def to_english(self):
cond = _assemble_agent_str(self.condition_entity).agent_str
target = _assemble_agent_str(self.target_entity).agent_str
if self.direction == 'up':
dir_verb = 'increases'
else:
dir_verb = 'decreases'
return f'{cond} {dir_verb} {target}.'
def to_english(self):
source_str = _assemble_agent_str(self.source)
target_str = _assemble_agent_str(self.target)
sb = SentenceBuilder()
if self.relation == 'is_ref':
rel_str = ' is a refinement of '
elif self.relation == 'has_ref':
rel_str = ' has a refinement '
sb.append_as_sentence([source_str, rel_str, target_str])
sb.make_sentence()
return sb.sentence
def test_agent_bound_mixed():
bc = BoundCondition(Agent('EGF'), True)
bc2 = BoundCondition(Agent('EGFR'), False)
a = Agent('EGFR', bound_conditions=[bc, bc2])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR bound to EGF and not bound to EGFR')
def plot_results(self, results, agent, obs_name, thresh=50):
plt.figure()
plt.ion()
max_val_lim = max(
max((numpy.max(results[0][1][obs_name]) +
0.25 * numpy.max(results[0][1][obs_name])), 101.0), thresh)
max_time = max([result[0][-1] for result in results])
lr = matplotlib.patches.Rectangle((0, 0),
max_time,
thresh,
color='red',
alpha=0.1)
hr = matplotlib.patches.Rectangle((0, thresh),
max_time,
max_val_lim - thresh,
color='green',
alpha=0.1)
ax = plt.gca()
ax.add_patch(lr)
ax.add_patch(hr)
if thresh + 0.05 * max_val_lim < max_val_lim:
plt.text(10, thresh + 0.05 * max_val_lim, 'High', fontsize=10)
plt.text(10, thresh - 0.05 * max_val_lim, 'Low')
for tspan, yobs in results:
plt.plot(tspan, yobs[obs_name])
plt.ylim(-5, max_val_lim)
plt.xlim(-100, 10100)
plt.xlabel('Time (s)')
plt.ylabel('Amount (molecules)')
agent_str = english_assembler._assemble_agent_str(agent).agent_str
plt.title('Simulation results for %s' % agent_str)
fig_path = get_img_path(obs_name + '.png')
plt.savefig(fig_path)
return fig_path
def test_agent_mod3():
mc = ModCondition('phosphorylation', 'tyrosine', '1111')
a = Agent('EGFR', mods=mc)
ag = ea._assemble_agent_str(a)
print(ag.agent_str)
assert ag.agent_str == 'EGFR phosphorylated on Y1111'
assert _substring_by_coords(ag.agent_str, ag.coords) == 'EGFR'
def test_agent_mods3():
mc1 = ModCondition('phosphorylation', 'tyrosine', '1111')
mc2 = ModCondition('phosphorylation')
a = Agent('EGFR', mods=[mc1, mc2])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR phosphorylated on Y1111 and an unknown residue')
def test_agent_mods_pos_only():
mc1 = ModCondition('phosphorylation', None, '1111')
a = Agent('EGFR', mods=[mc1])
ag = ea._assemble_agent_str(a)
print(ag.agent_str)
assert ag.agent_str == 'EGFR phosphorylated on amino acid 1111'
assert _substring_by_coords(ag.agent_str, ag.coords) == 'EGFR'
def test_agent_not_bound():
bc = BoundCondition(Agent('EGF'), False)
a = Agent('EGFR', bound_conditions=[bc])
ag = ea._assemble_agent_str(a)
print(ag.agent_str)
assert ag.agent_str == 'EGFR not bound to EGF'
assert _substring_by_coords(ag.agent_str, ag.coords) == 'EGFR'
def test_agent_mods3():
mc1 = ModCondition('phosphorylation', 'tyrosine', '1111')
mc2 = ModCondition('phosphorylation')
a = Agent('EGFR', mods=[mc1, mc2])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR phosphorylated on Y1111 and an unknown residue')
def test_agent_bound_mixed():
bc = BoundCondition(Agent('EGF'), True)
bc2 = BoundCondition(Agent('EGFR'), False)
a = Agent('EGFR', bound_conditions=[bc, bc2])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR bound to EGF and not bound to EGFR')
def plot_results(self, results, agent, obs_name, thresh=50):
plt.figure()
plt.ion()
max_val_lim = max(max(numpy.max(results[0][1][obs_name]), 101.0),
thresh)
max_time = max([result[0][-1] for result in results])
lr = matplotlib.patches.Rectangle((0, 0), max_time, thresh, color='red',
alpha=0.1)
hr = matplotlib.patches.Rectangle((0, thresh), max_time,
max_val_lim-thresh,
color='green', alpha=0.1)
ax = plt.gca()
ax.add_patch(lr)
ax.add_patch(hr)
if thresh + 5 < max_val_lim:
plt.text(10, thresh + 5, 'High', fontsize=10)
plt.text(10, thresh - 5, 'Low')
for tspan, yobs in results:
plt.plot(tspan, yobs[obs_name])
plt.ylim(-1, max_val_lim)
plt.xlim(-100, 10100)
plt.xlabel('Time (s)')
plt.ylabel('Amount (molecules)')
agent_str = english_assembler._assemble_agent_str(agent)
plt.title('Simulation results for %s' % agent_str)
fig_path = get_img_path(obs_name + '.png')
plt.savefig(fig_path)
return fig_path
def test_agent_bound_three():
bc = BoundCondition(Agent('EGF'), True)
bc2 = BoundCondition(Agent('EGFR'), True)
bc3 = BoundCondition(Agent('GRB2'), True)
a = Agent('EGFR', bound_conditions=[bc, bc2, bc3])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR bound to EGF, EGFR and GRB2')
def pybel_edge_to_english(pybel_edge):
source_str = _assemble_agent_str(pybel_edge.source)
target_str = _assemble_agent_str(pybel_edge.target)
sb = SentenceBuilder()
if pybel_edge.relation == 'partOf':
if pybel_edge.reverse:
rel_str = ' has a component '
else:
rel_str = ' is a part of '
elif pybel_edge.relation == 'hasVariant':
if pybel_edge.reverse:
rel_str = ' is a variant of '
else:
rel_str = ' has a variant '
sb.append_as_sentence([source_str, rel_str, target_str])
sb.make_sentence()
return sb.sentence
def test_agent_bound_mixed():
bc = BoundCondition(Agent('EGF'), True)
bc2 = BoundCondition(Agent('EGFR'), False)
a = Agent('EGFR', bound_conditions=[bc, bc2])
ag = ea._assemble_agent_str(a)
print(ag.agent_str)
assert ag.agent_str == 'EGFR bound to EGF and not bound to EGFR'
assert _substring_by_coords(ag.agent_str, ag.coords) == 'EGFR'
def test_agent_mods3():
mc1 = ModCondition('phosphorylation', 'tyrosine', '1111')
mc2 = ModCondition('phosphorylation')
a = Agent('EGFR', mods=[mc1, mc2])
ag = ea._assemble_agent_str(a)
print(ag.agent_str)
assert ag.agent_str == 'EGFR phosphorylated on Y1111 and an unknown residue'
assert ag.agent_str[ag.coords[0]:ag.coords[1]] == 'EGFR'
def test_agent_mut_plus():
a = Agent('BRAF',
mutations=[MutCondition('600', 'V', 'E')],
location='nucleus')
ag = ea._assemble_agent_str(a)
print(ag.agent_str)
assert ag.agent_str == 'BRAF-V600E in the nucleus'
assert _substring_by_coords(ag.agent_str, ag.coords) == 'BRAF'
def test_agent_bound_three():
bc = BoundCondition(Agent('EGF'), True)
bc2 = BoundCondition(Agent('EGFR'), True)
bc3 = BoundCondition(Agent('GRB2'), True)
a = Agent('EGFR', bound_conditions=[bc, bc2, bc3])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR bound to EGF, EGFR and GRB2')
def test_agent_mods():
mc1 = ModCondition('phosphorylation', 'tyrosine', '1111')
mc2 = ModCondition('phosphorylation', 'tyrosine', '1234')
a = Agent('EGFR', mods=[mc1, mc2])
ag = ea._assemble_agent_str(a)
print(ag.agent_str)
assert ag.agent_str == 'EGFR phosphorylated on Y1111 and Y1234'
assert _substring_by_coords(ag.agent_str, ag.coords) == 'EGFR'
def test_agent_bound_three():
bc = BoundCondition(Agent('EGF'), True)
bc2 = BoundCondition(Agent('EGFR'), True)
bc3 = BoundCondition(Agent('GRB2'), True)
a = Agent('EGFR', bound_conditions=[bc, bc2, bc3])
ag = ea._assemble_agent_str(a)
print(ag.agent_str)
assert ag.agent_str == 'EGFR bound to EGF, EGFR, and GRB2'
assert _substring_by_coords(ag.agent_str, ag.coords) == 'EGFR'
def plot_compare_conditions(self, ts, results, agent, obs_name):
plt.figure()
plt.ion()
plt.plot(ts, results[0][:len(ts)], label='Without condition')
plt.plot(ts, results[-1][:len(ts)], label='With condition')
plt.xlabel('Time (s)')
plt.ylabel('Amount (molecules)')
agent_str = english_assembler._assemble_agent_str(agent).agent_str
plt.title('Simulation results for %s' % agent_str)
plt.legend()
fig_path = get_img_path(obs_name + '.png')
plt.savefig(fig_path)
return fig_path
def plot_compare_conditions(self, ts, results, agent, obs_name):
plt.figure()
plt.ion()
plt.plot(ts, results[0][:len(ts)], label='Without condition')
plt.plot(ts, results[-1][:len(ts)], label='With condition')
plt.xlabel('Time (s)')
plt.ylabel('Amount (molecules)')
agent_str = english_assembler._assemble_agent_str(agent)
plt.title('Simulation results for %s' % agent_str)
plt.legend()
fig_path = get_img_path(obs_name + '.png')
plt.savefig(fig_path)
return fig_path
def to_english(self):
agent = _assemble_agent_str(self.entity).agent_str
if self.entity_role == 'subject':
verb = statement_base_verb(self.stmt_type.lower())
verb = verb[0].lower() + verb[1:]
sentence = f'What does {agent} {verb}?'
elif self.entity_role == 'object':
verb = statement_present_verb(self.stmt_type.lower())
verb = verb[0].lower() + verb[1:]
sentence = f'What {verb} {agent}?'
sentence = sentence[0].upper() + sentence[1:]
if self.terminal_ns:
sentence += f' ({", ".join(self.terminal_ns).upper()})'
return sentence
def to_english(self):
agent = _assemble_agent_str(self.entity).agent_str
agent = agent[0].upper() + agent[1:]
if self.pattern_type == 'always_value':
pattern = 'always'
elif self.pattern_type == 'eventual_value':
pattern = 'eventually'
elif self.pattern_type == 'sometime_value':
pattern = 'sometimes'
elif self.pattern_type == 'no_change':
pattern = 'not changing'
else:
pattern = self.pattern_type
if self.quant_value:
return f'{agent} is {pattern} {self.quant_value}.'
return f'{agent} is {pattern}.'
def test_agent_mut():
a = Agent('BRAF', mutations=[MutCondition('600','V', 'E')])
print(ea._assemble_agent_str(a))
assert ea._assemble_agent_str(a) == 'BRAF-V600E'
def test_agent_not_bound():
bc = BoundCondition(Agent('EGF'), False)
a = Agent('EGFR', bound_conditions=[bc])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR not bound to EGF')
def test_agent_not_bound():
bc = BoundCondition(Agent('EGF'), False)
a = Agent('EGFR', bound_conditions=[bc])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR not bound to EGF')
def test_agent_mut_plus():
a = Agent('BRAF', mutations=[MutCondition('600','V', 'E')],
location='nucleus')
print(ea._assemble_agent_str(a))
assert ea._assemble_agent_str(a) == 'BRAF-V600E in the nucleus'
def test_agent_basic():
s = ea._assemble_agent_str(Agent('EGFR'))
print(s)
assert (s == 'EGFR')
def test_agent_mod3():
mc = ModCondition('phosphorylation', 'tyrosine', '1111')
a = Agent('EGFR', mods=mc)
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR phosphorylated on Y1111')
def test_agent_mod3():
mc = ModCondition('phosphorylation', 'tyrosine', '1111')
a = Agent('EGFR', mods=mc)
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR phosphorylated on Y1111')
def test_agent_mut():
a = Agent('BRAF', mutations=[MutCondition('600', 'V', 'E')])
print(ea._assemble_agent_str(a))
assert ea._assemble_agent_str(a) == 'BRAF-V600E'
def test_agent_mut_plus():
a = Agent('BRAF',
mutations=[MutCondition('600', 'V', 'E')],
location='nucleus')
print(ea._assemble_agent_str(a))
assert ea._assemble_agent_str(a) == 'BRAF-V600E in the nucleus'
def test_agent_mut():
a = Agent('BRAF', mutations=[MutCondition('600', 'V', 'E')])
ag = ea._assemble_agent_str(a)
print(ag.agent_str)
assert ag.agent_str == 'BRAF-V600E'
assert _substring_by_coords(ag.agent_str, ag.coords) == 'BRAF'
def test_agent_loc():
a = Agent('BRAF', location='cytoplasm')
print(ea._assemble_agent_str(a))
assert ea._assemble_agent_str(a) == 'BRAF in the cytoplasm'
def test_agent_basic():
s = ea._assemble_agent_str(Agent('EGFR'))
print(s)
assert (s == 'EGFR')
def test_agent_activity():
a = Agent('BRAF', activity=ActivityCondition('activity', True))
print(ea._assemble_agent_str(a))
assert ea._assemble_agent_str(a) == 'active BRAF'
def test_agent_basic():
ag = ea._assemble_agent_str(Agent('EGFR'))
assert isinstance(ag, ea.AgentWithCoordinates)
print(ag.agent_str)
assert ag.agent_str == 'EGFR'
assert _substring_by_coords(ag.agent_str, ag.coords) == 'EGFR'
def test_agent_loc():
a = Agent('BRAF', location='cytoplasm')
print(ea._assemble_agent_str(a))
assert ea._assemble_agent_str(a) == 'BRAF in the cytoplasm'
def test_agent_activity():
a = Agent('BRAF', activity=ActivityCondition('activity', True))
print(ea._assemble_agent_str(a))
assert ea._assemble_agent_str(a) == 'active BRAF'
def test_agent_mods_pos_only():
mc1 = ModCondition('phosphorylation', None, '1111')
a = Agent('EGFR', mods=[mc1])
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'EGFR phosphorylated on amino acid 1111')
def test_agent_mod():
mc = ModCondition('phosphorylation')
a = Agent('EGFR', mods=mc)
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'phosphorylated EGFR')
def test_agent_activity():
a = Agent('BRAF', activity=ActivityCondition('activity', True))
ag = ea._assemble_agent_str(a)
print(ag.agent_str)
assert ag.agent_str == 'active BRAF'
assert _substring_by_coords(ag.agent_str, ag.coords) == 'BRAF'
def test_agent_mod():
mc = ModCondition('phosphorylation')
a = Agent('EGFR', mods=mc)
s = ea._assemble_agent_str(a)
print(s)
assert (s == 'phosphorylated EGFR')
