/usr/share/pyshared/Bio/Phylo/PhyloXMLIO.py is in python-biopython 1.58-1.
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# 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.
"""PhyloXML reader/parser, writer, and associated functions.
Instantiates tree elements from a parsed PhyloXML file, and constructs an XML
file from a `Bio.Phylo.PhyloXML` object.
About capitalization:
- phyloXML means the file format specification
- PhyloXML means the Biopython module `Bio.Phylo.PhyloXML` and its classes
- Phyloxml means the top-level class used by `PhyloXMLIO.read` (but not
`Bio.Phylo.read`!), containing a list of Phylogenies (objects derived from
`BaseTree.Tree`)
"""
__docformat__ = "restructuredtext en"
import sys
import warnings
from Bio.Phylo import PhyloXML as PX
if (3, 0, 0) <= sys.version_info[:3] <= (3, 1, 3):
# Workaround for cElementTree regression in python 3.0--3.1.3
# See http://bugs.python.org/issue9257
from xml.etree import ElementTree
else:
try:
from xml.etree import cElementTree as ElementTree
except ImportError:
# Alternative Python implementation, perhaps?
try:
from xml.etree import ElementTree as ElementTree
except ImportError:
# Python 2.4 -- check for 3rd-party implementations
try:
from lxml import etree as ElementTree
except ImportError:
try:
import cElementTree as ElementTree
except ImportError:
try:
from elementtree import ElementTree
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"No ElementTree module was found. "
"Use Python 2.5+, lxml or elementtree if you "
"want to use Bio.PhyloXML.")
# Keep the standard namespace prefixes when writing
# See http://effbot.org/zone/element-namespaces.htm
NAMESPACES = {
'phy': 'http://www.phyloxml.org',
'xs': 'http://www.w3.org/2001/XMLSchema',
}
try:
register_namespace = ElementTree.register_namespace
except AttributeError:
if not hasattr(ElementTree, '_namespace_map'):
# cElementTree needs the pure-Python xml.etree.ElementTree
# Py2.4 support: the exception handler can go away when Py2.4 does
try:
from xml.etree import ElementTree as ET_py
ElementTree._namespace_map = ET_py._namespace_map
except ImportError:
warnings.warn("Couldn't import xml.etree.ElementTree; "
"phyloXML namespaces may have unexpected abbreviations "
"in the output.",
# NB: ImportWarning was introduced in Py2.5
Warning, stacklevel=2)
ElementTree._namespace_map = {}
def register_namespace(prefix, uri):
ElementTree._namespace_map[uri] = prefix
for prefix, uri in NAMESPACES.iteritems():
register_namespace(prefix, uri)
class PhyloXMLError(Exception):
"""Exception raised when PhyloXML object construction cannot continue.
XML syntax errors will be found and raised by the underlying ElementTree
module; this exception is for valid XML that breaks the phyloXML
specification.
"""
pass
# ---------------------------------------------------------
# Public API
def read(file):
"""Parse a phyloXML file or stream and build a tree of Biopython objects.
The children of the root node are phylogenies and possibly other arbitrary
(non-phyloXML) objects.
:returns: a single `Bio.Phylo.PhyloXML.Phyloxml` object.
"""
return Parser(file).read()
def parse(file):
"""Iterate over the phylogenetic trees in a phyloXML file.
This ignores any additional data stored at the top level, but may be more
memory-efficient than the `read` function.
:returns: a generator of `Bio.Phylo.PhyloXML.Phylogeny` objects.
"""
return Parser(file).parse()
def write(obj, file, encoding='utf-8', indent=True):
"""Write a phyloXML file.
:Parameters:
obj
an instance of `Phyloxml`, `Phylogeny` or `BaseTree.Tree`, or an
iterable of either of the latter two. The object will be converted
to a Phyloxml object before serialization.
file
either an open handle or a file name.
"""
def fix_single(tree):
if isinstance(tree, PX.Phylogeny):
return tree
if isinstance(tree, PX.Clade):
return tree.to_phylogeny()
if isinstance(tree, PX.BaseTree.Tree):
return PX.Phylogeny.from_tree(tree)
if isinstance(tree, PX.BaseTree.Clade):
return PX.Phylogeny.from_tree(PX.BaseTree.Tree(root=tree))
else:
raise ValueError("iterable must contain Tree or Clade types")
if isinstance(obj, PX.Phyloxml):
pass
elif (isinstance(obj, PX.BaseTree.Tree) or
isinstance(obj, PX.BaseTree.Clade)):
obj = fix_single(obj).to_phyloxml()
elif hasattr(obj, '__iter__'):
obj = PX.Phyloxml({}, phylogenies=(fix_single(t) for t in obj))
else:
raise ValueError("First argument must be a Phyloxml, Phylogeny, "
"Tree, or iterable of Trees or Phylogenies.")
return Writer(obj).write(file, encoding=encoding, indent=indent)
# ---------------------------------------------------------
# Functions I wish ElementTree had
def _local(tag):
"""Extract the local tag from a namespaced tag name."""
if tag[0] == '{':
return tag[tag.index('}')+1:]
return tag
def _split_namespace(tag):
"""Split a tag into namespace and local tag strings."""
try:
return tag[1:].split('}', 1)
except:
return ('', tag)
def _ns(tag, namespace=NAMESPACES['phy']):
"""Format an XML tag with the given namespace."""
return '{%s}%s' % (namespace, tag)
def _get_child_as(parent, tag, construct):
"""Find a child node by tag, and pass it through a constructor.
Returns None if no matching child is found.
"""
child = parent.find(_ns(tag))
if child is not None:
return construct(child)
def _get_child_text(parent, tag, construct=unicode):
"""Find a child node by tag; pass its text through a constructor.
Returns None if no matching child is found.
"""
child = parent.find(_ns(tag))
if child is not None and child.text:
return construct(child.text)
def _get_children_as(parent, tag, construct):
"""Find child nodes by tag; pass each through a constructor.
Returns an empty list if no matching child is found.
"""
return [construct(child) for child in
parent.findall(_ns(tag))]
def _get_children_text(parent, tag, construct=unicode):
"""Find child nodes by tag; pass each node's text through a constructor.
Returns an empty list if no matching child is found.
"""
return [construct(child.text) for child in
parent.findall(_ns(tag))
if child.text]
def _indent(elem, level=0):
"""Add line breaks and indentation to ElementTree in-place.
Sources:
- http://effbot.org/zone/element-lib.htm#prettyprint
- http://infix.se/2007/02/06/gentlemen-indent-your-xml
"""
i = "\n" + level*" "
if len(elem):
if not elem.text or not elem.text.strip():
elem.text = i + " "
for e in elem:
_indent(e, level+1)
if not e.tail or not e.tail.strip():
e.tail = i + " "
if not e.tail or not e.tail.strip():
e.tail = i
else:
if level and (not elem.tail or not elem.tail.strip()):
elem.tail = i
# ---------------------------------------------------------
# INPUT
# ---------------------------------------------------------
def _str2bool(text):
if text == 'true':
return True
if text == 'false':
return False
raise ValueError('String could not be converted to boolean: ' + text)
def _dict_str2bool(dct, keys):
out = dct.copy()
for key in keys:
if key in out:
out[key] = _str2bool(out[key])
return out
def _int(text):
if text is not None:
try:
return int(text)
except Exception:
return None
def _float(text):
if text is not None:
try:
return float(text)
except Exception:
return None
def _collapse_wspace(text):
"""Replace all spans of whitespace with a single space character.
Also remove leading and trailing whitespace. See "Collapse Whitespace
Policy" in the phyloXML spec glossary:
http://phyloxml.org/documentation/version_100/phyloxml.xsd.html#Glossary
"""
if text is not None:
return ' '.join(text.split())
# NB: Not currently used
def _replace_wspace(text):
"""Replace tab, LF and CR characters with spaces, but don't collapse.
See "Replace Whitespace Policy" in the phyloXML spec glossary:
http://phyloxml.org/documentation/version_100/phyloxml.xsd.html#Glossary
"""
for char in ('\t', '\n', '\r'):
if char in text:
text = text.replace(char, ' ')
return text
class Parser(object):
"""Methods for parsing all phyloXML nodes from an XML stream.
To minimize memory use, the tree of ElementTree parsing events is cleared
after completing each phylogeny, clade, and top-level 'other' element.
Elements below the clade level are kept in memory until parsing of the
current clade is finished -- this shouldn't be a problem because clade is
the only recursive element, and non-clade nodes below this level are of
bounded size.
"""
def __init__(self, file):
# Get an iterable context for XML parsing events
context = iter(ElementTree.iterparse(file, events=('start', 'end')))
event, root = context.next()
self.root = root
self.context = context
def read(self):
"""Parse the phyloXML file and create a single Phyloxml object."""
phyloxml = PX.Phyloxml(dict((_local(key), val)
for key, val in self.root.items()))
other_depth = 0
for event, elem in self.context:
namespace, localtag = _split_namespace(elem.tag)
if event == 'start':
if namespace != NAMESPACES['phy']:
other_depth += 1
continue
if localtag == 'phylogeny':
phylogeny = self._parse_phylogeny(elem)
phyloxml.phylogenies.append(phylogeny)
if event == 'end' and namespace != NAMESPACES['phy']:
# Deal with items not specified by phyloXML
other_depth -= 1
if other_depth == 0:
# We're directly under the root node -- evaluate
otr = self.other(elem, namespace, localtag)
phyloxml.other.append(otr)
self.root.clear()
return phyloxml
def parse(self):
"""Parse the phyloXML file incrementally and return each phylogeny."""
phytag = _ns('phylogeny')
for event, elem in self.context:
if event == 'start' and elem.tag == phytag:
yield self._parse_phylogeny(elem)
# Special parsing cases -- incremental, using self.context
def _parse_phylogeny(self, parent):
"""Parse a single phylogeny within the phyloXML tree.
Recursively builds a phylogenetic tree with help from parse_clade, then
clears the XML event history for the phylogeny element and returns
control to the top-level parsing function.
"""
phylogeny = PX.Phylogeny(**_dict_str2bool(parent.attrib,
['rooted', 'rerootable']))
list_types = {
# XML tag, plural attribute
'confidence': 'confidences',
'property': 'properties',
'clade_relation': 'clade_relations',
'sequence_relation': 'sequence_relations',
}
for event, elem in self.context:
namespace, tag = _split_namespace(elem.tag)
if event == 'start' and tag == 'clade':
assert phylogeny.root is None, \
"Phylogeny object should only have 1 clade"
phylogeny.root = self._parse_clade(elem)
continue
if event == 'end':
if tag == 'phylogeny':
parent.clear()
break
# Handle the other non-recursive children
if tag in list_types:
getattr(phylogeny, list_types[tag]).append(
getattr(self, tag)(elem))
# Complex types
elif tag in ('date', 'id'):
setattr(phylogeny, tag, getattr(self, tag)(elem))
# Simple types
elif tag in ('name', 'description'):
setattr(phylogeny, tag, _collapse_wspace(elem.text))
# Unknown tags
elif namespace != NAMESPACES['phy']:
phylogeny.other.append(self.other(elem, namespace, tag))
parent.clear()
else:
# NB: This shouldn't happen in valid files
raise PhyloXMLError('Misidentified tag: ' + tag)
return phylogeny
_clade_complex_types = ['color', 'events', 'binary_characters', 'date']
_clade_list_types = {
'confidence': 'confidences',
'distribution': 'distributions',
'reference': 'references',
'property': 'properties',
}
_clade_tracked_tags = set(_clade_complex_types + _clade_list_types.keys()
+ ['branch_length', 'name', 'node_id', 'width'])
def _parse_clade(self, parent):
"""Parse a Clade node and its children, recursively."""
clade = PX.Clade(**parent.attrib)
if clade.branch_length is not None:
clade.branch_length = float(clade.branch_length)
# NB: Only evaluate nodes at the current level
tag_stack = []
for event, elem in self.context:
namespace, tag = _split_namespace(elem.tag)
if event == 'start':
if tag == 'clade':
clade.clades.append(self._parse_clade(elem))
continue
if tag == 'taxonomy':
clade.taxonomies.append(self._parse_taxonomy(elem))
continue
if tag == 'sequence':
clade.sequences.append(self._parse_sequence(elem))
continue
if tag in self._clade_tracked_tags:
tag_stack.append(tag)
if event == 'end':
if tag == 'clade':
elem.clear()
break
if tag != tag_stack[-1]:
continue
tag_stack.pop()
# Handle the other non-recursive children
if tag in self._clade_list_types:
getattr(clade, self._clade_list_types[tag]).append(
getattr(self, tag)(elem))
elif tag in self._clade_complex_types:
setattr(clade, tag, getattr(self, tag)(elem))
elif tag == 'branch_length':
# NB: possible collision with the attribute
if clade.branch_length is not None:
raise PhyloXMLError(
'Attribute branch_length was already set '
'for this Clade.')
clade.branch_length = _float(elem.text)
elif tag == 'width':
clade.width = _float(elem.text)
elif tag == 'name':
clade.name = _collapse_wspace(elem.text)
elif tag == 'node_id':
clade.node_id = PX.Id(elem.text.strip(),
elem.attrib.get('provider'))
elif namespace != NAMESPACES['phy']:
clade.other.append(self.other(elem, namespace, tag))
elem.clear()
else:
raise PhyloXMLError('Misidentified tag: ' + tag)
return clade
def _parse_sequence(self, parent):
sequence = PX.Sequence(**parent.attrib)
for event, elem in self.context:
namespace, tag = _split_namespace(elem.tag)
if event == 'end':
if tag == 'sequence':
parent.clear()
break
if tag in ('accession', 'mol_seq', 'uri',
'domain_architecture'):
setattr(sequence, tag, getattr(self, tag)(elem))
elif tag == 'annotation':
sequence.annotations.append(self.annotation(elem))
elif tag == 'name':
sequence.name = _collapse_wspace(elem.text)
elif tag in ('symbol', 'location'):
setattr(sequence, tag, elem.text)
elif namespace != NAMESPACES['phy']:
sequence.other.append(self.other(elem, namespace, tag))
parent.clear()
return sequence
def _parse_taxonomy(self, parent):
taxonomy = PX.Taxonomy(**parent.attrib)
for event, elem in self.context:
namespace, tag = _split_namespace(elem.tag)
if event == 'end':
if tag == 'taxonomy':
parent.clear()
break
if tag in ('id', 'uri'):
setattr(taxonomy, tag, getattr(self, tag)(elem))
elif tag == 'common_name':
taxonomy.common_names.append(_collapse_wspace(elem.text))
elif tag == 'synonym':
taxonomy.synonyms.append(elem.text)
elif tag in ('code', 'scientific_name', 'authority', 'rank'):
# ENH: check_str on rank
setattr(taxonomy, tag, elem.text)
elif namespace != NAMESPACES['phy']:
taxonomy.other.append(self.other(elem, namespace, tag))
parent.clear()
return taxonomy
def other(self, elem, namespace, localtag):
return PX.Other(localtag, namespace, elem.attrib,
value=elem.text and elem.text.strip() or None,
children=[self.other(child, *_split_namespace(child.tag))
for child in elem])
# Complex types
def accession(self, elem):
return PX.Accession(elem.text.strip(), elem.get('source'))
def annotation(self, elem):
return PX.Annotation(
desc=_collapse_wspace(_get_child_text(elem, 'desc')),
confidence=_get_child_as(elem, 'confidence', self.confidence),
properties=_get_children_as(elem, 'property', self.property),
uri=_get_child_as(elem, 'uri', self.uri),
**elem.attrib)
def binary_characters(self, elem):
def bc_getter(elem):
return _get_children_text(elem, 'bc')
return PX.BinaryCharacters(
type=elem.get('type'),
gained_count=_int(elem.get('gained_count')),
lost_count=_int(elem.get('lost_count')),
present_count=_int(elem.get('present_count')),
absent_count=_int(elem.get('absent_count')),
# Flatten BinaryCharacterList sub-nodes into lists of strings
gained=_get_child_as(elem, 'gained', bc_getter),
lost=_get_child_as(elem, 'lost', bc_getter),
present=_get_child_as(elem, 'present', bc_getter),
absent=_get_child_as(elem, 'absent', bc_getter))
def clade_relation(self, elem):
return PX.CladeRelation(
elem.get('type'), elem.get('id_ref_0'), elem.get('id_ref_1'),
distance=elem.get('distance'),
confidence=_get_child_as(elem, 'confidence', self.confidence))
def color(self, elem):
red, green, blue = (_get_child_text(elem, color, int) for color in
('red', 'green', 'blue'))
return PX.BranchColor(red, green, blue)
def confidence(self, elem):
return PX.Confidence(
_float(elem.text),
elem.get('type'))
def date(self, elem):
return PX.Date(
unit=elem.get('unit'),
desc=_collapse_wspace(_get_child_text(elem, 'desc')),
value=_get_child_text(elem, 'value', float),
minimum=_get_child_text(elem, 'minimum', float),
maximum=_get_child_text(elem, 'maximum', float),
)
def distribution(self, elem):
return PX.Distribution(
desc=_collapse_wspace(_get_child_text(elem, 'desc')),
points=_get_children_as(elem, 'point', self.point),
polygons=_get_children_as(elem, 'polygon', self.polygon))
def domain(self, elem):
return PX.ProteinDomain(elem.text.strip(),
int(elem.get('from')) - 1,
int(elem.get('to')),
confidence=_float(elem.get('confidence')),
id=elem.get('id'))
def domain_architecture(self, elem):
return PX.DomainArchitecture(
length=int(elem.get('length')),
domains=_get_children_as(elem, 'domain', self.domain))
def events(self, elem):
return PX.Events(
type=_get_child_text(elem, 'type'),
duplications=_get_child_text(elem, 'duplications', int),
speciations=_get_child_text(elem, 'speciations', int),
losses=_get_child_text(elem, 'losses', int),
confidence=_get_child_as(elem, 'confidence', self.confidence))
def id(self, elem):
provider = elem.get('provider') or elem.get('type')
return PX.Id(elem.text.strip(), provider)
def mol_seq(self, elem):
is_aligned = elem.get('is_aligned')
if is_aligned is not None:
is_aligned = _str2bool(is_aligned)
return PX.MolSeq(elem.text.strip(), is_aligned=is_aligned)
def point(self, elem):
return PX.Point(
elem.get('geodetic_datum'),
_get_child_text(elem, 'lat', float),
_get_child_text(elem, 'long', float),
alt=_get_child_text(elem, 'alt', float),
alt_unit=elem.get('alt_unit'))
def polygon(self, elem):
return PX.Polygon(
points=_get_children_as(elem, 'point', self.point))
def property(self, elem):
return PX.Property(elem.text.strip(),
elem.get('ref'), elem.get('applies_to'), elem.get('datatype'),
unit=elem.get('unit'),
id_ref=elem.get('id_ref'))
def reference(self, elem):
return PX.Reference(
doi=elem.get('doi'),
desc=_get_child_text(elem, 'desc'))
def sequence_relation(self, elem):
return PX.SequenceRelation(
elem.get('type'), elem.get('id_ref_0'), elem.get('id_ref_1'),
distance=_float(elem.get('distance')),
confidence=_get_child_as(elem, 'confidence', self.confidence))
def uri(self, elem):
return PX.Uri(elem.text.strip(),
desc=_collapse_wspace(elem.get('desc')),
type=elem.get('type'))
# ---------------------------------------------------------
# OUTPUT
# ---------------------------------------------------------
def _serialize(value):
"""Convert a Python primitive to a phyloXML-compatible Unicode string."""
if isinstance(value, float):
return unicode(value).upper()
elif isinstance(value, bool):
return unicode(value).lower()
return unicode(value)
def _clean_attrib(obj, attrs):
"""Create a dictionary from an object's specified, non-None attributes."""
out = {}
for key in attrs:
val = getattr(obj, key)
if val is not None:
out[key] = _serialize(val)
return out
def _handle_complex(tag, attribs, subnodes, has_text=False):
def wrapped(self, obj):
elem = ElementTree.Element(tag, _clean_attrib(obj, attribs))
for subn in subnodes:
if isinstance(subn, basestring):
# singular object: method and attribute names are the same
if getattr(obj, subn) is not None:
elem.append(getattr(self, subn)(getattr(obj, subn)))
else:
# list: singular method, pluralized attribute name
method, plural = subn
for item in getattr(obj, plural):
elem.append(getattr(self, method)(item))
if has_text:
elem.text = _serialize(obj.value)
return elem
wrapped.__doc__ = "Serialize a %s and its subnodes, in order." % tag
return wrapped
def _handle_simple(tag):
def wrapped(self, obj):
elem = ElementTree.Element(tag)
elem.text = _serialize(obj)
return elem
wrapped.__doc__ = "Serialize a simple %s node." % tag
return wrapped
class Writer(object):
"""Methods for serializing a PhyloXML object to XML."""
def __init__(self, phyloxml):
"""Build an ElementTree from a PhyloXML object."""
assert isinstance(phyloxml, PX.Phyloxml), "Not a Phyloxml object"
self._tree = ElementTree.ElementTree(self.phyloxml(phyloxml))
def write(self, file, encoding='utf-8', indent=True):
if indent:
_indent(self._tree.getroot())
self._tree.write(file, encoding)
return len(self._tree.getroot())
# Convert classes to ETree elements
def phyloxml(self, obj):
elem = ElementTree.Element(_ns('phyloxml'),
# NB: This is for XSD validation, which we don't do
# {_ns('schemaLocation', NAMESPACES['xsi']):
# obj.attributes['schemaLocation'],
# }
)
for tree in obj.phylogenies:
elem.append(self.phylogeny(tree))
for otr in obj.other:
elem.append(self.other(otr))
return elem
def other(self, obj):
elem = ElementTree.Element(_ns(obj.tag, obj.namespace), obj.attributes)
elem.text = obj.value
for child in obj.children:
elem.append(self.other(child))
return elem
phylogeny = _handle_complex(_ns('phylogeny'),
('rooted', 'rerootable', 'branch_length_unit', 'type'),
( 'name',
'id',
'description',
'date',
('confidence', 'confidences'),
'clade',
('clade_relation', 'clade_relations'),
('sequence_relation', 'sequence_relations'),
('property', 'properties'),
('other', 'other'),
))
clade = _handle_complex(_ns('clade'), ('id_source',),
( 'name',
'branch_length',
('confidence', 'confidences'),
'width',
'color',
'node_id',
('taxonomy', 'taxonomies'),
('sequence', 'sequences'),
'events',
'binary_characters',
('distribution', 'distributions'),
'date',
('reference', 'references'),
('property', 'properties'),
('clade', 'clades'),
('other', 'other'),
))
accession = _handle_complex(_ns('accession'), ('source',),
(), has_text=True)
annotation = _handle_complex(_ns('annotation'),
('ref', 'source', 'evidence', 'type'),
( 'desc',
'confidence',
('property', 'properties'),
'uri',
))
def binary_characters(self, obj):
"""Serialize a binary_characters node and its subnodes."""
elem = ElementTree.Element(_ns('binary_characters'),
_clean_attrib(obj,
('type', 'gained_count', 'lost_count',
'present_count', 'absent_count')))
for subn in ('gained', 'lost', 'present', 'absent'):
subelem = ElementTree.Element(_ns(subn))
for token in getattr(obj, subn):
subelem.append(self.bc(token))
elem.append(subelem)
return elem
clade_relation = _handle_complex(_ns('clade_relation'),
('id_ref_0', 'id_ref_1', 'distance', 'type'),
('confidence',))
color = _handle_complex(_ns('color'), (), ('red', 'green', 'blue'))
confidence = _handle_complex(_ns('confidence'), ('type',),
(), has_text=True)
date = _handle_complex(_ns('date'), ('unit',),
('desc', 'value', 'minimum', 'maximum'))
distribution = _handle_complex(_ns('distribution'), (),
( 'desc',
('point', 'points'),
('polygon', 'polygons'),
))
def domain(self, obj):
"""Serialize a domain node."""
elem = ElementTree.Element(_ns('domain'),
{'from': str(obj.start + 1), 'to': str(obj.end)})
if obj.confidence is not None:
elem.set('confidence', _serialize(obj.confidence))
if obj.id is not None:
elem.set('id', obj.id)
elem.text = _serialize(obj.value)
return elem
domain_architecture = _handle_complex(_ns('domain_architecture'),
('length',),
(('domain', 'domains'),))
events = _handle_complex(_ns('events'), (),
( 'type',
'duplications',
'speciations',
'losses',
'confidence',
))
id = _handle_complex(_ns('id'), ('provider',), (), has_text=True)
mol_seq = _handle_complex(_ns('mol_seq'), ('is_aligned',),
(), has_text=True)
node_id = _handle_complex(_ns('node_id'), ('provider',), (), has_text=True)
point = _handle_complex(_ns('point'), ('geodetic_datum', 'alt_unit'),
('lat', 'long', 'alt'))
polygon = _handle_complex(_ns('polygon'), (), (('point', 'points'),))
property = _handle_complex(_ns('property'),
('ref', 'unit', 'datatype', 'applies_to', 'id_ref'),
(), has_text=True)
reference = _handle_complex(_ns('reference'), ('doi',), ('desc',))
sequence = _handle_complex(_ns('sequence'),
('type', 'id_ref', 'id_source'),
( 'symbol',
'accession',
'name',
'location',
'mol_seq',
'uri',
('annotation', 'annotations'),
'domain_architecture',
('other', 'other'),
))
sequence_relation = _handle_complex(_ns('sequence_relation'),
('id_ref_0', 'id_ref_1', 'distance', 'type'),
('confidence',))
taxonomy = _handle_complex(_ns('taxonomy'),
('id_source',),
( 'id',
'code',
'scientific_name',
'authority',
('common_name', 'common_names'),
('synonym', 'synonyms'),
'rank',
'uri',
('other', 'other'),
))
uri = _handle_complex(_ns('uri'), ('desc', 'type'), (), has_text=True)
# Primitive types
# Floating point
alt = _handle_simple(_ns('alt'))
branch_length = _handle_simple(_ns('branch_length'))
lat = _handle_simple(_ns('lat'))
long = _handle_simple(_ns('long'))
maximum = _handle_simple(_ns('maximum'))
minimum = _handle_simple(_ns('minimum'))
value = _handle_simple(_ns('value'))
width = _handle_simple(_ns('width'))
# Integers
blue = _handle_simple(_ns('blue'))
duplications = _handle_simple(_ns('duplications'))
green = _handle_simple(_ns('green'))
losses = _handle_simple(_ns('losses'))
red = _handle_simple(_ns('red'))
speciations = _handle_simple(_ns('speciations'))
# Strings
bc = _handle_simple(_ns('bc'))
code = _handle_simple(_ns('code'))
common_name = _handle_simple(_ns('common_name'))
desc = _handle_simple(_ns('desc'))
description = _handle_simple(_ns('description'))
location = _handle_simple(_ns('location'))
mol_seq = _handle_simple(_ns('mol_seq'))
name = _handle_simple(_ns('name'))
rank = _handle_simple(_ns('rank'))
scientific_name = _handle_simple(_ns('scientific_name'))
symbol = _handle_simple(_ns('symbol'))
synonym = _handle_simple(_ns('synonym'))
type = _handle_simple(_ns('type'))
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