def test_nl_modeling():
# 1 code chunk
from indra.sources import trips
model_text = 'MAP2K1 phosphorylates MAPK1 and DUSP6 dephosphorylates MAPK1.'
tp = trips.process_text(model_text)
# 2nd code chunk
for st in tp.statements:
assert st.evidence[0].text # Replaces a print statement in the doc
# 3rd code chunk
from indra.assemblers.pysb import PysbAssembler
pa = PysbAssembler()
pa.add_statements(tp.statements)
pa.make_model(policies='two_step')
# 4th code chunk
for monomer in pa.model.monomers:
assert monomer # This replaces a print statements in the doc
# 5th code chunk
for rule in pa.model.rules:
assert rule # This replaces a print statements in the doc
# 6th code chunk
for parameter in pa.model.parameters:
assert parameter # This replaces a print statements in the doc
# 7th code chunk
for annotation in pa.model.annotations:
assert annotation # This replaces a print statements in the doc
# 8th code chunk (this code is currently in a commented out section)
pa.set_context('A375_SKIN')
for monomer_pattern, parameter in pa.model.initial_conditions:
assert monomer_pattern
assert parameter.value
# 9th code chunk
_ = pa.export_model('sbml')
assert _
_ = pa.export_model('bngl')
assert _
def contextualize_model(model, cell_line, genes):
"""Contextualize model at the level of a PySB model."""
# Here we just make a PysbAssembler to be able
# to apply set_context on the model being passed in
model.name = cell_line
cell_line_ccle = cell_line + '_SKIN'
pa = PysbAssembler()
pa.model = model
pa.set_context(cell_line_ccle)
# Set initial conditions for missense mutations
variants = read_ccle_variants(genes)
mutations = variants['missense'][cell_line_ccle]
for gene, mut_list in mutations.items():
for fres, loc, tres in mut_list:
site_name = fres + loc
for ic in model.initial_conditions:
if ic[0].monomer_patterns[0].monomer.name == gene:
sc = ic[0].monomer_patterns[0].site_conditions
if site_name in sc:
sc[site_name] = tres
return pa.model
