def test_create_tree(self):
"""take tax strings, create a tree"""
exp = {'name':'root',
'popcount':3,
'children':[
{'name':'k__1',
'popcount':3,
'children':[
{'name':'p__x',
'popcount':2,
'children':[
{'name':'c__1',
'popcount':1,
'children':[]},
{'name':'c__2',
'popcount':1,
'children':[]}
]
},
{'name':'p__y',
'popcount':3,
'children':[
{'name':'c__3',
'popcount':2,
'children':[]}
]
}
]}
]}
tax_strings = deepcopy(tax_strings_by_sample)
tax_strings[0].append(['k__[1]','p__x','c__'])
obs = update_tree(None, tax_strings)
self.assertEqual(obs, exp)
def test_create_tree(self):
"""take tax strings, create a tree"""
exp = {'name':'root',
'popcount':3,
'children':[
{'name':'k__1',
'popcount':3,
'children':[
{'name':'p__x',
'popcount':2,
'children':[
{'name':'c__1',
'popcount':1,
'children':[]},
{'name':'c__2',
'popcount':1,
'children':[]}
]
},
{'name':'p__y',
'popcount':3,
'children':[
{'name':'c__3',
'popcount':2,
'children':[]}
]
}
]}
]}
obs = update_tree(None, tax_strings_by_sample)
self.assertEqual(obs, exp)
def test_create_tree_ignore_contested(self):
"""take tax strings, create a tree"""
exp = {'name':'root',
'popcount':3,
'children':[
{'name':'k__1',
'popcount':3,
'children':[
{'name':'p__x',
'popcount':2,
'children':[
{'name':'c__1',
'popcount':1,
'children':[]},
{'name':'c__2',
'popcount':1,
'children':[]}
]
},
{'name':'p__y',
'popcount':3,
'children':[
{'name':'c__3',
'popcount':2,
'children':[]}
]
}
]}
]}
obs = update_tree(None, tax_strings_by_sample)
self.assertEqual(obs, exp)
def test_get_rare_unique(self):
t = update_tree(None, tax_strings_by_sample)
exp_unique = [['k__1','p__x','c__2']]
exp_rare = [['k__1','p__x','c__'],['k__1','p__y','c__3']]
obs_rare, obs_unique = get_rare_unique(t, sample_taxa, 0.7)
self.assertEqual(obs_rare, exp_rare)
self.assertEqual(obs_unique, exp_unique)
exp_unique = [['k__1','p__x','c__2']]
exp_rare = []
obs_rare, obs_unique = get_rare_unique(t, sample_taxa, 0.4)
self.assertEqual(obs_rare, exp_rare)
self.assertEqual(obs_unique, exp_unique)
def test_get_rare_unique(self):
t = update_tree(None, tax_strings_by_sample)
exp_unique = [['k__1', 'p__x', 'c__2']]
exp_rare = [['k__1', 'p__x', 'c__'], ['k__1', 'p__y', 'c__3']]
obs_rare, obs_unique = get_rare_unique(t, sample_taxa, 0.7)
self.assertEqual(obs_rare, exp_rare)
self.assertEqual(obs_unique, exp_unique)
exp_unique = [['k__1', 'p__x', 'c__2']]
exp_rare = []
obs_rare, obs_unique = get_rare_unique(t, sample_taxa, 0.4)
self.assertEqual(obs_rare, exp_rare)
self.assertEqual(obs_unique, exp_unique)
def test_sample_rare_unique(self):
t = update_tree(None, tax_strings_by_sample)
tax_by_sample = {
'a': tax_strings_by_sample[0],
'b': tax_strings_by_sample[1],
'c': tax_strings_by_sample[2]
}
exp = [('a', None, [['k__1', 'p__x', 'c__'],
['k__1', 'p__y',
'c__3']], [['k__1', 'p__x', 'c__1'],
['k__1', 'p__x', 'c__2']]),
('b', None, [['k__1', 'p__x', 'c__'], ['k__1', 'p__y',
'c__3']], []),
('c', None, [], [])]
obs = sample_rare_unique(t, None, tax_by_sample, 0.7)
self.assertEqual(sorted(obs), exp)
table_a = Table(array([[14, 15, 16]]), ['k__1; p__y; c__'],
['a', 'b', 'c'])
table_b = Table(
array([[1, 2, 3], [4, 5, 6], [14, 15, 16]]),
['k__1; p__x; c__1', 'k__1; p__x; c__2', 'k__1; p__y; c__'],
['a', 'b', 'c'],
)
table_c = Table(
array([[1, 2, 3], [4, 5, 6], [7, 8, 9], [10, 11, 12],
[14, 15, 16]]), [
'k__1; p__x; c__1', 'k__1; p__x; c__2',
'k__1; p__x; c__', 'k__1; p__y; c__3', 'k__1; p__y; c__'
], ['a', 'b', 'c'])
exp = [('a', table_a, [['k__1', 'p__x', 'c__'],
['k__1', 'p__y',
'c__3']], [['k__1', 'p__x', 'c__1'],
['k__1', 'p__x', 'c__2']]),
('b', table_b, [['k__1', 'p__x', 'c__'],
['k__1', 'p__y', 'c__3']], []),
('c', table_c, [], [])]
obs = sample_rare_unique(t, table, tax_by_sample, 0.7)
for o, e in zip(sorted(obs), exp):
self.assertEqual(o[0], e[0])
self.assertEqual(o[1], e[1])
self.assertEqual(o[2], e[2])
self.assertEqual(o[3], e[3])
def test_sample_rare_unique(self):
t = update_tree(None, tax_strings_by_sample)
tax_by_sample = {'a':tax_strings_by_sample[0],
'b':tax_strings_by_sample[1],
'c':tax_strings_by_sample[2]}
exp = [('a', None, [['k__1','p__x','c__'],['k__1','p__y','c__3']],
[['k__1','p__x','c__1'],['k__1','p__x','c__2']]),
('b', None, [['k__1','p__x','c__'],['k__1','p__y','c__3']], []),
('c', None, [], [])]
obs = sample_rare_unique(t, None, tax_by_sample, 0.7)
self.assertEqual(sorted(obs), exp)
table_a = Table(array([[14,15,16]]),
['k__1; p__y; c__'],
['a','b','c'])
table_b = Table(array([[1,2,3],
[4,5,6],
[14,15,16]]),
['k__1; p__x; c__1',
'k__1; p__x; c__2',
'k__1; p__y; c__'],
['a','b','c'], )
table_c = Table(array([[1,2,3],
[4,5,6],
[7,8,9],
[10,11,12],
[14,15,16]]),
['k__1; p__x; c__1',
'k__1; p__x; c__2',
'k__1; p__x; c__',
'k__1; p__y; c__3',
'k__1; p__y; c__'],
['a','b','c'])
exp = [('a', table_a, [['k__1','p__x','c__'],['k__1','p__y','c__3']],
[['k__1','p__x','c__1'],['k__1','p__x','c__2']]),
('b', table_b, [['k__1','p__x','c__'],['k__1','p__y','c__3']], []),
('c', table_c, [], [])]
obs = sample_rare_unique(t, table, tax_by_sample, 0.7)
for o,e in zip(sorted(obs), exp):
self.assertEqual(o[0], e[0])
self.assertEqual(o[1], e[1])
self.assertEqual(o[2], e[2])
self.assertEqual(o[3], e[3])
def test_traverse(self):
t = update_tree(None, tax_strings_by_sample)
exp = ['c__1','c__2','p__x','c__3','p__y','k__1','root']
obs = [n['name'] for n in traverse(t)]
self.assertEqual(obs, exp)
def test_traverse(self):
t = update_tree(None, tax_strings_by_sample)
exp = ['c__1', 'c__2', 'p__x', 'c__3', 'p__y', 'k__1', 'root']
obs = [n['name'] for n in traverse(t)]
self.assertEqual(obs, exp)
