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_collect_names_at_ranks_counts(self):
"""correctly returns total counts for names at ranks"""
input = "((a,b)c,(d,(e,f)g)h,(i,j)k)l;"
tipname_map = {
'a': ['1', '2', '3', '4', '5', '6', '7'],
'b': ['1', '2', '3', None, '5', '6', '8'],
'd': ['1', '2', '3', 'a', '5', '6', '9'],
'e': ['1', '2', '3', None, '5', '6', '9'],
'i': ['1', '2', '3', 'a', '5', '6', '9'],
'j': ['1', '2', '3', '4', '5', '6', '9']
}
tree = load_tree(input, tipname_map)
exp = {
0: {
'1': 6
},
1: {
'2': 6
},
2: {
'3': 6
},
3: {
'4': 2,
'a': 2
},
4: {
'5': 6
},
5: {
'6': 6
},
6: {
'7': 1,
'8': 1,
'9': 4
}
}
obs = collect_names_at_ranks_counts(tree)
self.assertEqual(obs, exp)
def test_collect_names_at_ranks_counts(self):
"""correctly returns total counts for names at ranks"""
input = "((a,b)c,(d,(e,f)g)h,(i,j)k)l;"
tipname_map = {'a':['1','2','3','4','5','6','7'],
'b':['1','2','3',None,'5','6','8'],
'd':['1','2','3','a','5','6','9'],
'e':['1','2','3',None,'5','6','9'],
'i':['1','2','3','a','5','6','9'],
'j':['1','2','3','4','5','6','9']}
tree = load_tree(input, tipname_map)
exp = {0:{'1':6},
1:{'2':6},
2:{'3':6},
3:{'4':2, 'a':2},
4:{'5':6},
5:{'6':6},
6:{'7':1,'8':1,'9':4}}
obs = collect_names_at_ranks_counts(tree)
self.assertEqual(obs, exp)
def generate_constrings(tree, tipname_map, verbose=False):
"""Assigns taxonomy to unidentified sequences in tree.
Returns all sequence IDs on tree."""
counts = nlevel.collect_names_at_ranks_counts(tree)
min_count = 2
nlevel.decorate_ntips(tree)
nlevel.decorate_name_relative_freqs(tree, counts, min_count)
nlevel.set_ranksafe(tree)
nlevel.pick_names(tree)
nlevel.name_node_score_fold(tree)
if verbose:
print "Tree score: ", nlevel.score_tree(tree)
nlevel.set_preliminary_name_and_rank(tree)
contree, contree_lookup = nlevel.make_consensus_tree(tipname_map.values())
nlevel.backfill_names_gap(tree, contree_lookup)
nlevel.commonname_promotion(tree)
nlevel.make_names_unique(tree, append_suffix=False)
constrings = nlevel.pull_consensus_strings(tree)
return constrings
