def test_ast_parse_fus():
assertion = AssertionStr(
entire="act(p(fus(HGNC:EWSR1, start, HGNC:FLI1, end)), ma(tscript))")
ast = bel.lang.ast.BELAst(assertion=assertion)
print("To String", ast.to_string())
assert (
ast.to_string() ==
"act(p(fus(HGNC:3508!EWSR1, start, HGNC:3749!FLI1, end)), ma(tscript))"
)
def test_ast_canonicalization(test_input, expected):
"""Test AST canonicalization and sorting function arguments
See issue: https://github.com/belbio/bel/issues/13
"""
assertion = AssertionStr(entire=test_input)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.canonicalize()
print("Canonicalized", ast.to_string())
assert ast.to_string() == expected
def test_ast_canonicalization_2():
"""Test AST canonicalization and sorting function arguments
See issue: https://github.com/belbio/bel/issues/13
"""
test_input = "path(DO:0080600!COVID-19)"
expected = "path(DO:0080600)"
assertion = AssertionStr(entire=test_input)
ast = bel.lang.ast.BELAst(assertion=assertion)
ast.canonicalize()
print("Canonicalized", ast.to_string())
assert ast.to_string() == expected
def test_ast_orthologization():
"""Test AST orthologization"""
assertion = AssertionStr(entire="p(HGNC:AKT1)")
ast = bel.lang.ast.BELAst(assertion=assertion)
if ast.orthologizable("TAX:10090"):
ast.orthologize("TAX:10090")
print("Orthologized to mouse", ast.to_string())
assert ast.to_string() == "p(EG:11651!Akt1)"
ast.decanonicalize()
print("Orthologized and decanonicalized to mouse", ast.to_string())
assert ast.to_string() == "p(MGI:87986!Akt1)"
else:
assert False, "Not orthologizable"
def test_ast_nested_orthologization():
assertion = AssertionStr(
entire="p(HGNC:AKT1) increases (p(HGNC:AKT1) increases p(HGNC:EGF))")
ast = bel.lang.ast.BELAst(assertion=assertion)
orthologizable = ast.orthologizable("TAX:10090")
print("Orthologizable", orthologizable)
ast.orthologize("TAX:10090").decanonicalize()
expected = "p(MGI:87986!Akt1) increases (p(MGI:87986!Akt1) increases p(MGI:95290!Egf))"
result = ast.to_string()
print("Result", result)
assert result == expected