def convert_fus(ast):
"""Convert BEL1 fus() to BEL2 fus()"""
parent_fn_name = ast.name_short
prefix_list = {"p": "p.", "r": "r.", "g": "c."}
prefix = prefix_list[parent_fn_name]
fus1_ns = ast.args[0].namespace
fus1_val = ast.args[0].value
arg_fus = ast.args[1]
fus_args = [None, "?", "?"]
for idx, arg in enumerate(arg_fus.args):
fus_args[idx] = arg
fus2_ns = fus_args[0].namespace
fus2_val = fus_args[0].value
if fus_args[1] == "?":
fus1_range = fus_args[1]
else:
fus1_range = f'"{prefix}1_{fus_args[1].value}"'
if fus_args[2] == "?":
fus2_range = fus_args[2]
else:
fus2_range = f'"{prefix}{fus_args[2].value}_?"'
fus = Function("fus", version=version, parent=ast)
fus.args = [
NSArg(fus1_ns, fus1_val, fus),
StrArg(fus1_range, fus),
NSArg(fus2_ns, fus2_val, fus),
StrArg(fus2_range, fus),
]
# Remove BEL
ast_args = ast.args
ast_args.pop(0)
ast_args.pop(0)
if ast_args == [None]:
ast_args = []
ast.args = []
ast.add_argument(fus)
if len(ast_args) > 0:
ast.args.extend(ast_args)
return ast
def convert_fus(ast):
"""Convert BEL1 fus() to BEL2 fus()"""
parent_fn_name = ast.name_short
prefix_list = {'p': 'p.', 'r': 'r.', 'g': 'c.'}
prefix = prefix_list[parent_fn_name]
fus1_ns = ast.args[0].namespace
fus1_val = ast.args[0].value
arg_fus = ast.args[1]
fus_args = [None, '?', '?']
for idx, arg in enumerate(arg_fus.args):
fus_args[idx] = arg
fus2_ns = fus_args[0].namespace
fus2_val = fus_args[0].value
if fus_args[1] == '?':
fus1_range = fus_args[1]
else:
fus1_range = f'"{prefix}1_{fus_args[1].value}"'
if fus_args[2] == '?':
fus2_range = fus_args[2]
else:
fus2_range = f'"{prefix}{fus_args[2].value}_?"'
fus = Function('fus', spec, parent_function=ast)
fus.args = [
NSArg(fus1_ns, fus1_val, fus),
StrArg(fus1_range, fus),
NSArg(fus2_ns, fus2_val, fus),
StrArg(fus2_range, fus),
]
# Remove BEL
ast_args = ast.args
ast_args.pop(0)
ast_args.pop(0)
if ast_args == [None]:
ast_args = []
ast.args = []
ast.add_argument(fus)
if len(ast_args) > 0:
ast.args.extend(ast_args)
return ast
def convert_trunc(trunc):
"""Convert BEL1 trunc() to BEL2 var()"""
parent_fn_name = trunc.parent_function.name_short
prefix_list = {"p": "p.", "r": "r.", "g": "c."}
prefix = prefix_list[parent_fn_name]
new_var_arg = f'"truncated at {trunc.args[0].value}"'
new_var = Function("var", version=version)
new_var.add_argument(StrArg(new_var_arg, new_var))
return new_var
def add_ast_fn(d, spec, parent_function=None):
"""Convert dict AST to object AST Function
Args:
ast_fn: AST object Function
d: AST as dictionary
spec: BEL Specification
Return:
ast_fn
"""
if d["type"] == "Function":
ast_fn = Function(d["function"]["name"],
spec,
parent_function=parent_function)
for arg in d["args"]:
if arg["type"] == "Function":
ast_fn.add_argument(
add_ast_fn(arg, spec, parent_function=ast_fn))
elif arg["type"] == "NSArg":
ast_fn.add_argument(
NSArg(arg["nsarg"]["ns"], arg["nsarg"]["ns_val"], ast_fn))
elif arg["type"] == "StrArg":
ast_fn.add_argument(StrArg(arg["arg"], ast_fn))
return ast_fn
def convert_activity(ast):
"""Convert BEL1 activities to BEL2 act()"""
if len(ast.args) > 1:
log.error(f"Activity should not have more than 1 argument {ast.to_string()}")
p_arg = ast.args[0] # protein argument
print("p_arg", p_arg)
ma_arg = Function("ma", bo.spec)
ma_arg.add_argument(StrArg(ast.name, ma_arg))
p_arg.change_parent_fn(ma_arg)
ast = Function("activity", bo.spec)
p_arg.change_parent_fn(ast)
ast.add_argument(p_arg)
ast.add_argument(ma_arg)
return ast
def convert_sub(sub):
"""Convert BEL1 sub() to BEL2 var()"""
args = sub.args
(ref_aa, pos, new_aa) = args
parent_fn_name = sub.parent_function.name_short
prefix_list = {"p": "p.", "r": "r.", "g": "c."}
prefix = prefix_list[parent_fn_name]
new_var_arg = f'"{prefix}{belspec["namespaces"]["AminoAcid"]["to_short"][ref_aa.value]}{pos.value}{belspec["namespaces"]["AminoAcid"]["to_short"][new_aa.value]}"'
new_var = Function("var", version=version)
new_var.add_argument(StrArg(new_var_arg, new_var))
return new_var
def convert_tloc(ast):
"""Convert BEL1 tloc() to BEL2"""
from_loc_arg = ast.args[1]
to_loc_arg = ast.args[2]
from_loc = Function("fromLoc", version=version, parent=ast)
from_loc.add_argument(
NSArg(from_loc_arg.namespace, from_loc_arg.value, parent=from_loc))
to_loc = Function("toLoc", version=version, parent=ast)
to_loc.add_argument(
NSArg(to_loc_arg.namespace, to_loc_arg.value, parent=to_loc))
ast.args[1] = from_loc
ast.args[2] = to_loc
return ast
def add_ast_fn(d, spec, parent_function=None):
"""Convert dict AST to object AST Function
Args:
ast_fn: AST object Function
d: AST as dictionary
spec: BEL Specification
Return:
ast_fn
"""
if d['type'] == 'Function':
ast_fn = Function(d['function']['name'], spec, parent_function=parent_function)
for arg in d['args']:
if arg['type'] == 'Function':
ast_fn.add_argument(add_ast_fn(arg, spec, parent_function=ast_fn))
elif arg['type'] == 'NSArg':
ast_fn.add_argument(NSArg(arg['nsarg']['ns'], arg['nsarg']['ns_val'], ast_fn))
elif arg['type'] == 'StrArg':
ast_fn.add_argument(StrArg(arg['arg'], ast_fn))
return ast_fn
def process_ast(edges, ast, spec):
if isinstance(ast, BELAst):
pass
# TODO composite is not being addressed right now
# TODO
elif isinstance(ast, Function):
if ast.name in ("complex", "complexAbundance"):
for arg in ast.args:
edges.append(BELAst(ast, "hasComponent", arg, spec))
elif ast.name in ("composite", "compositeAbundance"):
for arg in ast.args:
edges.append(BELAst(ast, "hasAssociation", arg, spec))
elif ast.name in ("act", "activity"):
subject = ast.args[0]
edge = BELAst(subject, "hasActivity", ast, spec)
edges.append(edge)
elif ast.name in ("pmod", "proteinModification"):
parent = ast.parent_function
src_abundance = Function(parent.name, spec)
src_abundance.add_argument(parent.args[0])
edges.append(BELAst(src_abundance, "hasModification", parent,
spec))
elif ast.name in ("var", "variant"):
parent = ast.parent_function
src_abundance = Function(parent.name, spec)
src_abundance.add_argument(parent.args[0])
edges.append(BELAst(src_abundance, "hasVariant", parent, spec))
elif ast.name in ("frag", "fragment"):
parent = ast.parent_function
src_abundance = Function(parent.name, spec)
src_abundance.add_argument(parent.args[0])
edges.append(BELAst(src_abundance, "hasFragment", parent, spec))
elif ast.name in ("loc", "location"):
parent = ast.parent_function
src_abundance = Function(parent.name, spec)
src_abundance.add_argument(parent.args[0])
edges.append(BELAst(src_abundance, "hasLocation", parent, spec))
elif ast.name in ("tloc", "translocation"):
src_abundance = ast.args[0]
from_abundance = copy.deepcopy(src_abundance)
from_loc = Function("loc", spec)
from_loc.add_argument(ast.args[1].args[0])
from_abundance.add_argument(from_loc)
to_abundance = copy.deepcopy(src_abundance)
to_loc = Function("loc", spec)
to_loc.add_argument(ast.args[2].args[0])
to_abundance.add_argument(to_loc)
edges.append(BELAst(ast, "decreases", from_abundance, spec))
edges.append(BELAst(ast, "increases", to_abundance, spec))
edges.append(
BELAst(src_abundance, "hasLocation", from_abundance, spec))
edges.append(
BELAst(src_abundance, "hasLocation", to_abundance, spec))
elif ast.name in ("sec", "cellSecretion", "surf",
"cellSurfaceExpression"):
target_loc = locations["extracellular"]
if ast.name in ("surf", "cellSurfaceExpression"):
target_loc = locations["cellsurface"]
src_abundance = ast.args[0]
to_abundance = copy.deepcopy(src_abundance)
to_loc = Function("loc", spec)
to_loc.add_argument(target_loc)
to_abundance.add_argument(to_loc)
edges.append(BELAst(ast, "increases", to_abundance, spec))
edges.append(
BELAst(src_abundance, "hasLocation", to_abundance, spec))
elif ast.name in ("deg", "degradation"):
edges.append(BELAst(ast, "directlyDecreases", ast.args[0], spec))
elif ast.name in ("fus", "fusion"):
parent = ast.parent_function
src_abundance = Function(parent.name, spec)
src_abundance.add_argument(ast.args[0])
edges.append(BELAst(src_abundance, "hasFusion", parent, spec))
src_abundance = Function(parent.name, spec)
src_abundance.add_argument(ast.args[2])
edges.append(BELAst(src_abundance, "hasFusion", parent, spec))
elif ast.name in ("reactants", "products"):
parent = ast.parent_function
relation = "hasProduct"
if ast.name == "reactants":
relation = "hasReactant"
for arg in ast.args:
edges.append(BELAst(parent, relation, arg, spec))
elif ast.name in ("product", "fusion"):
parent = ast.parent_function
src_abundance = Function(parent.name, spec)
src_abundance.add_argument(ast.args[0])
edges.append(BELAst(src_abundance, "hasFusion", parent, spec))
src_abundance = Function(parent.name, spec)
src_abundance.add_argument(ast.args[2])
edges.append(BELAst(src_abundance, "hasFusion", parent, spec))
# Recursively process every element by processing BELAst and Functions
if hasattr(ast, "args"):
for arg in ast.args:
process_ast(edges, arg, spec)
