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|
"""
Tests for `bx.phylo.newick`.
"""
import pytest
from bx.phylo.newick import (
Edge,
newick_parser,
Tree,
)
trees = [
r"(B:6.0,(A:5.0,C:3.0,'Foo ''bar':4.0)Q_X:5.0,D:11.0)label;",
"((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,(( monkey:100.85930,cat:47.14069):20.59201, weasel:18.87953):2.09460):3.87382,dog:25.46154);",
"(Bovine:0.69395,(Gibbon:0.36079,(Orang:0.33636,(Gorilla:0.17147,(Chimp:0.19268, Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460);",
"(Bovine:0.69395,(Hylobates:0.36079,(Pongo:0.33636,(G._Gorilla:0.17147, (P._paniscus:0.19268,H._sapiens:0.11927):0.08386):0.06124):0.15057):0.54939, Rodent:1.21460);",
"(B,(A,C,E),D);",
"(,(,,),);",
"(A,(B,C),D);",
"((A,D),(C,B));",
]
results = [
(
Tree(
"label",
[
Edge(6.0, Tree("B", None)),
Edge(
5.0,
Tree(
"Q X",
[Edge(5.0, Tree("A", None)), Edge(3.0, Tree("C", None)), Edge(4.0, Tree("Foo 'bar", None))],
),
),
Edge(11.0, Tree("D", None)),
],
)
),
(
Tree(
None,
[
Edge(
0.84599999999999997,
Tree(
None,
[Edge(19.199590000000001, Tree("raccoon", None)), Edge(6.8004100000000003, Tree("bear", None))],
),
),
Edge(
3.8738199999999998,
Tree(
None,
[
Edge(
7.5297299999999998,
Tree(None, [Edge(11.997, Tree("sea lion", None)), Edge(12.003, Tree("seal", None))]),
),
Edge(
2.0945999999999998,
Tree(
None,
[
Edge(
20.592009999999998,
Tree(
None,
[
Edge(100.8593, Tree("monkey", None)),
Edge(47.140689999999999, Tree("cat", None)),
],
),
),
Edge(18.879529999999999, Tree("weasel", None)),
],
),
),
],
),
),
Edge(25.461539999999999, Tree("dog", None)),
],
)
),
(
Tree(
None,
[
Edge(0.69394999999999996, Tree("Bovine", None)),
Edge(
0.54939000000000004,
Tree(
None,
[
Edge(0.36079, Tree("Gibbon", None)),
Edge(
0.15057000000000001,
Tree(
None,
[
Edge(0.33635999999999999, Tree("Orang", None)),
Edge(
0.061240000000000003,
Tree(
None,
[
Edge(0.17147000000000001, Tree("Gorilla", None)),
Edge(
0.083860000000000004,
Tree(
None,
[
Edge(0.19267999999999999, Tree("Chimp", None)),
Edge(0.11927, Tree("Human", None)),
],
),
),
],
),
),
],
),
),
],
),
),
Edge(1.2145999999999999, Tree("Mouse", None)),
],
)
),
(
Tree(
None,
[
Edge(0.69394999999999996, Tree("Bovine", None)),
Edge(
0.54939000000000004,
Tree(
None,
[
Edge(0.36079, Tree("Hylobates", None)),
Edge(
0.15057000000000001,
Tree(
None,
[
Edge(0.33635999999999999, Tree("Pongo", None)),
Edge(
0.061240000000000003,
Tree(
None,
[
Edge(0.17147000000000001, Tree("G. Gorilla", None)),
Edge(
0.083860000000000004,
Tree(
None,
[
Edge(0.19267999999999999, Tree("P. paniscus", None)),
Edge(0.11927, Tree("H. sapiens", None)),
],
),
),
],
),
),
],
),
),
],
),
),
Edge(1.2145999999999999, Tree("Rodent", None)),
],
)
),
(
Tree(
None,
[
Edge(None, Tree("B", None)),
Edge(
None,
Tree(None, [Edge(None, Tree("A", None)), Edge(None, Tree("C", None)), Edge(None, Tree("E", None))]),
),
Edge(None, Tree("D", None)),
],
)
),
(
Tree(
None,
[
Edge(None, Tree(None, None)),
Edge(
None,
Tree(
None, [Edge(None, Tree(None, None)), Edge(None, Tree(None, None)), Edge(None, Tree(None, None))]
),
),
Edge(None, Tree(None, None)),
],
)
),
(
Tree(
None,
[
Edge(None, Tree("A", None)),
Edge(None, Tree(None, [Edge(None, Tree("B", None)), Edge(None, Tree("C", None))])),
Edge(None, Tree("D", None)),
],
)
),
(
Tree(
None,
[
Edge(None, Tree(None, [Edge(None, Tree("A", None)), Edge(None, Tree("D", None))])),
Edge(None, Tree(None, [Edge(None, Tree("C", None)), Edge(None, Tree("B", None))])),
],
)
),
]
@pytest.mark.parametrize("tree,result", zip(trees, results))
def test_newick_tree(tree, result):
assert newick_parser.parse_string(tree) == result
|
