/usr/share/pyshared/Bio/Phylo/NewickIO.py is in python-biopython 1.58-1.
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# Based on Bio.Nexus, copyright 2005-2008 by Frank Kauff & Cymon J. Cox.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""I/O function wrappers for the Newick file format.
See: http://evolution.genetics.washington.edu/phylip/newick_doc.html
"""
__docformat__ = "restructuredtext en"
import warnings
from cStringIO import StringIO
from Bio import BiopythonDeprecationWarning
from Bio.Phylo import Newick
# Definitions retrieved from Bio.Nexus.Trees
NODECOMMENT_START = '[&'
NODECOMMENT_END = ']'
class NewickError(Exception):
"""Exception raised when Newick object construction cannot continue."""
pass
# ---------------------------------------------------------
# Public API
def parse(handle, **kwargs):
"""Iterate over the trees in a Newick file handle.
:returns: generator of Bio.Phylo.Newick.Tree objects.
"""
return Parser(handle).parse(**kwargs)
def write(trees, handle, plain=False, **kwargs):
"""Write a trees in Newick format to the given file handle.
:returns: number of trees written.
"""
return Writer(trees).write(handle, plain=plain, **kwargs)
# ---------------------------------------------------------
# Input
class Parser(object):
"""Parse a Newick tree given a file handle.
Based on the parser in `Bio.Nexus.Trees`.
"""
def __init__(self, handle):
self.handle = handle
@classmethod
def from_string(cls, treetext):
handle = StringIO(treetext)
return cls(handle)
def parse(self, values_are_confidence=False, rooted=False,
# XXX Deprecated kwarg -- remove after Biopython 1.58
values_are_support=None):
"""Parse the text stream this object was initialized with."""
# XXX Handling the deprecated kwarg -- remove after Biopython 1.58
if values_are_support is not None:
warnings.warn("use the argument values_are_confidence instead",
BiopythonDeprecationWarning)
values_are_confidence = values_are_support
self.values_are_confidence = values_are_confidence
self.rooted = rooted # XXX this attribue is useless
buf = ''
for line in self.handle:
buf += line.rstrip()
if buf.endswith(';'):
yield self._parse_tree(buf, rooted)
buf = ''
if buf:
# Last tree is missing a terminal ';' character -- that's OK
yield self._parse_tree(buf, rooted)
def _parse_tree(self, text, rooted):
"""Parses the text representation into an Tree object."""
# XXX Pass **kwargs along from Parser.parse?
return Newick.Tree(root=self._parse_subtree(text), rooted=self.rooted)
def _parse_subtree(self, text):
"""Parse ``(a,b,c...)[[[xx]:]yy]`` into subcomponents, recursively."""
text = text.strip().rstrip(';')
if text.count('(')!=text.count(')'):
raise NewickError("Parentheses do not match in (sub)tree: " + text)
# Text is now "(...)..." (balanced parens) or "..." (leaf node)
if text.count('(') == 0:
# Leaf/terminal node -- recursion stops here
return self._parse_tag(text)
# Handle one layer of the nested subtree
# XXX what if there's a paren in a comment or other string?
close_posn = text.rfind(')')
subtrees = []
# Locate subtrees by counting nesting levels of parens
plevel = 0
prev = 1
for posn in range(1, close_posn):
if text[posn] == '(':
plevel += 1
elif text[posn] == ')':
plevel -= 1
elif text[posn] == ',' and plevel == 0:
subtrees.append(text[prev:posn])
prev = posn + 1
subtrees.append(text[prev:close_posn])
# Construct a new clade from trailing text, then attach subclades
clade = self._parse_tag(text[close_posn+1:])
clade.clades = [self._parse_subtree(st) for st in subtrees]
return clade
def _parse_tag(self, text):
"""Extract the data for a node from text.
:returns: Clade instance containing any available data
"""
# Extract the comment
comment_start = text.find(NODECOMMENT_START)
if comment_start != -1:
comment_end = text.find(NODECOMMENT_END)
if comment_end == -1:
raise NewickError('Error in tree description: '
'Found %s without matching %s'
% (NODECOMMENT_START, NODECOMMENT_END))
comment = text[comment_start+len(NODECOMMENT_START):comment_end]
text = text[:comment_start] + text[comment_end+len(NODECOMMENT_END):]
else:
comment = None
clade = Newick.Clade(comment=comment)
# Extract name (taxon), and optionally support, branch length
# Float values are support and branch length, the string is name/taxon
values = []
for part in (t.strip() for t in text.split(':')):
if part:
try:
values.append(float(part))
except ValueError:
assert clade.name is None, "Two string taxonomies?"
clade.name = part
if len(values) == 1:
# Real branch length, or support as branch length
if self.values_are_confidence:
clade.confidence = values[0]
else:
clade.branch_length = values[0]
elif len(values) == 2:
# Two non-taxon values: support comes first. (Is that always so?)
clade.confidence, clade.branch_length = values
elif len(values) > 2:
raise NewickError("Too many colons in tag: " + text)
return clade
# ---------------------------------------------------------
# Output
class Writer(object):
"""Based on the writer in Bio.Nexus.Trees (str, to_string)."""
def __init__(self, trees):
self.trees = trees
def write(self, handle, **kwargs):
"""Write this instance's trees to a file handle."""
count = 0
for treestr in self.to_strings(**kwargs):
handle.write(treestr + '\n')
count += 1
return count
def to_strings(self, confidence_as_branch_length=False,
branch_length_only=False, plain=False,
plain_newick=True, ladderize=None, max_confidence=1.0,
format_confidence='%1.2f', format_branch_length='%1.5f',
# XXX Deprecated kwargs -- remove after Biopython 1.58
support_as_branchlengths=None, branchlengths_only=None,
max_support=None):
"""Return an iterable of PAUP-compatible tree lines."""
# XXX Handling the deprecated kwargs -- remove after Biopython 1.58
if support_as_branchlengths is not None:
warnings.warn(
"use the argument confidence_as_branch_length instead",
BiopythonDeprecationWarning)
confidence_as_branch_length = support_as_branchlengths
if branchlengths_only is not None:
warnings.warn("use the argument branch_length_only instead",
BiopythonDeprecationWarning)
branch_length_only = branchlengths_only
if max_support is not None:
warnings.warn("use the argument max_confidence instead",
BiopythonDeprecationWarning)
max_confidence = max_support
# If there's a conflict in the arguments, we override plain=True
if confidence_as_branch_length or branch_length_only:
plain = False
make_info_string = self._info_factory(plain,
confidence_as_branch_length, branch_length_only, max_confidence,
format_confidence, format_branch_length)
def newickize(clade):
"""Convert a node tree to a Newick tree string, recursively."""
if clade.is_terminal(): #terminal
return ((clade.name or '')
+ make_info_string(clade, terminal=True))
else:
subtrees = (newickize(sub) for sub in clade)
return '(%s)%s' % (','.join(subtrees),
make_info_string(clade))
# Convert each tree to a string
for tree in self.trees:
if ladderize in ('left', 'LEFT', 'right', 'RIGHT'):
# Nexus compatibility shim, kind of
tree.ladderize(reverse=(ladderize in ('right', 'RIGHT')))
rawtree = newickize(tree.root) + ';'
if plain_newick:
yield rawtree
continue
# Nexus-style (?) notation before the raw Newick tree
treeline = ['tree', (tree.name or 'a_tree'), '=']
if tree.weight != 1:
treeline.append('[&W%s]' % round(float(tree.weight), 3))
if tree.rooted:
treeline.append('[&R]')
treeline.append(rawtree)
yield ' '.join(treeline)
def _info_factory(self, plain, confidence_as_branch_length,
branch_length_only, max_confidence, format_confidence,
format_branch_length):
"""Return a function that creates a nicely formatted node tag."""
if plain:
# Plain tree only. That's easy.
def make_info_string(clade, terminal=False):
return ''
elif confidence_as_branch_length:
# Support as branchlengths (eg. PAUP), ignore actual branchlengths
def make_info_string(clade, terminal=False):
if terminal:
# terminal branches have 100% support
return ':' + format_confidence % max_confidence
else:
return ':' + format_confidence % clade.confidence
elif branch_length_only:
# write only branchlengths, ignore support
def make_info_string(clade, terminal=False):
return ':' + format_branch_length % clade.branch_length
else:
# write support and branchlengths (e.g. .con tree of mrbayes)
def make_info_string(clade, terminal=False):
if (terminal or
not hasattr(clade, 'confidence') or
clade.confidence is None):
return (':' + format_branch_length
) % (clade.branch_length or 0.0)
else:
return (format_confidence + ':' + format_branch_length
) % (clade.confidence, clade.branch_length or 0.0)
return make_info_string
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