def test_expand_families():
# Get the Expander
exp = ef.Expander(hierarchies)
# Declare some agents
akt = Agent('AKT', db_refs={'BE': 'AKT'})
raf = Agent('RAF', db_refs={'BE': 'RAF'})
mek = Agent('MEK', db_refs={'BE': 'MEK'})
mapk1 = Agent('MAPK1', db_refs={'BE': 'MAPK1'})
ampk = Agent('AMPK', db_refs={'BE': 'AMPK'})
# Test case where one agent is a family and the other is a gene
st = Phosphorylation(mek, mapk1)
expanded_stmts = exp.expand_families([st])
assert len(expanded_stmts) == 2
# Test for case involving None for one of the agents
st = Phosphorylation(None, akt)
expanded_stmts = exp.expand_families([st])
assert len(expanded_stmts) == 3
# Statement with two families: 3 Rafs x 2 Meks
st = Phosphorylation(raf, mek, 'S', '202')
expanded_stmts = exp.expand_families([st])
assert len(expanded_stmts) == 6
# Test also for case involving both family and complex relationships
st = Phosphorylation(ampk, mek)
expanded_stmts = exp.expand_families([st])
assert len(expanded_stmts) == 14
def test_db_ref_keys():
# test that expanded families get TEXT, UP, HGNC keys in their db_refs
# Get the Expander
exp = ef.Expander(hierarchies)
# Declare some agents
grb2 = Agent('GRB2',
db_refs={'TEXT': 'Grb2', 'UP': 'P62993', 'HGNC': '4566'})
shc = Agent('SHC', db_refs={'FPLX':'SHC'})
# Test case where one agent is a family and the other is a gene
st = Activation(grb2, shc)
expanded_stmts = exp.expand_families([st])
for st in expanded_stmts:
for agent in st.agent_list():
if agent is not None:
assert set(list(agent.db_refs)) == \
set(['TEXT','UP','HGNC'])
# Test for case involving None for one of the agents
st = Phosphorylation(None, shc)
expanded_stmts = exp.expand_families([st])
for st in expanded_stmts:
for agent in st.agent_list():
if agent is not None:
assert set(list(agent.db_refs)) == \
set(['TEXT','UP','HGNC'])
# Statement with two families: 4x4 SHC
st = Activation(shc, shc)
expanded_stmts = exp.expand_families([st])
for st in expanded_stmts:
for agent in st.agent_list():
if agent is not None:
assert set(list(agent.db_refs)) == \
set(['TEXT','UP','HGNC'])
def test_complexes_from_hierarchy():
exp = ef.Expander(hierarchies)
complexes = exp.complexes_from_hierarchy()
keys = [c.matches_key() for c in complexes]
probe_stmt = Complex([Agent('AMPK_alpha', db_refs={'FPLX':'AMPK_alpha'}),
Agent('AMPK_beta', db_refs={'FPLX':'AMPK_beta'}),
Agent('AMPK_gamma', db_refs={'FPLX':'AMPK_gamma'})])
assert probe_stmt.matches_key() in keys
def test_expanded_complexes_from_hierarchy():
exp = ef.Expander(hierarchies)
complexes = exp.expanded_complexes_from_hierarchy()
stmt_ag_names = []
for stmt in complexes:
sorted_names = tuple(sorted([ag.name for ag in stmt.agent_list()]))
stmt_ag_names.append(sorted_names)
ampk_alphas = ('PRKAA1', 'PRKAA2')
ampk_betas = ('PRKAB1', 'PRKAB2')
ampk_gammas = ('PRKAG1', 'PRKAG2', 'PRKAG3')
for alpha, beta, gamma in itertools.product(ampk_alphas, ampk_betas,
ampk_gammas):
assert tuple(sorted((alpha, beta, gamma))) in stmt_ag_names
def test_get_children():
exp = ef.Expander(hierarchies)
raf = Agent('RAF', db_refs={'BE': 'RAF'})
braf = Agent('BRAF', db_refs={'HGNC': '1097'})
# Look up RAF
rafs = exp.get_children(raf)
# Should get three family members
assert isinstance(rafs, list)
assert len(rafs) == 3
assert unicode_strs(rafs)
# The lookup of a gene-level entity should not return any additional
# entities
brafs = exp.get_children(braf)
assert isinstance(brafs, list)
assert len(brafs) == 0
assert unicode_strs(brafs)
# The lookup for a top-level family (e.g., MAPK, which has as children
# both the intermediate family ERK as well as all MAPK1-15 members)
# should not return the intermediate families when a filter is applied.
mapk = Agent('MAPK', db_refs={'BE': 'MAPK'})
mapks = exp.get_children(mapk, ns_filter=None)
assert len(mapks) == 12
assert ('HGNC', 'MAPK1') in mapks
assert ('HGNC', 'MAPK9') in mapks
assert ('BE', 'ERK') in mapks
assert ('BE', 'JNK') in mapks
assert unicode_strs(mapks)
# Now do the same expansion with a namespace filter
mapks = exp.get_children(mapk, ns_filter='HGNC')
assert unicode_strs(mapks)
assert len(mapks) == 9
assert ('HGNC', 'MAPK3') in mapks
assert ('HGNC', 'MAPK10') in mapks
assert ('BE', 'ERK') not in mapks
# Make sure we can also do this in a case involving both family and complex
# relationships
ampk = Agent('AMPK', db_refs={'BE': 'AMPK'})
ampks = exp.get_children(ampk, ns_filter=None)
assert len(ampks) == 22
ampks = exp.get_children(ampk, ns_filter='HGNC')
assert len(ampks) == 7
# Test that the default filter is HGNC
ampks = exp.get_children(ampk)
assert len(ampks) == 7
ag_none = None
none_children = exp.get_children(ag_none)
assert isinstance(none_children, list)
assert len(none_children) == 0
mod_map = {
'demethylate': 'Demethylation',
'methylate': 'Methylation',
'phosphorylate': 'Phosphorylation',
'dephosphorylate': 'Dephosphorylation',
'ubiquitinate': 'Ubiquitination',
'deubiquitinate': 'Deubiquitination',
'activate': 'Activation',
'inhibit': 'Inhibition'
}
affect_verbs = ['affect', 'regulate', 'control', 'target'] + \
list(mod_map.keys())
expander = expand_families.Expander()
def suggest_relevant_relations(groundings):
def make_nice_list(lst):
if len(lst) == 1:
return lst[0]
pre = ', '.join(lst[:-1])
full = '%s, or %s' % (pre, lst[-1])
return full
prefix1 = 'By the way, I recognized'
prefix2 = 'I also recognized'
msg_parts = []
for entity_txt, (dbn, dbi) in groundings.items():
if dbn == 'FPLX':
