def test_translocation(): st1 = Translocation(Agent('FOXO3A')) st2 = Translocation(Agent('FOXO3A'), 'cytoplasm') st3 = Translocation(Agent('FOXO3A'), None, 'nucleus') st4 = Translocation(Agent('FOXO3A'), 'cytoplasm', 'nucleus') e = ea.EnglishAssembler() e.add_statements([st1]) s = e.make_model() assert s == 'FOXO3A translocates.' assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'FOXO3A' e = ea.EnglishAssembler() e.add_statements([st2]) s = e.make_model() assert s == 'FOXO3A translocates from the cytoplasm.' assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'FOXO3A' e = ea.EnglishAssembler() e.add_statements([st3]) s = e.make_model() assert s == 'FOXO3A translocates to the nucleus.' assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'FOXO3A' e = ea.EnglishAssembler() e.add_statements([st4]) s = e.make_model() assert s == 'FOXO3A translocates from the cytoplasm to the nucleus.' assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'FOXO3A'
def test_agent_activity_stmt(): braf = Agent('BRAF', activity=ActivityCondition('activity', True)) mek = Agent('MAP2K1') st = Activation(braf, mek) e = ea.EnglishAssembler() e.add_statements([st]) s = e.make_model() print(s) assert s == 'Active BRAF activates MAP2K1.'
def test_agent_activity_stmt(): braf = Agent('BRAF', activity=ActivityCondition('activity', True)) mek = Agent('MAP2K1') st = Activation(braf, mek) e = ea.EnglishAssembler() e.add_statements([st]) s = e.make_model() print(s) assert s == 'Active BRAF activates MAP2K1.' assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'BRAF' assert _substring_by_coords(s, e.stmt_agents[0][1].coords) == 'MAP2K1'
def test_translocation(): st1 = Translocation(Agent('FOXO3A')) st2 = Translocation(Agent('FOXO3A'), 'cytoplasm') st3 = Translocation(Agent('FOXO3A'), None, 'nucleus') st4 = Translocation(Agent('FOXO3A'), 'cytoplasm', 'nucleus') e = ea.EnglishAssembler() e.add_statements([st1]) s = e.make_model() assert s == 'FOXO3A translocates.' e = ea.EnglishAssembler() e.add_statements([st2]) s = e.make_model() assert s == 'FOXO3A translocates from the cytoplasm.' e = ea.EnglishAssembler() e.add_statements([st3]) s = e.make_model() assert s == 'FOXO3A translocates to the nucleus.' e = ea.EnglishAssembler() e.add_statements([st4]) s = e.make_model() assert s == 'FOXO3A translocates from the cytoplasm to the nucleus.'
def test_assemble_more(): a = Agent('MAP2K1') b = Agent('PP2A') st1 = Dephosphorylation(b, a, 'serine', 222) b = Agent('BRAF') c = Agent('RAF1') st2 = Complex([a, b, c]) e = ea.EnglishAssembler() e.add_statements([st1, st2]) s = e.make_model() print(s) assert s == \ 'PP2A dephosphorylates MAP2K1 on S222. MAP2K1 binds BRAF and RAF1.'
def test_assemble_more(): a = Agent('MAP2K1') b = Agent('PP2A') st1 = Dephosphorylation(b, a, 'serine', 222) b = Agent('BRAF') c = Agent('RAF1') st2 = Complex([a, b, c]) e = ea.EnglishAssembler() e.add_statements([st1, st2]) s = e.make_model() print(s) assert s == \ 'PP2A dephosphorylates MAP2K1 on S222. MAP2K1 binds BRAF and RAF1.' assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'PP2A' assert _substring_by_coords(s, e.stmt_agents[0][1].coords) == 'MAP2K1' assert _substring_by_coords(s, e.stmt_agents[1][0].coords) == 'MAP2K1' assert _substring_by_coords(s, e.stmt_agents[1][1].coords) == 'BRAF' assert _substring_by_coords(s, e.stmt_agents[1][2].coords) == 'RAF1'
def _stmt_to_text(st): e = ea.EnglishAssembler() e.add_statements([st]) s = e.make_model() print(s) return s