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# Copyright 2013 by Leighton Pritchard. 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.
"""This module provides classes and functions to parse a KGML pathway map.
The KGML pathway map is parsed into the object structure defined in
KGML_Pathway.py in this module.
Classes:
- KGMLParser Parses KGML file
Functions:
- read Returns a single Pathway object, using KGMLParser
internally
"""
from __future__ import print_function
try:
import xml.etree.cElementTree as ElementTree
except ImportError:
import xml.etree.ElementTree as ElementTree
from Bio._py3k import StringIO
from Bio.KEGG.KGML.KGML_pathway import *
def read(handle, debug=0):
"""Parses a single KEGG Pathway from given file handle.
Returns a single Pathway object. There should be one and only
one pathway in each file, but there may well be pathological
examples out there.
"""
iterator = parse(handle, debug)
try:
first = next(iterator)
except StopIteration:
first = None
if first is None:
raise ValueError("No pathways found in handle")
try:
second = next(iterator)
except StopIteration:
second = None
if second is not None:
raise ValueError("More than one pathway found in handle")
return first
def parse(handle, debug=0):
"""Returns an iterator over Pathway elements.
Arguments:
- handle - file handle to a KGML file for parsing
- debug - integer for amount of debug information to print
This is a generator for the return of multiple Pathway objects.
"""
# Check handle
if not hasattr(handle, 'read'):
if isinstance(handle, str):
handle = StringIO(handle)
else:
exc_txt = "An XML-containing handle or an XML string " +\
"must be provided"
raise Exception(exc_txt)
# Parse XML and return each Pathway
for event, elem in \
ElementTree.iterparse(handle, events=('start', 'end')):
if event == "end" and elem.tag == "pathway":
yield KGMLParser(elem).parse()
elem.clear()
class KGMLParser(object):
"""Parses a KGML XML Pathway entry into a Pathway object."""
def __init__(self, elem):
self.entry = elem
def parse(self):
"""Parse the input elements."""
def _parse_pathway(attrib):
for k, v in attrib.items():
self.pathway.__setattr__(k, v)
def _parse_entry(element):
new_entry = Entry()
for k, v in element.attrib.items():
new_entry.__setattr__(k, v)
for subelement in element.getchildren():
if subelement.tag == 'graphics':
_parse_graphics(subelement, new_entry)
elif subelement.tag == 'component':
_parse_component(subelement, new_entry)
self.pathway.add_entry(new_entry)
def _parse_graphics(element, entry):
new_graphics = Graphics(entry)
for k, v in element.attrib.items():
new_graphics.__setattr__(k, v)
entry.add_graphics(new_graphics)
def _parse_component(element, entry):
new_component = Component(entry)
for k, v in element.attrib.items():
new_component.__setattr__(k, v)
entry.add_component(new_component)
def _parse_reaction(element):
new_reaction = Reaction()
for k, v in element.attrib.items():
new_reaction.__setattr__(k, v)
for subelement in element.getchildren():
if subelement.tag == 'substrate':
new_reaction.add_substrate(int(subelement.attrib['id']))
elif subelement.tag == 'product':
new_reaction.add_product(int(subelement.attrib['id']))
self.pathway.add_reaction(new_reaction)
def _parse_relation(element):
new_relation = Relation()
new_relation.entry1 = int(element.attrib['entry1'])
new_relation.entry2 = int(element.attrib['entry2'])
new_relation.type = element.attrib['type']
for subtype in element.getchildren():
name, value = subtype.attrib['name'], subtype.attrib['value']
if name in ('compound', 'hidden compound'):
new_relation.subtypes.append((name, int(value)))
else:
new_relation.subtypes.append((name, value))
self.pathway.add_relation(new_relation)
# ==========
# Initialise Pathway
self.pathway = Pathway()
# Get information about the pathway itself
_parse_pathway(self.entry.attrib)
for element in self.entry.getchildren():
if element.tag == 'entry':
_parse_entry(element)
elif element.tag == 'reaction':
_parse_reaction(element)
elif element.tag == 'relation':
_parse_relation(element)
# Parsing of some elements not implemented - no examples yet
else:
# This should warn us of any unimplemented tags
import warnings
from Bio import BiopythonParserWarning
warnings.warn("Warning: tag %s not implemented in parser" %
element.tag, BiopythonParserWarning)
return self.pathway
if __name__ == '__main__':
# Check large metabolism
pathway = read(open('ko01100.xml', 'rU'))
print(pathway)
for k, v in list(pathway.entries.items())[:20]:
print(v)
for r in list(pathway.reactions)[:20]:
print(r)
print(len(pathway.maps))
# Check relations
pathway = read(open('ko_metabolic/ko00010.xml', 'rU'))
print(pathway)
for k, v in list(pathway.entries.items())[:20]:
print(v)
for r in list(pathway.reactions[:20]):
print(r)
for r in list(pathway.relations[:20]):
print(r)
print(len(pathway.maps))
# Check components
pathway = read(open('ko_metabolic/ko00253.xml', 'rU'))
print(pathway)
for k, v in pathway.entries.items():
print(v)
print(len(pathway.maps))
# Test XML representation
print(pathway.get_KGML())
# Test bounds of pathway
print(pathway.bounds)
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