k__k1','p__p1','c__c2',None,'f__f2','g__g1','s__s2'],
'c':[None,None,None,None,None,None,None],
'd':['k__k2','p__x','c__c1','o__o10','f__f2','g__g2','s__s3']}
rep1 = {'a':['k__k1','p__p1','c__c1','o__o1','f__f1','g__g1','s__s1'],
'c':[None,None,None,None,None,None,None],
'd':['k__k2','','c__c1','f__f2','f__f2','g__g2','s__s3']}
rep2 = {'a':['k__k1','p__p1','c__c1','o__o1','f__f1','g__g1','s__s1'],
'b':['k__k1','p__p1','c__c2',None,'f__f2','g__g1','s__s9'],
'c':[None,None,None,None,None,None,None]}
rep3 = {'a':['k__k1','p__p1','c__c1','o__o1','f__f1','g__g1','s__s1'],
'b':['k__k1','p__p1','c__c2',None,'f__f2','g__g1','s__s2'],
'd':['k__k2','','c__c1','f__f2','f__f2','g__g2','s__s3']}
rep4 = {'a':['k__k1','p__p1','c__c1','o__o1','f__f1','g__g1','s__s1'],
'b':['k__k1','p__p1','c__c10',None,'f__f2','g__g1','s__s2'],
'c':[None,None,None,None,None,None,None],
'd':['k__k1','','c__c1','f__f2','f__f2','g__g2','s__s3']}
# if malformed, as in rep3 rep4 for d, count as contridiction
exp = {'a':[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],
'b':[1.0, 1.0, 0.75, 1.0, 1.0, 1.0, 0.75],
'c':[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],
'd':[0.75, 0.25, 1.0, 0.25, 1.0, 1.0, 1.0]}
obs = taxa_score(master, [rep1,rep2,rep3,rep4])
self.assertEqual(obs, exp)
def test_merge_taxa_strings_and_scores(self):
"""merge taxa scores and the strings"""
master = {'a':['k__k1','p__p1','c__c1','o__o1','f__f1','g__g1','s__s1'],
'b':['k__k1','p__p1','c__c2',None,'f__f2','g__g1','s__s2'],
'c':[None,None,None,None,None,None,None],
'd':['k__k2','p__x','c__c1','o__o10','f__f2','g__g2','s__s3']}
rep1 = {'a':['k__k1','p__p1','c__c1','o__o1','f__f1','g__g1','s__s1'],
'c':[None,None,None,None,None,None,None],
'd':['k__k2','','c__c1','f__f2','f__f2','g__g2','s__s3']}
rep2 = {'a':['k__k1','p__p1','c__c1','o__o1','f__f1','g__g1','s__s1'],
'b':['k__k1','p__p1','c__c2',None,'f__f2','g__g1','s__s9'],
'c':[None,None,None,None,None,None,None]}
rep3 = {'a':['k__k1','p__p1','c__c1','o__o1','f__f1','g__g1','s__s1'],
'b':['k__k1','p__p1','c__c2',None,'f__f2','g__g1','s__s2'],
'd':['k__k2','','c__c1','f__f2','f__f2','g__g2','s__s3']}
rep4 = {'a':['k__k1','p__p1','c__c1','o__o1','f__f1','g__g1','s__s1'],
'b':['k__k1','p__p1','c__c10',None,'f__f2','g__g1','s__s2'],
'c':[None,None,None,None,None,None,None],
'd':['k__k1','','c__c1','f__f2','f__f2','g__g2','s__s3']}
scores = taxa_score(master, [rep1, rep2, rep3, rep4])
exp = {'a':[('k__k1',1.0), ('p__p1',1.0), ('c__c1',1.0), ('o__o1',1.0),
('f__f1',1.0), ('g__g1',1.0), ('s__s1',1.0)],
'b':[('k__k1',1.0), ('p__p1',1.0), ('c__c2',0.75), (None,1.0),
('f__f2',1.0), ('g__g1',1.0), ('s__s2',0.75)],
'c':[(None,1.0), (None,1.0), (None,1.0), (None,1.0), (None,1.0),
(None,1.0), (None,1.0)],
'd':[('k__k2',0.75), ('p__x',0.25), ('c__c1',1.0),
('o__o10',0.25), ('f__f2',1.0), ('g__g2',1.0),
('s__s3',1.0)]}
obs = merge_taxa_strings_and_scores(master, scores)
self.assertEqual(obs,exp)
def test_merge_taxa_strings_and_scores(self):
"""merge taxa scores and the strings"""
master = {
'a':
['k__k1', 'p__p1', 'c__c1', 'o__o1', 'f__f1', 'g__g1', 's__s1'],
'b': ['k__k1', 'p__p1', 'c__c2', None, 'f__f2', 'g__g1', 's__s2'],
'c': [None, None, None, None, None, None, None],
'd':
['k__k2', 'p__x', 'c__c1', 'o__o10', 'f__f2', 'g__g2', 's__s3']
}
rep1 = {
'a':
['k__k1', 'p__p1', 'c__c1', 'o__o1', 'f__f1', 'g__g1', 's__s1'],
'c': [None, None, None, None, None, None, None],
'd': ['k__k2', '', 'c__c1', 'f__f2', 'f__f2', 'g__g2', 's__s3']
}
rep2 = {
'a':
['k__k1', 'p__p1', 'c__c1', 'o__o1', 'f__f1', 'g__g1', 's__s1'],
'b': ['k__k1', 'p__p1', 'c__c2', None, 'f__f2', 'g__g1', 's__s9'],
'c': [None, None, None, None, None, None, None]
}
rep3 = {
'a':
['k__k1', 'p__p1', 'c__c1', 'o__o1', 'f__f1', 'g__g1', 's__s1'],
'b': ['k__k1', 'p__p1', 'c__c2', None, 'f__f2', 'g__g1', 's__s2'],
'd': ['k__k2', '', 'c__c1', 'f__f2', 'f__f2', 'g__g2', 's__s3']
}
rep4 = {
'a':
['k__k1', 'p__p1', 'c__c1', 'o__o1', 'f__f1', 'g__g1', 's__s1'],
'b': ['k__k1', 'p__p1', 'c__c10', None, 'f__f2', 'g__g1', 's__s2'],
'c': [None, None, None, None, None, None, None],
'd': ['k__k1', '', 'c__c1', 'f__f2', 'f__f2', 'g__g2', 's__s3']
}
scores = taxa_score(master, [rep1, rep2, rep3, rep4])
exp = {
'a':
[('k__k1', 1.0), ('p__p1', 1.0), ('c__c1', 1.0), ('o__o1', 1.0),
('f__f1', 1.0), ('g__g1', 1.0), ('s__s1', 1.0)],
'b': [('k__k1', 1.0), ('p__p1', 1.0), ('c__c2', 0.75), (None, 1.0),
('f__f2', 1.0), ('g__g1', 1.0), ('s__s2', 0.75)],
'c': [(None, 1.0), (None, 1.0), (None, 1.0), (None, 1.0),
(None, 1.0), (None, 1.0), (None, 1.0)],
'd': [('k__k2', 0.75), ('p__x', 0.25), ('c__c1', 1.0),
('o__o10', 0.25), ('f__f2', 1.0), ('g__g2', 1.0),
('s__s3', 1.0)]
}
obs = merge_taxa_strings_and_scores(master, scores)
self.assertEqual(obs, exp)
def test_taxa_score(self):
"""score taxa strings in the face of replicates"""
master = {
'a':
['k__k1', 'p__p1', 'c__c1', 'o__o1', 'f__f1', 'g__g1', 's__s1'],
'b': ['k__k1', 'p__p1', 'c__c2', None, 'f__f2', 'g__g1', 's__s2'],
'c': [None, None, None, None, None, None, None],
'd':
['k__k2', 'p__x', 'c__c1', 'o__o10', 'f__f2', 'g__g2', 's__s3']
}
rep1 = {
'a':
['k__k1', 'p__p1', 'c__c1', 'o__o1', 'f__f1', 'g__g1', 's__s1'],
'c': [None, None, None, None, None, None, None],
'd': ['k__k2', '', 'c__c1', 'f__f2', 'f__f2', 'g__g2', 's__s3']
}
rep2 = {
'a':
['k__k1', 'p__p1', 'c__c1', 'o__o1', 'f__f1', 'g__g1', 's__s1'],
'b': ['k__k1', 'p__p1', 'c__c2', None, 'f__f2', 'g__g1', 's__s9'],
'c': [None, None, None, None, None, None, None]
}
rep3 = {
'a':
['k__k1', 'p__p1', 'c__c1', 'o__o1', 'f__f1', 'g__g1', 's__s1'],
'b': ['k__k1', 'p__p1', 'c__c2', None, 'f__f2', 'g__g1', 's__s2'],
'd': ['k__k2', '', 'c__c1', 'f__f2', 'f__f2', 'g__g2', 's__s3']
}
rep4 = {
'a':
['k__k1', 'p__p1', 'c__c1', 'o__o1', 'f__f1', 'g__g1', 's__s1'],
'b': ['k__k1', 'p__p1', 'c__c10', None, 'f__f2', 'g__g1', 's__s2'],
'c': [None, None, None, None, None, None, None],
'd': ['k__k1', '', 'c__c1', 'f__f2', 'f__f2', 'g__g2', 's__s3']
}
# if malformed, as in rep3 rep4 for d, count as contridiction
exp = {
'a': array([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]),
'b': array([1.0, 1.0, 0.75, 1.0, 1.0, 1.0, 0.75]),
'c': array([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]),
'd': array([0.75, 0.25, 1.0, 0.25, 1.0, 1.0, 1.0])
}
obs = taxa_score(master, [rep1, rep2, rep3, rep4])
self.assertEqual(obs.keys(), exp.keys())
for k in exp:
self.assertTrue(array_equal(obs[k], exp[k]))
