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|
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import io
import unittest
from skbio import TreeNode
from skbio.io import NewickFormatError
from skbio.io.format.newick import (
_newick_to_tree_node, _tree_node_to_newick, _newick_sniffer)
class TestNewick(unittest.TestCase):
def _assert_node_equal(self, n1, n2):
self.assertEqual(n1.name, n2.name)
self.assertEqual(n1.length, n2.length)
self.assertEqual(len(n1.children), len(n2.children))
def _assert_equal(self, n1, n2):
def name(x):
return (str(x.name),
float(x.length) if x.length is not None else 0,
len(x.children))
self._assert_node_equal(n1, n2)
for c1, c2 in zip(sorted(n1.children, key=name),
sorted(n2.children, key=name)):
self.assertTrue(c1.parent is n1)
self.assertTrue(c2.parent is n2)
self._assert_equal(c1, c2)
def _setup_tree(self, kwargs_list):
trees = []
for kwargs in kwargs_list:
trees.append(TreeNode(**kwargs))
trees[4].extend([trees[2], trees[3]])
trees[5].extend([trees[0], trees[1], trees[4]])
return trees[5]
def _setup_linked_list(self, kwargs_list):
last_node = None
for idx, kwargs in enumerate(kwargs_list):
new_node = TreeNode(**kwargs)
if last_node is not None:
new_node.append(last_node)
last_node = new_node
return last_node
def _setup_balanced_binary(self, kwargs_list):
trees = []
for kwargs in kwargs_list:
trees.append(TreeNode(**kwargs))
trees[0].extend([trees[2], trees[3]])
trees[1].extend([trees[4], trees[5]])
trees[6].extend([trees[0], trees[1]])
return trees[6]
def setUp(self):
# Using the factory functions above, we will construct different tree
# instances. Each tree is expected to serialize to the first newick
# string in the list. Each string in the list is expected to
# deserialize into an equivilent rotation of the constructed instance.
tree_blank = (self._setup_tree([
{}, {}, {}, {}, {}, {}
]), [
"(,,(,));\n",
"(,(,),);",
"((,),,);",
" ((,[ this is a comment ]) , , ) ; ",
"((,[ i_can_do_this[0] or escape unmatched '[ ]),[more words],);",
])
tree_leaves_named = (self._setup_tree([
{'name': 'a_'},
{'name': 'b'},
{'name': 'c'},
{'name': 'd'},
{},
{}
]), [
"('a_',b,(c,d));\n",
"(b,(c,d),'a_');",
"(b\n,'a_'\n ,(d \t,c) ) ;",
])
tree_all_named = (self._setup_tree([
{'name': 'a'},
{'name': 'b'},
{'name': 'c'},
{'name': '[whaaat!\']'},
{'name': 'e'},
{'name': 'f'}
]), [
"(a,b,(c,'[whaaat!'']')e)f;\n",
"(b,(c,'[whaaat!'']')e,a)f;",
"(b,[comment] \na,('[whaaat!'']',c)e)f;",
])
tree_all_but_root_distances = (self._setup_tree([
{'length': 0.1},
{'length': 0.2},
{'length': 0.3},
{'length': 0.4},
{'length': 0.5},
{}
]), [
"(:0.1,:0.2,(:0.3,:0.4):0.5);\n",
"(:0.2,(:0.3,:0.4):0.5,:0.1);",
"(:0.2,:0.1,(:0.4,:0.3):0.5);",
])
tree_all_distances = (self._setup_tree([
{'length': 0.1},
{'length': 0.2},
{'length': 0.3},
{'length': 0.4},
{'length': 0.5},
{'length': 0.0}
]), [
"(:0.1,:0.2,(:0.3,:0.4):0.5):0.0;\n",
"(:0.2,(:0.3,:0.4):0.5,:0.1):0.0;",
"(:0.2,\n:0.1,(:0.4,\n:0.3):0.5)\n:0.0;",
])
tree_all_leaves_named_with_distances = (self._setup_tree([
{'name': 'a', 'length': 0.1},
{'name': 'b_a\'', 'length': 0.2},
{'name': 'c', 'length': 0.3},
{'name': 'de d', 'length': 0.4},
{'length': 0.5},
{'length': 0.0}
]), [
"(a:0.1,'b_a''':0.2,(c:0.3,de_d:0.4):0.5):0.0;\n",
"('b_a''':0.2,(c:0.3,'de d':0.4):0.5,a:0.1):0.0;",
"('b_a''':0.2,a:0.1,('de d'[why not]:0.4,c:0.3):0.5):0.0;",
])
tree_all_leaves_named_with_distances_no_root = (self._setup_tree([
{'name': 'a', 'length': 0.1},
{'name': 'b_a\'', 'length': 0.2},
{'name': 'c', 'length': 0.3},
{'name': 'de d', 'length': 0.4},
{'length': 0.5},
{}
]), [
"(a:0.1,'b_a''':0.2,(c:0.3,de__d:0.4):0.5);\n",
"('b_a''':0.2\n[comment ahoy]\n,(c:0.3,'de d':0.4):0.5,a:0.1);",
"('b_a''':0.2,a:0.1,(de__d:0.4,c:0.3):0.5);"
])
tree_all = (self._setup_tree([
{'name': 'a', 'length': 0.1},
{'name': 'b_a\'', 'length': 0.2},
{'name': 'c', 'length': 0.3},
{'name': 'de\' d', 'length': 0.4},
{'name': 'e', 'length': 0.5},
{'name': 'f', 'length': 0.0}
]), [
"(a:0.1,'b_a''':0.2,(c:0.3,de''_d:0.4)e:0.5)f:0.0;\n",
"('b_a''':0.2,(c:0.3,de''_d:0.4)e:0.5,a:0.1)f:0.0;",
"((de''_d:0.4, c:0.3)e:0.5, 'b_a''':0.2, a:0.1)f:0.0;"
])
balanced_blank = (self._setup_balanced_binary([
{}, {}, {}, {}, {}, {}, {}
]), [
"((,),(,));\n",
])
balanced_named = (self._setup_balanced_binary([
{'name': 'a'},
{'name': 'b'},
{'name': 'c'},
{'name': 'd'},
{'name': 'e'},
{'name': 'f'},
{'name': 'g'}
]), [
"((c,d)a,(e,f)b)g;\n",
])
balanced_distances = (self._setup_balanced_binary([
{'length': 1.0},
{'length': 2.0},
{'length': 3.0},
{'length': 4.0},
{'length': 5.0},
{'length': 6.0},
{'length': 0.0}
]), [
"((:3.0,:4.0):1.0,(:5.0,:6.0):2.0):0.0;\n",
])
blanaced_all = (self._setup_balanced_binary([
{'name': 'a', 'length': 1.0},
{'name': 'b', 'length': 2.0},
{'name': 'c', 'length': 3.0},
{'name': 'd', 'length': 4.0},
{'name': 'e', 'length': 5.0},
{'name': 'f:f\'f', 'length': 6.0},
{'name': 'g', 'length': 0.0}
]), [
"((c:3.0,d:4.0)a:1.0,(e:5.0,'f:f''f':6.0)b:2.0)g:0.0;\n",
])
linked_list_blank = (self._setup_linked_list([
{}, {}, {}, {}, {}
]), [
"(((())));\n",
"[(((())));](((())));",
"[[(((())));](((())));](((())));\t\t\n"
])
linked_list_named = (self._setup_linked_list([
{'name': 'aaa'},
{'name': 'b_a\''},
{'name': 'c'},
{'name': 'de d'},
{'name': 'e'},
]), [
"((((aaa)'b_a''')c)de_d)e;\n"
])
inked_list_distances = (self._setup_linked_list([
{'length': 0.4},
{'length': 0.3},
{'length': 0.2},
{'length': 0.1},
{'length': 0.0},
]), [
"((((:0.4):0.3):0.2):0.1):0.0;\n",
"((((:0.4)[not a label]:0.3):0.2):0.1):0.0;\t\t\n"
])
linked_list_all = (self._setup_linked_list([
{'name': 'a', 'length': 0.4},
{'name': 'b_a\'', 'length': 0.3},
{'name': 'c', 'length': 0.2},
{'name': 'de d', 'length': 0.1},
{'name': 'eee', 'length': 0.0},
]), [
"((((a:0.4)'b_a''':0.3)c:0.2)de_d:0.1)eee:0.0;\n"
])
single_empty = (TreeNode(), [";\n", "[comment about the root"
" and its properties];"])
single_named = (TreeNode(name='athing'), ["athing;\n"])
single_distance = (TreeNode(length=200.0), [":200.0;\n"])
single_all = (TreeNode(name='[a]', length=200.0), ["'[a]':200.0;\n"])
self.trees_newick_lists = [
tree_blank,
tree_leaves_named,
tree_all_named,
tree_all_but_root_distances,
tree_all_distances,
tree_all_leaves_named_with_distances,
tree_all_leaves_named_with_distances_no_root,
tree_all,
balanced_blank,
balanced_named,
balanced_distances,
blanaced_all,
linked_list_blank,
linked_list_named,
inked_list_distances,
linked_list_all,
single_empty,
single_named,
single_distance,
single_all
]
# Invalid newick strings and list of error fragments that should be
# a part of the error message when read.
self.invalid_newicks = [
("", ['root']),
("This is not a newick file.", ['whitespace', 'label']),
("((();", ['Parenthesis', 'unbalanced']),
("(,,,)(,);\n", ['unnested', 'children']),
("(()());", ['unnested', 'children']),
("(():,,)", ['length']),
("[][[]('comment is the gotcha':0.2,,);", ['unbalanced', 'root']),
("#SampleID\tHeaderA\tHeaderB\n0\t'yellow'\t0.45;", ['whitespace',
'label']),
("))();", ['Parenthesis', 'unbalanced']),
("((,,),((,,));", ['Parenthesis', 'unbalanced']),
("\n".join([",".join(str(i) for i in range(100))
for _ in range(100)]), ['whitespace', 'label'])
]
def test_newick_to_tree_node_valid_files(self):
for tree, newicks in self.trees_newick_lists:
for newick in newicks:
fh = io.StringIO(newick)
read_tree = _newick_to_tree_node(fh)
self._assert_equal(tree, read_tree)
fh.close()
def test_newick_to_tree_node_invalid_files(self):
for invalid, error_fragments in self.invalid_newicks:
fh = io.StringIO(invalid)
with self.assertRaises(NewickFormatError) as cm:
_newick_to_tree_node(fh)
for frag in error_fragments:
self.assertIn(frag, str(cm.exception))
fh.close()
def test_tree_node_to_newick(self):
for tree, newicks in self.trees_newick_lists:
newick = newicks[0]
fh = io.StringIO()
_tree_node_to_newick(tree, fh)
self.assertEqual(newick, fh.getvalue())
fh.close()
def test_roundtrip(self):
for tree, newicks in self.trees_newick_lists:
newick = newicks[0]
fh = io.StringIO(newick)
tree = _newick_to_tree_node(fh)
fh2 = io.StringIO()
_tree_node_to_newick(tree, fh2)
fh2.seek(0)
tree2 = _newick_to_tree_node(fh2)
self.assertEqual(newick, fh2.getvalue())
self._assert_equal(tree, tree2)
fh.close()
fh2.close()
def test_newick_to_tree_node_convert_underscores(self):
fh = io.StringIO('(_:0.1, _a, _b)__;')
tree = _newick_to_tree_node(fh, convert_underscores=False)
fh2 = io.StringIO()
_tree_node_to_newick(tree, fh2)
self.assertEqual(fh2.getvalue(), "('_':0.1,'_a','_b')'__';\n")
fh2.close()
fh.close()
def test_newick_sniffer_valid_files(self):
for _, newicks in self.trees_newick_lists:
for newick in newicks:
fh = io.StringIO(newick)
self.assertEqual(_newick_sniffer(fh), (True, {}))
fh.close()
def test_newick_sniffer_invalid_files(self):
for invalid, _ in self.invalid_newicks:
fh = io.StringIO(invalid)
self.assertEqual(_newick_sniffer(fh), (False, {}))
fh.close()
if __name__ == '__main__':
unittest.main()
|
