def add_observables(model):
data = process_data.read_data()
ab_map = process_data.get_antibody_map(data)
for ab_name, agents in ab_map.items():
patterns = []
for agent in agents:
try:
monomer = model.monomers[agent.name]
except KeyError:
continue
if agent.mods:
mc = agent.mods[0]
site_names = ['phospho', mc.residue]
if mc.position is not None:
site_names.append(mc.residue + mc.position)
for site_name in site_names:
try:
pattern = monomer(**{site_name: 'p'})
patterns.append(ComplexPattern([pattern], None))
except Exception:
pass
else:
patterns.append(ComplexPattern([monomer()], None))
if patterns:
if model.monomers.get(ab_name) is not None:
obs_name = ab_name + '_obs'
else:
obs_name = ab_name
if not re.match(r'[_a-z][_a-z0-9]*\Z', obs_name, re.IGNORECASE):
obs_name = obs_name.replace('-', '_')
if not re.match(r'[_a-z][_a-z0-9]*\Z', obs_name, re.IGNORECASE):
obs_name = 'p' + obs_name
o = Observable(obs_name, ReactionPattern(patterns))
model.add_component(o)
'''
def run(dec_thresh=-1, inc_thresh=1):
data = pd.read_data(pd.data_file)
ab_agents = pd.get_antibody_map(data)
# If filtering is to be done based on thresholds only,
# set this to None
drug_ab_combs = get_eval_drug_ab_combs(data)
#drug_ab_combs = None
stmts, values = make_stmts(data,
ab_agents,
drug_ab_combs=drug_ab_combs,
thresh=[dec_thresh, inc_thresh])
# Now, preassemble the statements to remove duplicates
pa_dict = preassemble_stmts(stmts)
with open('data_stmts.pkl', 'wb') as f:
pickle.dump((pa_dict, values), f, protocol=2)
return (stmts, values)
if json_dict[drug].get(ab) is None:
json_dict[drug][ab] = {}
for idx, path in enumerate(paths):
path_stmts = []
for rule_name, sign in path[:-1]:
stmt = _stmt_from_rule(model, rule_name, stmts)
path_stmts.append(stmt.uuid)
json_dict[drug][ab][idx] = path_stmts
return json_dict
if __name__ == '__main__':
print("Processing data")
data = process_data.read_data(process_data.data_file)
data_genes = process_data.get_all_gene_names(data)
ab_map = process_data.get_antibody_map(data)
print('Loading data statements.')
data_stmts, data_values = make_stmts.run(dec_thresh=0.5, inc_thresh=1.5)
all_data_stmts = [values.values() for values in data_stmts.values()]
all_data_stmts = itertools.chain.from_iterable(all_data_stmts)
all_data_stmts = list(itertools.chain.from_iterable(all_data_stmts))
print('We will check the following drug-ab combinations:\n============')
for drug, stmtd in data_stmts.items():
print(drug)
for ab in stmtd.keys():
print('-'+ ab)
agent_obs = list(itertools.chain.from_iterable(ab_map.values()))
# Here we need to cross-reference the antbody map with the data values