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from unittest import TestCase, main
from bp import parse_newick, to_skbio_treenode, write_newick, parse_jplace
import re
import json
import pandas as pd
import pandas.testing as pdt
import os
import skbio
import io
import numpy as np
import numpy.testing as npt
class NewickTests(TestCase):
def test_parse_newick_simple_edge_numbers(self):
# from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009
# but without edge labels
# 0 1 2 3 4 5 6 7 8 9
# 1 1 1 0 1 0 0 1 0 0
in_ = '((A:.01{0}, B:.01{1})D:.01{3}, C:.01{4}) {5};'
exp_sk = '((A:.01, B:.01)D:.01, C:.01);' # skbio doesn't know about edge numbers
obs = parse_newick(in_)
obs_sk = to_skbio_treenode(obs)
exp_sk = skbio.TreeNode.read([exp_sk])
self.assertEqual(obs_sk.compare_rfd(exp_sk), 0)
self.assertEqual(obs.edge(2), 0)
self.assertEqual(obs.edge(4), 1)
self.assertEqual(obs.edge(1), 3)
self.assertEqual(obs.edge(7), 4)
self.assertEqual(obs.edge(0), 5)
self.assertEqual(obs.edge_from_number(0), 2)
self.assertEqual(obs.edge_from_number(1), 4)
self.assertEqual(obs.edge_from_number(3), 1)
self.assertEqual(obs.edge_from_number(4), 7)
self.assertEqual(obs.edge_from_number(5), 0)
def _compare_newick(self, obs, exp):
a = skbio.TreeNode.read([obs])
b = skbio.TreeNode.read([exp])
self.assertEqual(a.compare_rfd(b), 0)
npt.assert_equal(a.tip_tip_distances().data,
b.tip_tip_distances().data)
def test_write_newick_cases(self):
tests = ['((foo"bar":1,baz:2)x:3)r;',
"(((a:1,b:2.5)c:6,d:8,(e),(f,g,(h:1,i:2)j:1)k:1.2)l,m:2)r;",
"(((a)b)c,((d)e)f)r;",
"((a,(b,c):5)'d','e; foo':10,((f))g)r;"]
for test in tests:
buf = io.StringIO()
obs = write_newick(parse_newick(test), buf, False)
buf.seek(0)
obs = buf.read()
self._compare_newick(obs, test)
def test_write_newick_edges(self):
test_a = '((foo"bar":1{0},baz:2{1})x:3{2})r;'
test_b = "(((a)b)c,((d)e)f)r;"
buf = io.StringIO()
obs = write_newick(parse_newick(test_a), buf, True)
buf.seek(0)
obs = to_skbio_treenode(parse_newick(buf.read()))
self.assertEqual(obs.find('foo"bar"').edge_num, 0)
self.assertEqual(obs.find('baz').edge_num, 1)
self.assertEqual(obs.find('x').edge_num, 2)
buf = io.StringIO()
obs = write_newick(parse_newick(test_b), buf, True)
buf.seek(0)
obs = to_skbio_treenode(parse_newick(buf.read()))
for o in obs.traverse():
self.assertEqual(o.edge_num, 0)
def test_parse_newick_singlenode_bug(self):
# https://github.com/wasade/improved-octo-waddle/issues/29
test = 'i:1;'
# let's not allow this edge case
with self.assertRaises(ValueError):
parse_newick(test)
def test_parse_newick_no_semicolon_bug(self):
# https://github.com/wasade/improved-octo-waddle/issues/26
test = "((h:1, i:1, j:1, k:1, l: 1),(e:1,f:1),(n:1,o:1,p:1))a:1"
with self.assertRaises(ValueError):
parse_newick(test)
# make sure we work with a newline
test = "((h:1, i:1, j:1, k:1, l: 1),(e:1,f:1),(n:1,o:1,p:1))a:1;\n"
parse_newick(test)
def test_write_newick_underscore_bug(self):
test = "(((a)b)'c_foo',((d)e)f)r;"
buf = io.StringIO()
obs = write_newick(parse_newick(test), buf, False)
buf.seek(0)
self.assertIn("'c_foo'", test)
def test_parse_newick_nested_quotes(self):
# bug: quotes are removed
in_ = '((foo"bar":1,baz:2)x:3)r;'
exp = skbio.TreeNode.read([in_])
obs = to_skbio_treenode(parse_newick(in_))
self.assertEqual(obs.compare_subsets(exp), 0.0)
def test_parse_newick_with_commas(self):
# bug: comma is getting interpreted even if in quotes
in_ = "(('foo,bar':1,baz:2)x:3)r;"
exp = skbio.TreeNode.read([in_])
obs = to_skbio_treenode(parse_newick(in_))
self.assertEqual(obs.compare_subsets(exp), 0.0)
def test_parse_newick_with_parens(self):
# bug: parens are getting interpreted even if in quotes
in_ = "(('foo(b)ar':1,baz:2)x:3)r;"
exp = skbio.TreeNode.read([in_])
obs = to_skbio_treenode(parse_newick(in_))
self.assertEqual(obs.compare_subsets(exp), 0.0)
def test_parse_newick(self):
in_ = "((a:2,b):1,(c:4,d)y:20,e)r;"
exp_bp = [1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0]
exp_n = ['r', None, 'a', None, 'b', None, None, 'y', 'c', None, 'd',
None, None, 'e', None, None]
exp_l = [0, 1, 2, 0, 0, 0, 0, 20, 4, 0, 0, 0, 0, 0, 0, 0]
obs_bp = parse_newick(in_)
npt.assert_equal(obs_bp.B, np.asarray(exp_bp, dtype=bool))
for i, (e_n, e_l) in enumerate(zip(exp_n, exp_l)):
self.assertEqual(obs_bp.name(i), e_n)
self.assertEqual(obs_bp.length(i), e_l)
def test_parse_newick_complex(self):
in_ = "(((a:1,b:2.5)c:6,d:8,(e),(f,g,(h:1,i:2)j:1)k:1.2)l,m:2)r;"
# 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
exp_bp = [1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1,
1, 0, 1, 0, 0, 0, 0, 1, 0, 0]
exp_n = ['r', 'l', 'c', 'a', None, 'b', None, None, 'd', None, None,
'e', None, None, 'k', 'f', None, 'g', None, 'j', 'h', None,
'i', None, None, None, None, 'm', None, None]
exp_l = [0, 0, 6, 1, 0, 2.5, 0, 0, 8, 0, 0, 0, 0, 0, 1.2, 0, 0, 0, 0,
1, 1, 0, 2, 0, 0, 0, 0, 2, 0, 0]
obs_bp = parse_newick(in_)
npt.assert_equal(obs_bp.B, np.asarray(exp_bp, dtype=bool))
for i, (e_n, e_l) in enumerate(zip(exp_n, exp_l)):
self.assertEqual(obs_bp.name(i), e_n)
self.assertEqual(obs_bp.length(i), e_l)
def test_parse_newick_singledesc(self):
in_ = "(((a)b)c,((d)e)f)r;"
# 0 1 2 3 4 5 6 7 8 9 10 11 12 13
exp_bp = [1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0]
exp_n = ['r', 'c', 'b', 'a', None, None, None, 'f', 'e', 'd', None,
None, None, None]
obs_bp = parse_newick(in_)
npt.assert_equal(obs_bp.B, np.asarray(exp_bp, dtype=bool))
for i, e_n in enumerate(exp_n):
self.assertEqual(obs_bp.name(i), e_n)
def test_parse_newick_unnamed_singledesc(self):
in_ = "((a,b)c,d,(e))r;"
exp_bp = [1, 1, 1, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0]
exp_n = ['r', 'c', 'a', None, 'b', None, None, 'd', None, None, 'e',
None, None, None]
obs_bp = parse_newick(in_)
npt.assert_equal(obs_bp.B, np.asarray(exp_bp, dtype=bool))
for i, e_n in enumerate(exp_n):
self.assertEqual(obs_bp.name(i), e_n)
def test_parse_newick_name_with_semicolon(self):
in_ = "((a,(b,c):5)'d','e; foo':10,((f))g)r;"
exp_bp = [1, 1, 1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0]
exp_n = ['r', 'd', 'a', None, None, 'b', None, 'c', None, None, None,
'e; foo', None, 'g', None, 'f', None, None, None, None]
exp_l = [0, 0, 0, 0, 5, 0, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0, 0, 0, 0, 0]
obs_bp = parse_newick(in_)
npt.assert_equal(obs_bp.B, np.asarray(exp_bp, dtype=bool))
for i, (e_n, e_l) in enumerate(zip(exp_n, exp_l)):
self.assertEqual(obs_bp.name(i), e_n)
self.assertEqual(obs_bp.length(i), e_l)
class JPlaceParseTests(TestCase):
package = 'bp.tests'
def setUp(self):
with open(self.get_data_path('200/placement.jplace'), 'r') as file:
self.jplacedata = file.read()
no_edge_numbers = re.sub(r"{\d+}", '',
json.loads(self.jplacedata)['tree'])
self.tree = skbio.TreeNode.read([no_edge_numbers])
def get_data_path(self, filename):
current_directory = os.getcwd()
return current_directory + "/tests/data/" + filename
def test_place_jplace_square_braces(self):
self.jplacedata = json.loads(self.jplacedata)
treestr = self.jplacedata['tree']
treestr = re.sub(r"{(\d+)}", r"[\1]", treestr)
self.jplacedata['tree'] = treestr
self.jplacedata = json.dumps(self.jplacedata)
exp_tree = self.tree
obs_df, obs_tree = parse_jplace(self.jplacedata)
obs_tree = to_skbio_treenode(obs_tree)
self.assertEqual(obs_tree.compare_rfd(exp_tree), 0)
for n in obs_tree.traverse(include_self=False):
self.assertTrue(n.edge_num >= 0)
def test_parse_jplace_simple(self):
columns = ['fragment', 'edge_num', 'likelihood', 'like_weight_ratio',
'distal_length', 'pendant_length']
exp_df = [["82", 361, 0.01013206496780672, 1, 0.02652932626620403,
0.039354548684623215],
["99", 308, 0.04520741687623886, 1, 0.11020044356641526,
0.06550337922097477],
["43", 309, 0.04054866161921744, 1, 0.010712923050783987,
0.020946988900520196],
["195", 277, 0.01918907908397749, 1, 0.03065741838803451,
0.04513513498399864],
["162", 55, 0.01758935282545493, 1, 0.0033199487685078776,
0.05388735804976052],
["56", 81, 0.2366882303770561, 1, 0.04172580852519453,
0.0007060238727097983],
["91", 105, 0.0001863393767883581, 1, 0.04578898721138839,
0.08655004339151215],
["174", 89, 0.01216463967379211, 1, 0.04707020642820376,
0.045206727542450205],
["5", 143, 0.012162345471765756, 1, 0.023797389484252734,
0.10447375403452556],
["55", 139, 0.09563944060686769, 1, 0.014593217782258146,
0.04537214236560885]]
exp_df = pd.DataFrame(exp_df, columns=columns)
exp_tree = self.tree
obs_df, obs_tree = parse_jplace(self.jplacedata)
obs_tree = to_skbio_treenode(obs_tree)
pdt.assert_frame_equal(obs_df, exp_df)
self.assertEqual(obs_tree.compare_rfd(exp_tree), 0)
def test_parse_jplace_multiple_per_fragment(self):
columns = ['fragment', 'edge_num', 'likelihood', 'like_weight_ratio',
'distal_length', 'pendant_length']
exp_df = [["82", 361, 0.01013206496780672, 1, 0.02652932626620403,
0.039354548684623215],
["99", 308, 0.04520741687623886, 1, 0.11020044356641526,
0.06550337922097477],
# tied on like_weight_ratio but lower pendant
["99", 309, 0.04520741687623886, 1, 0.11020044356641526,
0.00550337922097477],
["55", 139, 0.09563944060686769, 1, 0.014593217782258146,
0.04537214236560885],
# tied higher like_weight_ratio
["55", 138, 0.09563944060686769, 10, 0.014593217782258146,
0.04537214236560885]]
exp_df = pd.DataFrame(exp_df, columns=columns)
# ...adjust jplace data
data = json.loads(self.jplacedata)
keep = []
for placement in data['placements']:
if placement['n'][0] == '82':
keep.append(placement)
elif placement['n'][0] == '99':
placement['p'].append([309, 0.04520741687623886, 1,
0.11020044356641526,
0.00550337922097477])
keep.append(placement)
elif placement['n'][0] == '55':
placement['p'].append([138, 0.09563944060686769, 10,
0.014593217782258146,
0.04537214236560885])
keep.append(placement)
data['placements'] = keep
data = json.dumps(data)
exp_tree = self.tree
obs_df, obs_tree = parse_jplace(data)
obs_tree = to_skbio_treenode(obs_tree)
pdt.assert_frame_equal(obs_df, exp_df)
self.assertEqual(obs_tree.compare_rfd(exp_tree), 0)
if __name__ == '__main__':
main()
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