def test_best_name_freqs_for_nodes(self):
"""correctly gets the frequencies per name per node"""
data = StringIO(u"((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', 'b', '5', '6', '8'],
'd': ['1', '2', '3', '4', '5', '6', '7'],
'e': ['1', '2', '3', 'b', 'a', 'foo', '7'],
'i': ['1', '2', '3', '4', 'a', 'foo', '8'],
'j': ['1', '2', '3', 'b', 'a', 'foo', '8']}
total_counts = {0: {'1': 10, 'foo': 5},
1: {'2': 10},
2: {'3': 10},
3: {'4': 4, 'b': 5},
4: {'5': 7, 'a': 5},
5: {'6': 3, 'foo': 3},
6: {'7': 3, '8': 4}}
tree = load_tree(data, tipname_map)
decorate_ntips(tree)
decorate_name_relative_freqs(tree, total_counts, 1)
set_ranksafe(tree)
pick_names(tree)
# result = best_name_freqs_for_nodes(tree)
cnode = tree.children[0]
hnode = tree.children[1]
knode = tree.children[2]
def test_name_node_score_fold(self):
"""hate taxonomy"""
data = StringIO(u"((a,b)c,(d,(e,f)g)h,(i,j)k)l;")
tipname_map = {'a': ['1', '2', '3', '4', '5', '6', '8'],
'b': ['1', '2', '3', '4', '5', '6', '8'],
'd': ['1', '2', '3', 'f', 'e', 'c', '9'],
'e': ['1', '2', '3', 'f', 'e', 'c', '9'],
'i': ['1', '2', '3', 'g', 'a', 'h', '11'],
'j': ['1', '2', '3', 'g', 'a', 'h', '12']}
total_counts = {0: {'1': 10, 'foo': 5},
1: {'2': 10},
2: {'3': 10},
3: {'4': 3, 'f': 5, 'g': 5},
4: {'5': 7, 'a': 5, 'e': 4},
5: {'6': 3, 'c': 3, 'd': 2, 'h': 3},
6: {'8': 3, '9': 2, '10': 2, '11': 2, '12': 2}}
tree = load_tree(data, tipname_map)
decorate_ntips(tree)
decorate_name_relative_freqs(tree, total_counts, 1)
set_ranksafe(tree)
pick_names(tree)
name_node_score_fold(tree)
exp_root = ['1', '2', '3', None, None, None, None]
expc0 = [None, None, None, '4', None, None, None]
expc1 = [None, None, None, None, 'e', 'c', '9']
expc2 = [None, None, None, None, None, 'h', None]
expc1c1 = [None] * 7
self.assertEqual(tree.RankNames, exp_root)
self.assertEqual(tree.children[0].RankNames, expc0)
self.assertEqual(tree.children[1].RankNames, expc1)
self.assertEqual(tree.children[2].RankNames, expc2)
self.assertEqual(tree.children[1].children[1].RankNames, expc1c1)
def test_validate_all_paths(self):
"""complains correctly about badpaths"""
data = StringIO(u"(((((1,2)s__,(3,4)s__)g__)p__),((5,6)f__)f__,((7,8)c__)o__);")
t = load_tree(data, {})
exp = [n for n in t.tips() if n.name in ['5', '6', '7', '8']]
obs = validate_all_paths(t)
self.assertEqual(obs, exp)
def test_set_ranksafe(self):
"""correctly set ranksafe on tree"""
data = StringIO(u"((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', 'b', '5', '6', '8'],
'd': ['1', '2', '3', '4', '5', '6', '8'],
'e': ['1', '2', '3', 'b', 'a', '6', '7'],
'i': ['1', '2', '3', '4', 'a', '6', '7'],
'j': ['1', '2', '3', 'b', 'a', '6', '8']}
total_counts = {0: {'1': 10, 'foo': 5},
1: {'2': 20},
2: {'3': 10},
3: {'4': 4, 'b': 5},
4: {'5': 7, 'a': 5},
5: {'6': 6},
6: {'7': 3, '8': 3}}
tree = load_tree(data, tipname_map)
decorate_ntips(tree)
decorate_name_relative_freqs(tree, total_counts, 1)
set_ranksafe(tree)
exp_root = [True, False, True, False, True, True, False]
self.assertEqual(tree.RankSafe, exp_root)
def test_decorate_name_relative_freqs(self):
"""correctly decorate relative frequency information on a tree"""
data = StringIO(u"((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', '4', '5', '6', '8'],
'd': ['1', '2', '3', '4', '5', '6', '8'],
'e': ['1', '2', '3', '4', 'a', '6', '7'],
'i': ['1', '2', '3', '4', 'a', None, '7'],
'j': ['1', '2', '3', '4', 'a', None, '8']}
total_counts = {0: {'1': 10, 'foo': 5},
1: {'2': 6},
2: {'3': 12},
3: {'4': 6, 'bar': 5},
4: {'5': 6, 'a': 3},
5: {'6': 6},
6: {'7': 3, '8': 3}}
tree = load_tree(data, tipname_map)
decorate_ntips(tree)
decorate_name_relative_freqs(tree, total_counts, 1)
exp_root = {0: {'1': .6},
1: {'2': 1.0},
2: {'3': .5},
3: {'4': 1.0},
4: {'5': .5, 'a': 1.0},
5: {'6': 4.0 / 6},
6: {'7': 1.0, '8': 1.0}}
self.assertEqual(tree.ConsensusRelFreq, exp_root)
def test_load_tree(self):
"""correctly loads and decorates tiplook info on a tree"""
data = StringIO(u"((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', '4', '5', '6', '8'],
'd': ['1', '2', '3', '4', '5', '6', '9'],
'e': ['1', '2', '3', '4', '5', '6', '10'],
'i': ['1', '2', '3', '4', '5', '6', '12'],
'j': ['1', '2', '3', '4', '5', '6', '13']}
# exp in Name: (tipstart, tipstop, consensus)
exp = {'a': (0, 0, ['1', '2', '3', '4', '5', '6', '7']),
'b': (1, 1, ['1', '2', '3', '4', '5', '6', '8']),
'c': (0, 1, [None] * 7),
'd': (2, 2, ['1', '2', '3', '4', '5', '6', '9']),
'e': (3, 3, ['1', '2', '3', '4', '5', '6', '10']),
'f': (4, 4, [None] * 7),
'g': (3, 4, [None] * 7),
'h': (2, 4, [None] * 7),
'i': (5, 5, ['1', '2', '3', '4', '5', '6', '12']),
'j': (6, 6, ['1', '2', '3', '4', '5', '6', '13']),
'k': (5, 6, [None] * 7),
'l': (0, 6, [None] * 7)}
obstree = load_tree(data, tipname_map)
obs = {}
for node in obstree.traverse(include_self=True):
obs[node.name] = (node.TipStart, node.TipStop, node.Consensus)
self.assertEqual(obs, exp)
def test_pick_names(self):
"""correctly pick names to retain on a tree"""
data = StringIO(u"((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', 'b', '5', '6', '8'],
'd': ['1', '2', '3', '4', '5', '6', '7'],
'e': ['1', '2', '3', 'b', 'a', 'foo', '7'],
'i': ['1', '2', '3', '4', 'a', 'foo', '8'],
'j': ['1', '2', '3', 'b', 'a', 'foo', '8']}
total_counts = {0: {'1': 10, 'foo': 5},
1: {'2': 10},
2: {'3': 10},
3: {'4': 4, 'b': 5},
4: {'5': 7, 'a': 5},
5: {'6': 3, 'foo': 3},
6: {'7': 3, '8': 4}}
tree = load_tree(data, tipname_map)
decorate_ntips(tree)
decorate_name_relative_freqs(tree, total_counts, 1)
set_ranksafe(tree)
pick_names(tree)
exp_root = ['1', '2', '3', None, None, None, None]
self.assertEqual(tree.RankNames, exp_root)
expc0 = [None, None, None, None, None, '6', None]
expc1 = [None, None, None, None, None, None, '7']
expc2 = [None, None, None, None, None, 'foo', '8']
expc1c1 = [None] * 7
self.assertEqual(tree.children[0].RankNames, expc0)
self.assertEqual(tree.children[1].RankNames, expc1)
self.assertEqual(tree.children[2].RankNames, expc2)
self.assertEqual(tree.children[1].children[1].RankNames, expc1c1)
def test_pick_names(self):
"""correctly pick names to retain on a tree"""
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','b','5','6','8'],
'd':['1','2','3','4','5','6','7'],
'e':['1','2','3','b','a','foo','7'],
'i':['1','2','3','4','a','foo','8'],
'j':['1','2','3','b','a','foo','8']}
total_counts = {0:{'1':10, 'foo':5},
1:{'2':10},
2:{'3':10},
3:{'4':4,'b':5},
4:{'5':7,'a':5},
5:{'6':3,'foo':3},
6:{'7':3,'8':4}}
tree = load_tree(input,tipname_map)
decorate_ntips(tree)
decorate_name_relative_freqs(tree, total_counts, 1)
set_ranksafe(tree)
pick_names(tree)
exp_root = ['1','2','3',None,None,None,None]
self.assertEqual(tree.RankNames, exp_root)
expc0 = [None,None,None,None,None,'6',None]
expc1 = [None,None,None,None,None,None,'7']
expc2 = [None,None,None,None,None,'foo','8']
expc1c1 = [None] * 7
self.assertEqual(tree.Children[0].RankNames, expc0)
self.assertEqual(tree.Children[1].RankNames, expc1)
self.assertEqual(tree.Children[2].RankNames, expc2)
self.assertEqual(tree.Children[1].Children[1].RankNames, expc1c1)
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_best_name_freqs_for_nodes(self):
"""correctly gets the frequencies per name per node"""
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','b','5','6','8'],
'd':['1','2','3','4','5','6','7'],
'e':['1','2','3','b','a','foo','7'],
'i':['1','2','3','4','a','foo','8'],
'j':['1','2','3','b','a','foo','8']}
total_counts = {0:{'1':10, 'foo':5},
1:{'2':10},
2:{'3':10},
3:{'4':4,'b':5},
4:{'5':7,'a':5},
5:{'6':3,'foo':3},
6:{'7':3,'8':4}}
tree = load_tree(input,tipname_map)
decorate_ntips(tree)
decorate_name_relative_freqs(tree, total_counts, 1)
set_ranksafe(tree)
pick_names(tree)
#result = best_name_freqs_for_nodes(tree)
cnode = tree.Children[0]
hnode = tree.Children[1]
knode = tree.Children[2]
def test_name_node_score_fold(self):
"""hate taxonomy"""
input = "((a,b)c,(d,(e,f)g)h,(i,j)k)l;"
tipname_map = {'a':['1','2','3','4','5','6','8'],
'b':['1','2','3','4','5','6','8'],
'd':['1','2','3','f','e','c','9'],
'e':['1','2','3','f','e','c','9'],
'i':['1','2','3','g','a','h','11'],
'j':['1','2','3','g','a','h','12']}
total_counts = {0:{'1':10, 'foo':5},
1:{'2':10},
2:{'3':10},
3:{'4':3,'f':5,'g':5},
4:{'5':7,'a':5,'e':4},
5:{'6':3,'c':3,'d':2,'h':3},
6:{'8':3,'9':2,'10':2,'11':2,'12':2}}
tree = load_tree(input,tipname_map)
decorate_ntips(tree)
decorate_name_relative_freqs(tree, total_counts, 1)
set_ranksafe(tree)
pick_names(tree)
name_node_score_fold(tree)
exp_root = ['1','2','3',None,None,None,None]
expc0 = [None, None, None, '4',None,None,None]
expc1 = [None, None, None, None,'e','c','9']
expc2 = [None, None, None, None, None,'h',None]
expc1c1 = [None] * 7
self.assertEqual(tree.RankNames, exp_root)
self.assertEqual(tree.Children[0].RankNames, expc0)
self.assertEqual(tree.Children[1].RankNames, expc1)
self.assertEqual(tree.Children[2].RankNames, expc2)
self.assertEqual(tree.Children[1].Children[1].RankNames, expc1c1)
def test_decorate_name_relative_freqs(self):
"""correctly decorate relative frequency information on a tree"""
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','4','5','6','8'],
'd':['1','2','3','4','5','6','8'],
'e':['1','2','3','4','a','6','7'],
'i':['1','2','3','4','a',None,'7'],
'j':['1','2','3','4','a',None,'8']}
total_counts = {0:{'1':10, 'foo':5},
1:{'2':6},
2:{'3':12},
3:{'4':6,'bar':5},
4:{'5':6,'a':3},
5:{'6':6},
6:{'7':3,'8':3}}
tree = load_tree(input, tipname_map)
decorate_ntips(tree)
decorate_name_relative_freqs(tree, total_counts, 1)
exp_root = {0:{'1':.6},
1:{'2':1.0},
2:{'3':.5},
3:{'4':1.0},
4:{'5':.5, 'a':1.0},
5:{'6':4.0/6},
6:{'7':1.0,'8':1.0}}
self.assertFloatEqual(tree.ConsensusRelFreq, exp_root)
def test_set_ranksafe(self):
"""correctly set ranksafe on tree"""
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','b','5','6','8'],
'd':['1','2','3','4','5','6','8'],
'e':['1','2','3','b','a','6','7'],
'i':['1','2','3','4','a','6','7'],
'j':['1','2','3','b','a','6','8']}
total_counts = {0:{'1':10, 'foo':5},
1:{'2':20},
2:{'3':10},
3:{'4':4,'b':5},
4:{'5':7,'a':5},
5:{'6':6},
6:{'7':3,'8':3}}
tree = load_tree(input, tipname_map)
decorate_ntips(tree)
decorate_name_relative_freqs(tree, total_counts, 1)
set_ranksafe(tree)
#exp_root = ['Yes','Majority','Yes','No','Yes','Yes','No']
exp_root = [True,False,True,False,True,True,False]
self.assertEqual(tree.RankSafe, exp_root)
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_load_tree(self):
"""correctly loads and decorates tiplook info on a tree"""
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','4','5','6','8'],
'd':['1','2','3','4','5','6','9'],
'e':['1','2','3','4','5','6','10'],
'i':['1','2','3','4','5','6','12'],
'j':['1','2','3','4','5','6','13']}
# exp in Name: (tipstart, tipstop, consensus)
exp = {'a':(0,0,['1','2','3','4','5','6','7']),
'b':(1,1,['1','2','3','4','5','6','8']),
'c':(0,1,[None] * 7),
'd':(2,2,['1','2','3','4','5','6','9']),
'e':(3,3,['1','2','3','4','5','6','10']),
'f':(4,4,[None] * 7),
'g':(3,4,[None] * 7),
'h':(2,4,[None] * 7),
'i':(5,5,['1','2','3','4','5','6','12']),
'j':(6,6,['1','2','3','4','5','6','13']),
'k':(5,6,[None] * 7),
'l':(0,6,[None] * 7)}
obstree = load_tree(input, tipname_map, verbose=False)
obs = {}
for node in obstree.traverse(include_self=True):
obs[node.Name] = (node.TipStart, node.TipStop, node.Consensus)
self.assertEqual(obs, exp)
def test_validate_all_paths(self):
"""complains correctly about badpaths"""
input = "(((((1,2)s__,(3,4)s__)g__)p__),((5,6)f__)f__,((7,8)c__)o__);"
t = load_tree(input, {})
exp = [n for n in t.tips() if n.name in ['5', '6', '7', '8']]
obs = validate_all_paths(t)
self.assertEqual(obs, exp)
def test_validate_all_paths(self):
"""complains correctly about badpaths"""
input = "(((((1,2)s__,(3,4)s__)g__)p__),((5,6)f__)f__,((7,8)c__)o__);"
t = load_tree(input, {})
exp = [t.getNodeMatchingName('5'),
t.getNodeMatchingName('6'),
t.getNodeMatchingName('7'),
t.getNodeMatchingName('8')]
obs = validate_all_paths(t)
self.assertEqual(obs, exp)
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_generate_constrings_valid_input(self):
"""Tests generate_constrings with standard valid input.
Checks that our output mirrors nlevel (tax2tree's interface)."""
exp = test_results
determine_rank_order(test_cons[0].split('\t')[1])
cons_map = load_consensus_map(test_cons, False)
tree = load_tree(test_tree, cons_map)
obs = generate_constrings(tree, cons_map)
self.assertEqual(obs, exp)
def test_generate_constrings_valid_input(self):
"""Tests generate_constrings with standard valid input.
Checks that our output mirrors nlevel (tax2tree's interface)."""
exp = test_results
determine_rank_order(test_cons[0].split('\t')[1])
cons_map = load_consensus_map(test_cons, False)
tree = load_tree(test_tree, cons_map)
obs = generate_constrings(tree, cons_map)
self.assertEqual(obs, exp)
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 __call__(self, seq_path=None, result_path=None, log_path=None):
"""Returns a dict mapping {seq_id:(taxonomy, confidence)} for each seq
Keep in mind, "confidence" is only done for consistency and in fact
all assignments will have a score of 0 because a method for determining
confidence is not currently implemented.
Parameters:
seq_path: path to file of sequences. The sequences themselves are
never actually used, but they are needed for their ids.
result_path: path to file of results. If specified, dumps the
result to the desired path instead of returning it.
log_path: path to log, which should include dump of params.
"""
# initialize the logger
logger = self._get_logger(log_path)
logger.info(str(self))
with open(seq_path, 'U') as f:
seqs = dict(parse_fasta(f))
consensus_map = tax2tree.prep_consensus(
open(self.Params['id_to_taxonomy_fp']),
seqs.keys())
seed_con = consensus_map[0].strip().split('\t')[1]
determine_rank_order(seed_con)
tipnames_map = load_consensus_map(consensus_map, False)
tree = load_tree(open(self.Params['tree_fp']), tipnames_map)
results = tax2tree.generate_constrings(tree, tipnames_map)
results = tax2tree.clean_output(results, seqs.keys())
if result_path:
# if the user provided a result_path, write the
# results to file
with open(result_path, 'w') as f:
for seq_id, (lineage, confidence) in results.iteritems():
f.write('%s\t%s\t%s\n' % (seq_id, lineage, confidence))
logger.info('Result path: %s' % result_path)
return results
def __call__(self, seq_path=None, result_path=None, log_path=None):
"""Returns a dict mapping {seq_id:(taxonomy, confidence)} for each seq
Keep in mind, "confidence" is only done for consistency and in fact
all assignments will have a score of 0 because a method for determining
confidence is not currently implemented.
Parameters:
seq_path: path to file of sequences. The sequences themselves are
never actually used, but they are needed for their ids.
result_path: path to file of results. If specified, dumps the
result to the desired path instead of returning it.
log_path: path to log, which should include dump of params.
"""
# initialize the logger
logger = self._get_logger(log_path)
logger.info(str(self))
with open(seq_path, 'U') as f:
seqs = dict(MinimalFastaParser(f))
consensus_map = tax2tree.prep_consensus(
open(self.Params['id_to_taxonomy_fp']),
seqs.keys())
seed_con = consensus_map[0].strip().split('\t')[1]
determine_rank_order(seed_con)
tipnames_map = load_consensus_map(consensus_map, False)
tree = load_tree(open(self.Params['tree_fp']), tipnames_map)
results = tax2tree.generate_constrings(tree, tipnames_map)
results = tax2tree.clean_output(results, seqs.keys())
if result_path:
# if the user provided a result_path, write the
# results to file
with open(result_path, 'w') as f:
for seq_id, (lineage, confidence) in results.iteritems():
f.write('%s\t%s\t%s\n' % (seq_id, lineage, confidence))
logger.info('Result path: %s' % result_path)
return results
def test_decorate_name_counts(self):
"""correctly decorate relative frequency information on a tree"""
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', '4', '5', '6', '8'],
'd': ['1', '2', '3', '4', '5', '6', '8'],
'e': ['1', '2', '3', '4', 'a', '6', '7'],
'i': ['1', '2', '3', '4', 'a', None, '7'],
'j': ['1', '2', '3', '4', 'a', None, '8']
}
tree = load_tree(input, tipname_map)
decorate_ntips(tree)
decorate_name_counts(tree)
exp_root = {
0: {
'1': 6
},
1: {
'2': 6
},
2: {
'3': 6
},
3: {
'4': 6
},
4: {
'5': 3,
'a': 3
},
5: {
'6': 4
},
6: {
'7': 3,
'8': 3
}
}
self.assertEqual(tree.TaxaCount, exp_root)
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 test_decorate_name_counts(self):
"""correctly decorate relative frequency information on a tree"""
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', '4', '5', '6', '8'],
'd': ['1', '2', '3', '4', '5', '6', '8'],
'e': ['1', '2', '3', '4', 'a', '6', '7'],
'i': ['1', '2', '3', '4', 'a', None, '7'],
'j': ['1', '2', '3', '4', 'a', None, '8']}
tree = load_tree(input, tipname_map)
decorate_ntips(tree)
decorate_name_counts(tree)
exp_root = {0: {'1': 6},
1: {'2': 6},
2: {'3': 6},
3: {'4': 6},
4: {'5': 3, 'a': 3},
5: {'6': 4},
6: {'7': 3, '8': 3}}
self.assertEqual(tree.TaxaCount, exp_root)
