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()