/
test_taxtree.py
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/
test_taxtree.py
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#!/usr/bin/env python
from unittest import TestCase, main
from copy import deepcopy
from numpy import array
from biom import Table
from americangut.taxtree import create_node, add_node, get_node, update_tree, \
get_rare_unique, traverse, sample_rare_unique, \
build_persample_tree_from_taxontable, set_relative_freqs, \
update_per_sample_tree
__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2013, The American Gut Project"
__credits__ = ["Daniel McDonald"]
__license__ = "BSD"
__version__ = "unversioned"
__maintainer__ = "Daniel McDonald"
__email__ = "mcdonadt@colorado.edu"
class TaxTreeTests(TestCase):
def setUp(self):
ta = {'name': 'root',
'count': 36,
'freq': 1.0,
'children': [{'name': 'k__1',
'count': 36,
'freq': 1.0,
'children': [{'name': 'p__x',
'count': 12,
'freq': 12.0 / 36.0,
'children': [{'name': 'c__1',
'count': 1,
'freq': 1.0 / 36,
'children': []},
{'name': 'c__2',
'count': 4,
'freq': 4.0 / 36,
'children': []},
{'name': 'c__',
'count': 7,
'freq': 7.0 / 36,
'children': []}]},
{'name': 'p__y',
'count': 24,
'freq': 24.0 / 36.0,
'children': [{'name': 'c__3',
'count': 10,
'freq': 10.0 / 36.0,
'children': []},
{'name': 'c__',
'count': 14,
'freq': 14.0 / 36.0,
'children': []}]}]}]}
self.persample = ta
def test_build_persample_tree_from_taxontable(self):
exp_a = ('a', self.persample)
obs_a = build_persample_tree_from_taxontable(table).next()
self.assertEqual(obs_a, exp_a)
def test_set_relative_freqs(self):
persample_copy = deepcopy(self.persample)
self.persample['freq'] = None
for node in traverse(self.persample):
node['freq'] = None
set_relative_freqs(self.persample)
self.assertEqual(persample_copy, self.persample)
def test_update_per_sample_tree(self):
taxons = (('k__a', 'p__x'),
('k__a', 'p__x'),
('k__a', 'p__y'), # indep of p__x; c__1
('k__b', 'p__z'))
counts = (5, 7, 9, 11)
exp = {'name': 'root',
'count': 32,
'freq': None,
'children': [{'name': 'k__a',
'count': 21,
'freq': None,
'children': [{'name': 'p__x',
'count': 12,
'freq': None,
'children': []},
{'name': 'p__y',
'count': 9,
'freq': None,
'children': []}]},
{'name': 'k__b',
'count': 11,
'freq': None,
'children': [{'name': 'p__z',
'count': 11,
'freq': None,
'children': []}]}]}
tree = create_node('root', count=0, freq=None)
update_per_sample_tree(tree, taxons[0], counts[0])
update_per_sample_tree(tree, taxons[1], counts[1])
update_per_sample_tree(tree, taxons[2], counts[2])
update_per_sample_tree(tree, taxons[3], counts[3])
self.assertEqual(tree, exp)
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_create_node(self):
exp = {'name':'foo','children':[]}
obs = create_node('foo')
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)
def test_add_node(self):
exp = {'name':'foo','popcount':1,'children':[
{'name':'bar', 'popcount':2, 'children':[]}
]
}
foo = create_node('foo', popcount=1)
bar = create_node('bar', popcount=2)
add_node(foo,bar)
self.assertEqual(foo, exp)
def test_get_node(self):
tree = {'name':'foo','popcount':0,'children':[
{'name':'bar', 'popcount':0, 'children':[]}
]}
self.assertEqual(get_node(tree, 'does not exist'), None)
self.assertEqual(get_node(tree, 'bar'), tree['children'][0])
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_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)
tax_strings_by_sample = [
[
['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__x','c__'],
['k__1','p__y','c__3']
],
[
['k__1','p__y','c__']
]
]
table = 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'])
sample_taxa = [
['k__1','p__x','c__2'],
['k__1','p__x','c__'],
['k__1','p__y','c__3']
]
if __name__ == '__main__':
main()