def test_simple_assembly():
st1 = Activation(Agent('a'), Agent('b'))
st2 = Inhibition(Agent('a'), Agent('c'))
sa = SifAssembler([st1, st2])
sa.make_model()
assert len(sa.graph.nodes()) == 3
assert len(sa.graph.edges()) == 2
def test_modification():
st1 = Phosphorylation(Agent('BRAF'), Agent('MAP2K1'), 'S', '222')
sa = SifAssembler([st1])
sa.make_model(True, True, True)
assert len(sa.graph.nodes()) == 2
assert len(sa.graph.edges()) == 1
sa.save_model('test_sif.sif', True)
with open('test_sif.sif', 'rb') as fh:
txt = fh.read().decode('utf-8')
assert txt == 'BRAF 0 MAP2K1\n', txt
def test_evidence_assembly():
ev1 = Evidence(pmid='1')
ev2 = Evidence(pmid='2')
ev3 = Evidence(pmid='3')
Evidence(pmid='4')
st1 = Activation(Agent('a'), Agent('b'), evidence=[ev1])
st2 = Inhibition(Agent('a'), Agent('c'), evidence=[ev1, ev2, ev3])
sa = SifAssembler([st1, st2])
sa.make_model()
assert len(sa.graph.nodes()) == 3
assert len(sa.graph.edges()) == 2
sa.set_edge_weights('support_pmid')
def assemble_loopy():
"""Assemble INDRA Statements into a Loopy model using SIF Assembler."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
stmts_json = body.get('statements')
stmts = stmts_from_json(stmts_json)
sa = SifAssembler(stmts)
sa.make_model(use_name_as_key=True)
model_str = sa.print_loopy(as_url=True)
res = {'loopy_url': model_str}
return res
def assemble_loopy():
"""Assemble INDRA Statements into a Loopy model using SIF Assembler."""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
stmts_json = body.get('statements')
stmts = stmts_from_json(stmts_json)
sa = SifAssembler(stmts)
sa.make_model(use_name_as_key=True)
model_str = sa.print_loopy(as_url=True)
res = {'loopy_url': model_str}
return res
def assemble_pysb(stmts, data_genes, out_file):
"""Return an assembled PySB model."""
base_file, _ = os.path.splitext(out_file)
#stmts = ac.load_statements('%s.pkl' % base_file)
stmts = preprocess_stmts(stmts, data_genes)
# Make a SIF model equivalent to the PySB model
# Useful for making direct comparisons in pathfinding
sa = SifAssembler(stmts)
sa.make_model(use_name_as_key=True, include_mods=True,
include_complexes=True)
sif_str = sa.print_model(include_unsigned_edges=True)
with open('%s_pysb.sif' % base_file, 'wt') as f:
f.write(sif_str)
# This is the "final" set of statements going into the assembler so it
# makes sense to cache these.
# This is also the point where index cards can be generated
ac.dump_statements(stmts, '%s_before_pa.pkl' % base_file)
assemble_index_cards(stmts, 'output/index_cards')
# Save a version of statements with no evidence for faster loading
for s in stmts:
s.evidence = []
for ss in s.supports + s.supported_by:
ss.evidence = []
ac.dump_statements(stmts, '%s_no_evidence.pkl' % base_file)
# Assemble model
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model(reverse_effects=False)
#ac.dump_statements(pa.statements, '%s_after_pa.pkl' % base_file)
# Set context
set_context(pa)
# Add observables
add_observables(pa.model)
pa.save_model(out_file)
with open('korkut_pysb.pkl', 'wb') as fh:
pickle.dump(pa.model, fh)
#pa.export_model('kappa', '%s.ka' % base_file)
return pa.model
def post(self):
"""Assemble INDRA Statements into a Loopy model using SIF Assembler.
Parameters
----------
statements : list[indra.statements.Statement.to_json()]
A list of INDRA Statements to assemble.
Returns
-------
loopy_url : str
Assembled Loopy model string.
"""
args = request.json
stmts_json = args.get('statements')
stmts = stmts_from_json(stmts_json)
sa = SifAssembler(stmts)
sa.make_model(use_name_as_key=True)
model_str = sa.print_loopy(as_url=True)
res = {'loopy_url': model_str}
return res
from indra.util import _require_python3
from indra.assemblers.sif import SifAssembler
import indra.tools.assemble_corpus as ac
stmts = ac.load_statements('output/preassembled.pkl')
stmts = ac.filter_belief(stmts, 0.95)
stmts = ac.filter_direct(stmts)
sa = SifAssembler(stmts)
sa.make_model(True, True, False)
sa.set_edge_weights('support_all')
fname = 'model_high_belief_v2.sif'
with open(fname, 'wt') as fh:
for s, t, d in sa.graph.edges(data=True):
source = sa.graph.nodes[s]['name']
target = sa.graph.nodes[t]['name']
fh.write('%s %f %s\n' % (source, d['weight'], target))
def assemble_sif(stmts, data, out_file):
"""Return an assembled SIF."""
# Filter for high-belief statements
stmts = ac.filter_belief(stmts, 0.99)
stmts = ac.filter_top_level(stmts)
# Filter for Activation / Inhibition
stmts_act = ac.filter_by_type(stmts, Activation)
stmts_inact = ac.filter_by_type(stmts, Inhibition)
stmts = stmts_act + stmts_inact
# Get Ras227 and filter statments
ras_genes = process_data.get_ras227_genes()
#ras_genes = [x for x in ras_genes if x not in ['YAP1']]
stmts = ac.filter_gene_list(stmts, ras_genes, 'all')
# Get the drugs inhibiting their targets as INDRA
# statements
def get_drug_statements():
drug_targets = process_data.get_drug_targets()
drug_stmts = []
for dn, tns in drug_targets.items():
da = Agent(dn + ':Drugs')
for tn in tns:
ta = Agent(tn)
drug_stmt = Inhibition(da, ta)
drug_stmts.append(drug_stmt)
return drug_stmts
drug_stmts = get_drug_statements()
stmts = stmts + drug_stmts
# Rewrite statements to replace genes with their corresponding
# antibodies when possible
stmts = rewrite_ab_stmts(stmts, data)
def filter_ab_edges(st, policy='all'):
st_out = []
for s in st:
if policy == 'all':
all_ab = True
for a in s.agent_list():
if a is not None:
if a.name.find('_p') == -1 and \
a.name.find('Drugs') == -1:
all_ab = False
break
if all_ab:
st_out.append(s)
elif policy == 'one':
any_ab = False
for a in s.agent_list():
if a is not None and a.name.find('_p') != -1:
any_ab = True
break
if any_ab:
st_out.append(s)
return st_out
stmts = filter_ab_edges(stmts, 'all')
# Get a list of the AB names that end up being covered in the prior network
# This is important because other ABs will need to be taken out of the
# MIDAS file to work.
def get_ab_names(st):
prior_abs = set()
for s in st:
for a in s.agent_list():
if a is not None:
if a.name.find('_p') != -1:
prior_abs.add(a.name)
return sorted(list(prior_abs))
pkn_abs = get_ab_names(stmts)
def get_drug_names(st):
prior_drugs = set()
for s in st:
for a in s.agent_list():
if a is not None:
if a.name.find('Drugs') != -1:
prior_drugs.add(a.name.split(':')[0])
return sorted(list(prior_drugs))
pkn_drugs = get_drug_names(stmts)
print('Boolean PKN contains these antibodies: %s' % ', '.join(pkn_abs))
# Because of a bug in CNO,
# node names containing AND need to be replaced
# node names containing - need to be replaced
# node names starting in a digit need to be replaced
# must happen before SIF assembly, but not sooner as that will drop
# names from the MIDAS file
def rename_nodes(st):
for s in st:
for a in s.agent_list():
if a is not None:
if a.name.find('AND') != -1:
a.name = a.name.replace('AND', 'A_ND')
if a.name.find('-') != -1:
a.name = a.name.replace('-', '_')
if a.name[0].isdigit():
a.name = 'abc_' + a.name
rename_nodes(stmts)
# Make the SIF model
sa = SifAssembler(stmts)
sa.make_model(use_name_as_key=True)
sif_str = sa.print_model()
# assemble and dump a cx of the sif
ca = CxAssembler()
ca.add_statements(stmts)
model = ca.make_model()
ca.save_model('sif.cx')
with open(out_file, 'wb') as fh:
fh.write(sif_str.encode('utf-8'))
# Make the MIDAS data file used for training the model
midas_data = process_data.get_midas_data(data, pkn_abs, pkn_drugs)
return sif_str
coll = boolean2.util.Collector()
bn_str = boolean2.modify_states(bn_str, turnon=on, turnoff=off)
model = boolean2.Model(text=bn_str, mode='async')
for i in range(nsim):
model.initialize()
model.iterate(steps=nsteps)
coll.collect(states=model.states, nodes=model.nodes)
avgs = coll.get_averages(normalize=True)
return avgs
if __name__ == '__main__':
# Build Boolean net for basic pathway
st = ac.load_statements('ras_pathway.pkl')
sa = SifAssembler(st)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway.sif')
bn_str = sa.print_boolean_net('ras_pathway_bn.txt')
# Build Boolean net for extended pathway
st_ext = ac.load_statements('ras_pathway_extension.pkl')
sa = SifAssembler(st + st_ext)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway_extension.sif')
bn_str = sa.print_boolean_net('ras_pathway_extension_bn.txt')
# Condition 1
off = []
on = ['GROWTH-FACTOR']
avgs = get_sim_avgs(bn_str, off=off, on=on)
jun_basic_noinh = avgs['JUN']
coll = boolean2.util.Collector()
bn_str = boolean2.modify_states(bn_str, turnon=on, turnoff=off)
model = boolean2.Model(text=bn_str, mode='async')
for i in range(nsim):
model.initialize()
model.iterate(steps=nsteps)
coll.collect(states=model.states, nodes=model.nodes)
avgs = coll.get_averages(normalize=True)
return avgs
if __name__ == '__main__':
# Build Boolean net for basic pathway
st = ac.load_statements('ras_pathway.pkl')
sa = SifAssembler(st)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway.sif')
bn_str = sa.print_boolean_net('ras_pathway_bn.txt')
# Build Boolean net for extended pathway
st_ext = ac.load_statements('ras_pathway_extension.pkl')
sa = SifAssembler(st + st_ext)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway_extension.sif')
bn_str = sa.print_boolean_net('ras_pathway_extension_bn.txt')
# Condition 1
off = []
on = ['GROWTH-FACTOR']
avgs = get_sim_avgs(bn_str, off=off, on=on)
jun_basic_noinh = avgs['JUN']