def process_belrdf(rdf_filename):
# Parse the RDF
g = rdflib.Graph()
g.parse(rdf_filename, format='nt')
# Build BelPy statements from RDF
bp = BelProcessor(g)
bp.get_complexes()
bp.get_activating_subs()
bp.get_modifications()
bp.get_dephosphorylations()
bp.get_activating_mods()
bp.get_composite_activating_mods()
bp.get_activity_activity()
# Print some output about the process
bp.print_statement_coverage()
print "\n--- Converted BelPy Statements -------------"
bp.print_statements()
return bp
def process_belrdf(rdf_str):
# Parse the RDF
g = rdflib.Graph()
g.parse(data=rdf_str, format='nt')
# Build BelPy statements from RDF
bp = BelProcessor(g)
bp.get_complexes()
bp.get_activating_subs()
bp.get_modifications()
bp.get_dephosphorylations()
bp.get_activating_mods()
bp.get_composite_activating_mods()
bp.get_activity_activity()
# Print some output about the process
bp.print_statement_coverage()
print "\n--- Converted BelPy Statements -------------"
bp.print_statements()
return bp
def process_belrdf(rdf_str):
"""Return a BelProcessor for a BEL/RDF string.
Parameters
----------
rdf_str : str
A BEL/RDF string to be processed. This will usually come from reading
a .rdf file.
Returns
-------
bp : BelProcessor
A BelProcessor object which contains INDRA Statements in bp.statements.
Notes
-----
This function calls all the specific get_type_of_mechanism()
functions of the newly constructed BelProcessor to extract
INDRA Statements.
"""
g = rdflib.Graph()
try:
g.parse(data=rdf_str, format="nt")
except ParseError:
logger.error("Could not parse rdf.")
return None
# Build INDRA statements from RDF
bp = BelProcessor(g)
bp.get_complexes()
bp.get_activating_subs()
bp.get_modifications()
bp.get_dephosphorylations()
bp.get_activating_mods()
bp.get_composite_activating_mods()
bp.get_activation()
# Print some output about the process
bp.print_statement_coverage()
logger.debug("\n--- Converted INDRA Statements -------------")
bp.print_statements()
return bp
