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Merged
kayjan merged 2 commits into from
Jan 3, 2024
Merged

Newick changes #149

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ed64e05
Changed: Misc docstring update
kayjan Jan 3, 2024
f8c1540
Added: More test case for tree_to_newick
kayjan Jan 3, 2024
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4 changes: 2 additions & 2 deletions bigtree/tree/export.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1207,8 +1207,8 @@ def tree_to_newick(
Args:
tree (Node): tree to be exported
intermediate_node_name (bool): indicator if intermediate nodes have node names, defaults to True
length_attr (str): node attribute to extract into outside of bracket, optional
length_sep (str): separate between node name and length, used if length_attr is non-empty, defaults to ":"
length_attr (str): node length attribute to extract to beside name, optional
length_sep (str): separator between node name and length, used if length_attr is non-empty, defaults to ":"
attr_list (Iterable[str]): list of node attributes to extract into square bracket, optional
attr_prefix (str): prefix before all attributes, within square bracket, used if attr_list is non-empty, defaults to "&&NHX:"
attr_sep (str): separator between attributes, within square brackets, used if attr_list is non-empty, defaults to ":"
Expand Down
35 changes: 35 additions & 0 deletions tests/conftest.py
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Expand Up @@ -502,6 +502,41 @@ def binarytree_node():
return a


@pytest.fixture
def phylogenetic_tree():
"""
Example taken from: https://www.cs.mcgill.ca/~birch/doc/forester/NHX.pdf
"""
root = Node("placeholder_root", E="1.1.1.1", D="N")
metazoa = Node(
"placeholder_metazoa",
length=0.1,
S="Metazoa",
E="1.1.1.1",
D="N",
parent=root,
)
primates = Node(
"placeholder_primates",
length=0.05,
S="Primates",
E="1.1.1.1",
D="Y",
B="100",
parent=metazoa,
)
_ = Node("ADH2", length=0.1, S="human", E="1.1.1.1", parent=primates)
_ = Node("ADH1", length=0.11, S="human", E="1.1.1.1", parent=primates)
_ = Node("ADHY", length=0.1, S="nematode", E="1.1.1.1", parent=metazoa)
_ = Node("ADHX", length=0.12, S="insect", E="1.1.1.1", parent=metazoa)
fungi = Node("placeholder_fungi", length=0.1, S="Fungi", parent=root)
_ = Node("ADH4", length=0.09, S="yeast", E="1.1.1.1", parent=fungi)
_ = Node("ADH3", length=0.13, S="yeast", E="1.1.1.1", parent=fungi)
_ = Node("ADH2", length=0.12, S="yeast", E="1.1.1.1", parent=fungi)
_ = Node("ADH1", length=0.11, S="yeast", E="1.1.1.1", parent=fungi)
return root


def assert_print_statement(func, expected, *args, **kwargs):
captured_output = io.StringIO()
sys.stdout = captured_output
Expand Down
59 changes: 20 additions & 39 deletions tests/tree/test_export.py
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@@ -1,7 +1,6 @@
import pandas as pd
import pytest

from bigtree.node.node import Node
from bigtree.tree.construct import dataframe_to_tree, dict_to_tree, nested_dict_to_tree
from bigtree.tree.export import (
print_tree,
Expand Down Expand Up @@ -1384,13 +1383,13 @@ class TestTreeToNewick:
@staticmethod
def test_tree_to_newick(tree_node):
newick_str = tree_to_newick(tree_node)
expected_str = """((d,(g,h)e)b,(f)c)a"""
expected_str = "((d,(g,h)e)b,(f)c)a"
assert newick_str == expected_str

@staticmethod
def test_tree_to_newick_length(tree_node):
newick_str = tree_to_newick(tree_node, length_attr="age")
expected_str = """((d:40,(g:10,h:6)e:35)b:65,(f:38)c:60)a"""
expected_str = "((d:40,(g:10,h:6)e:35)b:65,(f:38)c:60)a"
assert newick_str == expected_str

@staticmethod
Expand All @@ -1402,13 +1401,13 @@ def test_tree_to_newick_length_invalid_error(tree_node):
@staticmethod
def test_tree_to_newick_length_sep(tree_node):
newick_str = tree_to_newick(tree_node, length_attr="age", length_sep=";")
expected_str = """((d;40,(g;10,h;6)e;35)b;65,(f;38)c;60)a"""
expected_str = "((d;40,(g;10,h;6)e;35)b;65,(f;38)c;60)a"
assert newick_str == expected_str

@staticmethod
def test_tree_to_newick_attr_list(tree_node):
newick_str = tree_to_newick(tree_node, attr_list=["age"])
expected_str = """((d[&&NHX:age=40],(g[&&NHX:age=10],h[&&NHX:age=6])e[&&NHX:age=35])b[&&NHX:age=65],(f[&&NHX:age=38])c[&&NHX:age=60])a[&&NHX:age=90]"""
expected_str = "((d[&&NHX:age=40],(g[&&NHX:age=10],h[&&NHX:age=6])e[&&NHX:age=35])b[&&NHX:age=65],(f[&&NHX:age=38])c[&&NHX:age=60])a[&&NHX:age=90]"
assert newick_str == expected_str

@staticmethod
Expand All @@ -1420,54 +1419,36 @@ def test_tree_to_newick_attr_list_invalid(tree_node):
@staticmethod
def test_tree_to_newick_attr_prefix(tree_node):
newick_str = tree_to_newick(tree_node, attr_list=["age"], attr_prefix="")
expected_str = """((d[age=40],(g[age=10],h[age=6])e[age=35])b[age=65],(f[age=38])c[age=60])a[age=90]"""
expected_str = "((d[age=40],(g[age=10],h[age=6])e[age=35])b[age=65],(f[age=38])c[age=60])a[age=90]"
assert newick_str == expected_str

@staticmethod
def test_tree_to_newick_intermediate_node_name(tree_node):
newick_str = tree_to_newick(
tree_node, intermediate_node_name=False, attr_list=["age"]
)
expected_str = """((d[&&NHX:age=40],(g[&&NHX:age=10],h[&&NHX:age=6])[&&NHX:age=35])[&&NHX:age=65],(f[&&NHX:age=38])[&&NHX:age=60])[&&NHX:age=90]"""
expected_str = "((d[&&NHX:age=40],(g[&&NHX:age=10],h[&&NHX:age=6])[&&NHX:age=35])[&&NHX:age=65],(f[&&NHX:age=38])[&&NHX:age=60])[&&NHX:age=90]"
assert newick_str == expected_str

@staticmethod
def test_tree_to_newick_phylogenetic():
"""
Example taken from: https://www.cs.mcgill.ca/~birch/doc/forester/NHX.pdf
"""
root = Node("placeholder_root", E="1.1.1.1", D="N")
metazoa = Node(
"placeholder_metazoa",
length=0.1,
S="Metazoa",
E="1.1.1.1",
D="N",
parent=root,
)
primates = Node(
"placeholder_primates",
length=0.05,
S="Primates",
E="1.1.1.1",
D="Y",
B="100",
parent=metazoa,
def test_tree_to_newick_phylogenetic(phylogenetic_tree):
newick_str = tree_to_newick(
phylogenetic_tree,
intermediate_node_name=False,
length_attr="length",
attr_list=["S", "E", "D", "B"],
)
_ = Node("ADH2", length=0.1, S="human", E="1.1.1.1", parent=primates)
_ = Node("ADH1", length=0.11, S="human", E="1.1.1.1", parent=primates)
_ = Node("ADHY", length=0.1, S="nematode", E="1.1.1.1", parent=metazoa)
_ = Node("ADHX", length=0.12, S="insect", E="1.1.1.1", parent=metazoa)
fungi = Node("placeholder_fungi", length=0.1, S="Fungi", parent=root)
_ = Node("ADH4", length=0.09, S="yeast", E="1.1.1.1", parent=fungi)
_ = Node("ADH3", length=0.13, S="yeast", E="1.1.1.1", parent=fungi)
_ = Node("ADH2", length=0.12, S="yeast", E="1.1.1.1", parent=fungi)
_ = Node("ADH1", length=0.11, S="yeast", E="1.1.1.1", parent=fungi)
expected_str = "(((ADH2:0.1[&&NHX:S=human:E=1.1.1.1],ADH1:0.11[&&NHX:S=human:E=1.1.1.1]):0.05[&&NHX:S=Primates:E=1.1.1.1:D=Y:B=100],ADHY:0.1[&&NHX:S=nematode:E=1.1.1.1],ADHX:0.12[&&NHX:S=insect:E=1.1.1.1]):0.1[&&NHX:S=Metazoa:E=1.1.1.1:D=N],(ADH4:0.09[&&NHX:S=yeast:E=1.1.1.1],ADH3:0.13[&&NHX:S=yeast:E=1.1.1.1],ADH2:0.12[&&NHX:S=yeast:E=1.1.1.1],ADH1:0.11[&&NHX:S=yeast:E=1.1.1.1]):0.1[&&NHX:S=Fungi])[&&NHX:E=1.1.1.1:D=N]"
assert newick_str == expected_str

@staticmethod
def test_tree_to_newick_phylogenetic_attr_sep(phylogenetic_tree):
newick_str = tree_to_newick(
root,
phylogenetic_tree,
intermediate_node_name=False,
length_attr="length",
attr_list=["S", "E", "D", "B"],
attr_sep=";",
)
expected_str = """(((ADH2:0.1[&&NHX:S=human:E=1.1.1.1],ADH1:0.11[&&NHX:S=human:E=1.1.1.1]):0.05[&&NHX:S=Primates:E=1.1.1.1:D=Y:B=100],ADHY:0.1[&&NHX:S=nematode:E=1.1.1.1],ADHX:0.12[&&NHX:S=insect:E=1.1.1.1]):0.1[&&NHX:S=Metazoa:E=1.1.1.1:D=N],(ADH4:0.09[&&NHX:S=yeast:E=1.1.1.1],ADH3:0.13[&&NHX:S=yeast:E=1.1.1.1],ADH2:0.12[&&NHX:S=yeast:E=1.1.1.1],ADH1:0.11[&&NHX:S=yeast:E=1.1.1.1]):0.1[&&NHX:S=Fungi])[&&NHX:E=1.1.1.1:D=N]"""
expected_str = "(((ADH2:0.1[&&NHX:S=human;E=1.1.1.1],ADH1:0.11[&&NHX:S=human;E=1.1.1.1]):0.05[&&NHX:S=Primates;E=1.1.1.1;D=Y;B=100],ADHY:0.1[&&NHX:S=nematode;E=1.1.1.1],ADHX:0.12[&&NHX:S=insect;E=1.1.1.1]):0.1[&&NHX:S=Metazoa;E=1.1.1.1;D=N],(ADH4:0.09[&&NHX:S=yeast;E=1.1.1.1],ADH3:0.13[&&NHX:S=yeast;E=1.1.1.1],ADH2:0.12[&&NHX:S=yeast;E=1.1.1.1],ADH1:0.11[&&NHX:S=yeast;E=1.1.1.1]):0.1[&&NHX:S=Fungi])[&&NHX:E=1.1.1.1;D=N]"
assert newick_str == expected_str