def test_consistency_unrooted(self):
"""Test consistency of taxa with a taxa that is only monophyletic in unrooted tree"""
seed_con = 'f__Lachnospiraceae; g__Bacteroides; s__'
nl.determine_rank_order(seed_con)
tipname_map = {'a': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides pectinophilus'],
'b': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides pectinophilus'],
'c': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides pectinophilus'],
'd': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides acidifaciens'],
'e': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides acidifaciens']}
tree = nl.load_tree(StringIO(u'((a,b),(c,(d,e)));'), tipname_map)
counts = nl.collect_names_at_ranks_counts(tree)
nl.decorate_ntips_rank(tree)
nl.decorate_name_counts(tree)
# determine taxonomic consistency of rooted tree
#expected_consistency_index
c = Consistency(counts, len(nl.RANK_ORDER))
consistency_index = c.calculate(tree, rooted=True)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides pectinophilus'], 0.66666666)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides acidifaciens'], 1.0)
#determine consistency of unrooted tree
consistency_index = c.calculate(tree, rooted=False)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides acidifaciens'], 1.0)
def test_consistency_missing(self):
"""Test consistency of taxa in tree with missing taxa"""
seed_con = 'f__Lachnospiraceae; g__Bacteroides; s__'
nl.determine_rank_order(seed_con)
tipname_map = {'a': ['f__Lachnospiraceae', 'g__Bacteroides', None],
'c': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides pectinophilus'],
'b': ['f__Lachnospiraceae', 'g__Bacteroides', None], 'e': [None, None, None],
'd': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides pectinophilus'],
'g': [None, None, None], 'f': ['f__Lachnospiraceae', 'g__Lachnospira', None],
'h': ['f__Lachnospiraceae', 'g__Lachnospira', 's__Bacteroides pectinophilus']}
tree = nl.load_tree(StringIO(u'(((a,b),(c,d)),((e,f),(g,h)));'), tipname_map)
counts = nl.collect_names_at_ranks_counts(tree)
nl.decorate_ntips_rank(tree)
nl.decorate_name_counts(tree)
# determine taxonomic consistency of rooted tree
#expected_consistency_index
c = Consistency(counts, len(nl.RANK_ORDER))
consistency_index = c.calculate(tree, rooted=True)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Lachnospira'], 1.0)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
#determine consistency of unrooted tree
consistency_index = c.calculate(tree, rooted=False)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Lachnospira'], 1.0)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
def test_consistency_unrooted(self):
"""Test consistency of taxa with a taxa that is only monophyletic in unrooted tree"""
seed_con = 'f__Lachnospiraceae; g__Bacteroides; s__'
nl.determine_rank_order(seed_con)
tipname_map = {
'a': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides pectinophilus'
],
'b': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides pectinophilus'
],
'c': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides pectinophilus'
],
'd': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides acidifaciens'
],
'e': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides acidifaciens'
]
}
tree = nl.load_tree('((a,b),(c,(d,e)));', tipname_map)
counts = nl.collect_names_at_ranks_counts(tree)
nl.decorate_ntips_rank(tree)
nl.decorate_name_counts(tree)
# determine taxonomic consistency of rooted tree
#expected_consistency_index
c = Consistency(counts, len(nl.RANK_ORDER))
consistency_index = c.calculate(tree, rooted=True)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides pectinophilus'], 0.66666666)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides acidifaciens'], 1.0)
#determine consistency of unrooted tree
consistency_index = c.calculate(tree, rooted=False)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides acidifaciens'], 1.0)
def test_consistency_missing(self):
"""Test consistency of taxa in tree with missing taxa"""
seed_con = 'f__Lachnospiraceae; g__Bacteroides; s__'
nl.determine_rank_order(seed_con)
tipname_map = {
'a': ['f__Lachnospiraceae', 'g__Bacteroides', None],
'c': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides pectinophilus'
],
'b': ['f__Lachnospiraceae', 'g__Bacteroides', None],
'e': [None, None, None],
'd': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides pectinophilus'
],
'g': [None, None, None],
'f': ['f__Lachnospiraceae', 'g__Lachnospira', None],
'h': [
'f__Lachnospiraceae', 'g__Lachnospira',
's__Bacteroides pectinophilus'
]
}
tree = nl.load_tree('(((a,b),(c,d)),((e,f),(g,h)));', tipname_map)
counts = nl.collect_names_at_ranks_counts(tree)
nl.decorate_ntips_rank(tree)
nl.decorate_name_counts(tree)
# determine taxonomic consistency of rooted tree
#expected_consistency_index
c = Consistency(counts, len(nl.RANK_ORDER))
consistency_index = c.calculate(tree, rooted=True)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Lachnospira'], 1.0)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
#determine consistency of unrooted tree
consistency_index = c.calculate(tree, rooted=False)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Lachnospira'], 1.0)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
def test_decorate_ntips_rank(self):
"""correctly decorate the tree with the NumTipsRank param"""
input = "(((a,b)c,(d,e,f)g)h,(i,j)k)l;"
tree = TreeNode.from_newick(input)
tips = dict([(tip.name, tip) for tip in tree.tips()])
tips['a'].Consensus = [1, 2, 3, 4, 5, 6, 7]
tips['b'].Consensus = [None, None, None, 5, None, None, None]
tips['d'].Consensus = [1, 2, 3, 4, 5, 6, 8]
tips['e'].Consensus = [None, None, None, None, None, None, None]
tips['f'].Consensus = [1, 2, 3, 4, 5, 6, 8]
tips['i'].Consensus = [1, 2, 3, 4, 5, 6, 8]
tips['j'].Consensus = [1, 2, 3, 4, 5, 6, 8]
decorate_ntips_rank(tree)
self.assertEqual(tree.NumTipsRank[0], 5)
self.assertEqual(tree.NumTipsRank[1], 5)
self.assertEqual(tree.NumTipsRank[2], 5)
self.assertEqual(tree.NumTipsRank[3], 6)
self.assertEqual(tree.NumTipsRank[4], 5)
self.assertEqual(tree.NumTipsRank[5], 5)
self.assertEqual(tree.NumTipsRank[6], 5)
def test_decorate_ntips_rank(self):
"""correctly decorate the tree with the NumTipsRank param"""
data = StringIO(u"(((a,b)c,(d,e,f)g)h,(i,j)k)l;")
tree = TreeNode.read(data)
tips = dict([(tip.name, tip) for tip in tree.tips()])
tips['a'].Consensus = [1, 2, 3, 4, 5, 6, 7]
tips['b'].Consensus = [None, None, None, 5, None, None, None]
tips['d'].Consensus = [1, 2, 3, 4, 5, 6, 8]
tips['e'].Consensus = [None, None, None, None, None, None, None]
tips['f'].Consensus = [1, 2, 3, 4, 5, 6, 8]
tips['i'].Consensus = [1, 2, 3, 4, 5, 6, 8]
tips['j'].Consensus = [1, 2, 3, 4, 5, 6, 8]
decorate_ntips_rank(tree)
self.assertEqual(tree.NumTipsRank[0], 5)
self.assertEqual(tree.NumTipsRank[1], 5)
self.assertEqual(tree.NumTipsRank[2], 5)
self.assertEqual(tree.NumTipsRank[3], 6)
self.assertEqual(tree.NumTipsRank[4], 5)
self.assertEqual(tree.NumTipsRank[5], 5)
self.assertEqual(tree.NumTipsRank[6], 5)