diff --git a/CHANGELOG.md b/CHANGELOG.md
index ed832efc82a8dc48a18229e142e5289cc371b158..a08564833f39f7b9ed3c0e71e7f3ada2d6c1f628 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,11 @@ The `newick` package adheres to [Semantic Versioning](http://semver.org/spec/v2.
## [Unreleased]
+## [v1.3.1] - 2021-10-14
+
+Fixed support for node annotations for the case when annotations are between `:` and length.
+
+
## [v1.3.0] - 2021-05-04
Added support for reading and writing of node annotations (in comments).
diff --git a/README.md b/README.md
index 96ff265214443f8fb7b101ac6bb27fb073ece386..0b09547b966d2000848fb454e4d4c66fedf624e3 100644
--- a/README.md
+++ b/README.md
@@ -66,6 +66,19 @@ The `newick` package allows to deal with comments in two ways.
>>> newick.loads('(a[annotation],b)c;')[0].newick
'(a[annotation],b)c'
```
+ Annotations may come before or after the `:` which separates node label and length:
+- ```python
+ >>> newick.loads('(a[annotation]:2,b)c;')[0].descendants[0].length
+ 2.0
+ >>> newick.loads('(a:[annotation]2,b)c;')[0].descendants[0].length
+ 2.0
+ ```
+ but if they preceed the colon, they must not contain `:`:
+- ```python
+ >>> newick.loads('(a[annotation:]:2,b)c;')[0].descendants[0].comment
+ ...
+ ValueError: Node names or branch lengths must not contain ":"
+ ```
Note that square brackets inside *quoted labels* will **not** be interpreted as comments
or annotations:
diff --git a/setup.py b/setup.py
index 2bb6fe7e8178b871065a8e60abb644c4cc35c514..00c50052c20b20631d14706e009a695352415aea 100755
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@ from setuptools import setup, find_packages
setup(
name='newick',
- version="1.3.1.dev0",
+ version="1.3.1",
description='A python module to read and write the Newick format',
long_description=open("README.md").read(),
long_description_content_type="text/markdown",
diff --git a/src/newick.py b/src/newick.py
index f28341a7b17b0f8110074ea14db0869f37c2e3d2..170e3258955696e62d25a59cf2051112d4562652 100644
--- a/src/newick.py
+++ b/src/newick.py
@@ -6,7 +6,7 @@ Functionality to read and write the Newick serialization format for trees.
import re
import pathlib
-__version__ = "1.3.1.dev0"
+__version__ = "1.3.1"
RESERVED_PUNCTUATION = ':;,()'
COMMENT = re.compile(r'\[[^]]*]')
@@ -39,8 +39,7 @@ class Node(object):
"""
for char in RESERVED_PUNCTUATION:
if (name and char in name) or (length and char in length):
- raise ValueError(
- 'Node names or branch lengths must not contain "%s"' % char)
+ raise ValueError('Node names or branch lengths must not contain "{}"'.format(char))
self.name = name
self.comment = comment
self._length = length
@@ -48,6 +47,7 @@ class Node(object):
self.ancestor = None
self._length_parser = kw.pop('length_parser', length_parser)
self._length_formatter = kw.pop('length_formatter', length_formatter)
+ self._colon_before_comment = kw.pop('colon_before_comment', False)
def __repr__(self):
return 'Node("%s")' % self.name
@@ -86,11 +86,17 @@ class Node(object):
@property
def newick(self):
"""The representation of the Node in Newick format."""
+ colon_done = False
label = self.name or ''
if self.comment:
+ if self._length and self._colon_before_comment:
+ label += ':'
+ colon_done = True
label += '[{}]'.format(self.comment)
if self._length:
- label += ':' + self._length
+ if not colon_done:
+ label += ':'
+ label += self._length
descendants = ','.join([n.newick for n in self.descendants])
if descendants:
descendants = '(' + descendants + ')'
@@ -426,16 +432,27 @@ def write(tree, fname, encoding='utf8'):
def _parse_name_and_length(s):
- length, comment = None, None
+ length, comment, colon_before_comment = None, None, False
if ':' in s:
- parts = s.split(':')
- if ']' not in parts[-1]: # A ] in length doesn't make sense - the : must be in a comment.
- s = ':'.join(parts[:-1])
- length = parts[-1]
+ # Comments may be placed between ":" and length, or between name and ":"!
+ # In any case, we interpret the first occurrence of ":" as separator for length, i.e.
+ # a ":" in an annotation **before** the length separator will screw things up.
+ before, _, after = s.partition(':')
+ if before.endswith(']'):
+ assert '[' in before and '[' not in after, s
+ s, comment = before[:-1].split('[', maxsplit=1)
+ length = after
+ elif after.startswith('['):
+ assert ']' in after and '[' not in before, s
+ colon_before_comment = True
+ comment, length = after[1:].split(']', maxsplit=1)
+ s = before
+ else:
+ s, length = before, after
if '[' in s and s.endswith(']'): # This looks like a node annotation in a comment.
s, comment = s.split('[', maxsplit=1)
comment = comment[:-1]
- return s or None, length or None, comment
+ return s or None, length or None, comment, colon_before_comment
def _parse_siblings(s, **kw):
@@ -484,5 +501,11 @@ def parse_node(s, strip_comments=False, **kw):
raise ValueError('unmatched braces %s' % parts[0][:100])
descendants = list(_parse_siblings(')'.join(parts[:-1])[1:], **kw))
label = parts[-1]
- name, length, comment = _parse_name_and_length(label)
- return Node.create(name=name, length=length, comment=comment, descendants=descendants, **kw)
+ name, length, comment, colon_before_comment = _parse_name_and_length(label)
+ return Node.create(
+ name=name,
+ length=length,
+ comment=comment,
+ colon_before_comment=colon_before_comment,
+ descendants=descendants,
+ **kw)
diff --git a/tests/test_newick.py b/tests/test_newick.py
index 24b40780c4795d1565e91c83b514308ff8de669f..103f1caa761880c99df8858470f3a35f85001fc2 100644
--- a/tests/test_newick.py
+++ b/tests/test_newick.py
@@ -391,4 +391,58 @@ def test_with_comments():
tree = loads(nwk)[0]
assert tree.comment.startswith('y')
assert tree.descendants[0].name == '1' and tree.descendants[0].comment.startswith('x')
- assert tree.newick == nwk
\ No newline at end of file
+ assert tree.newick == nwk
+
+
+def test_with_comments_beast():
+ nwk = "((((20:[&rate=9.363171791537587E-5]1320.9341043566992,(21:[&rate=9.363171791537587E-5]" \
+ "1225.8822690335624,(((((15:[&rate=9.363171791537587E-5]638.1949811891477,16:[&rate=" \
+ "9.363171791537587E-5]638.1949811891477):[&rate=9.363171791537587E-5]257.76795318129564" \
+ ",8:[&rate=9.363171791537587E-5]895.9629343704433):[&rate=9.363171791537587E-5]" \
+ "41.795862802882425,12:[&rate=9.363171791537587E-5]937.7587971733258):" \
+ "[&rate=9.363171791537587E-5]95.6952785114238,14:[&rate=9.363171791537587E-5]" \
+ "1033.4540756847496):[&rate=9.363171791537587E-5]59.28887326566064,((25:" \
+ "[&rate=9.363171791537587E-5]368.1724945784702,28:[&rate=9.363171791537587E-" \
+ "5]368.1724945784702):[&rate=9.363171791537587E-5]618.1292632448451,(13:[&rate=" \
+ "9.363171791537587E-5]894.6169275367406,((22:[&rate=9.363171791537587E-5]532." \
+ "4463352965287,33:[&rate=9.363171791537587E-5]532.4463352965287):[&rate=9." \
+ "363171791537587E-5]124.75991679524702,19:[&rate=9.363171791537587E-5]657." \
+ "2062520917757):[&rate=9.363171791537587E-5]237.4106754449649):[&rate=9." \
+ "363171791537587E-5]91.68483028657465):[&rate=9.363171791537587E-5]106.44119112709495):" \
+ "[&rate=9.363171791537587E-5]133.13932008315214):[&rate=9.363171791537587E-5]95." \
+ "05183532313686):[&rate=9.363171791537587E-5]239.53051384576952,((23:[&rate=9." \
+ "363171791537587E-5]886.6590941437129,2:[&rate=9.363171791537587E-5]886.6590941437129):" \
+ "[&rate=9.363171791537587E-5]318.065540579532,((6:[&rate=9.363171791537587E-5]1128." \
+ "8289029154403,37:[&rate=9.363171791537587E-5]1128.8289029154403):[&rate=9." \
+ "363171791537587E-5]17.349382774569676,((((((3:[&rate=9.363171791537587E-5]459." \
+ "5487115479798,36:[&rate=9.363171791537587E-5]459.5487115479798):[&rate=9." \
+ "363171791537587E-5]306.57918484718175,(31:[&rate=9.363171791537587E-5]485." \
+ "4575256190764,34:[&rate=9.363171791537587E-5]485.4575256190764):[&rate=9." \
+ "363171791537587E-5]280.6703707760851):[&rate=9.363171791537587E-5]15.246829791795335," \
+ "(30:[&rate=9.363171791537587E-5]543.1657161064542,1:[&rate=9.363171791537587E-5]543." \
+ "1657161064542):[&rate=9.363171791537587E-5]238.2090100805027):[&rate=9." \
+ "363171791537587E-5]118.69392508203657,((7:[&rate=9.363171791537587E-5]520." \
+ "3998734304117,35:[&rate=9.363171791537587E-5]520.3998734304117):[&rate=9." \
+ "363171791537587E-5]238.7668559806733,(32:[&rate=9.363171791537587E-5]720." \
+ "2892667226898,17:[&rate=9.363171791537587E-5]720.2892667226898):[&rate=9." \
+ "363171791537587E-5]38.87746268839521):[&rate=9.363171791537587E-5]140.9019218579084)" \
+ ":[&rate=9.363171791537587E-5]52.21797041264119,26:[&rate=9.363171791537587E-5]" \
+ "952.2866216816346):[&rate=9.363171791537587E-5]163.25701515522496,((18:[&rate=9." \
+ "363171791537587E-5]720.6233628054213,10:[&rate=9.363171791537587E-5]720.6233628054213):" \
+ "[&rate=9.363171791537587E-5]119.64362661776931,(29:[&rate=9.363171791537587E-5]617." \
+ "5158316030422,(9:[&rate=9.363171791537587E-5]593.9192324440043,(11:[&rate=9." \
+ "363171791537587E-5]472.3642192781455,27:[&rate=9.363171791537587E-5]472.3642192781455)" \
+ ":[&rate=9.363171791537587E-5]121.55501316585872):[&rate=9.363171791537587E-5]23." \
+ "596599159037964):[&rate=9.363171791537587E-5]222.75115782014836):[&rate=9." \
+ "363171791537587E-5]275.276647413669):[&rate=9.363171791537587E-5]30.63464885315034):" \
+ "[&rate=9.363171791537587E-5]58.54634903323495):[&rate=9.363171791537587E-5]355." \
+ "73998347922384):[&rate=9.363171791537587E-5]1186.6682306101936,24:[&rate=9." \
+ "363171791537587E-5]2747.1328488126624):[&rate=9.363171791537587E-5]301.4581721015056," \
+ "(38:[&rate=9.363171791537587E-5]963.0459960655501,(5:[&rate=9.363171791537587E-5]500." \
+ "66376645282014,4:[&rate=9.363171791537587E-5]500.66376645282014):[&rate=9." \
+ "363171791537587E-5]462.38222961272993):[&rate=9.363171791537587E-5]2085.5450248486177)"
+ tree = loads(nwk)[0]
+ assert tree.descendants[0].comment == '&rate=9.363171791537587E-5'
+ assert tree.descendants[0].name is None
+ assert tree.descendants[0].length == pytest.approx(301.4581721015056)
+ assert tree.newick == nwk