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)
# ==========
# Initialize 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
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:
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:
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:
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)
# ==========
# Initialize Pathway
self.pathway = Pathway()
# Get information about the pathway itself
_parse_pathway(self.entry.attrib)
for element in self.entry:
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