def main(argv):
if len(sys.argv) != 3:
print "Usage: %s model_filename cm_filename" % __file__
return 1
model_filename = argv[1]
cm_filename = argv[2]
# Sanity checks on filename
if not os.path.exists(model_filename):
raise Exception("File '%s' doesn't exist" % model_filename)
if not re.search(r'\.py$', model_filename):
raise Exception("File '%s' is not a .py file" % model_filename)
sys.path.insert(0, os.path.dirname(model_filename))
model_name = re.sub(r'\.py$', '', os.path.basename(model_filename))
# import it
try:
# FIXME if the model has the same name as some other "real" module
# which we use, there will be trouble (use the imp package and import
# as some safe name?)
model_module = __import__(model_name)
except StandardError as e:
print "Error in model script:\n"
raise
# grab the 'model' variable from the module
try:
model = model_module.__dict__['model']
except KeyError:
raise Exception("File '%s' isn't a model file" % model_filename)
# Make the contact map
kappa.contact_map(model, base_filename=cm_filename)
return 0
def make_contact_map(pysb_model, model_id):
"""Generate a Kappa contact map."""
try:
cm = kappa.contact_map(pysb_model)
fname = 'model%d_cm' % model_id
abs_path = os.path.abspath(os.getcwd())
full_path = os.path.join(abs_path, fname + '.png')
cm.draw(full_path, prog='dot')
except Exception:
return None
return full_path
lopez_modules.momp_monomers()
Observable('aBax', Bax(state='A'))
Observable('cSmac', Smac(state='C'))
# The specific MOMP model to use
lopez_modules.embedded(do_pore_transport=False)
# Set Bid initial condition to be tBid
model.update_initial_condition_pattern(Bid(state='U', bf=None),
Bid(state='T', bf=None))
# Get rid of CytoC and Smac
model.parameters['Smac_0'].value = 0
model.parameters['CytoC_0'].value = 0
# Put some Noxa at the membrane
Initial(Noxa(state='M', bf=None), Parameter('mNoxa_0', 1))
Initial(Bad(state='M', bf=None), Parameter('mBad_0', 1))
# Generate the contact map
output_dir = os.path.abspath(os.path.dirname(__file__))
contact_map(model, output_dir, 'fig5d')
try:
# Remove the extra output files we don't need
os.unlink('fig5d.ka')
os.unlink('fig5d_cm.jpg')
except OSError:
pass
print()
print("Generated fig5d_cm.dot in", output_dir)
lopez_modules.momp_monomers()
Observable('aBax', Bax(state='A'))
Observable('cSmac', Smac(state='C'))
# The specific MOMP model to use
lopez_modules.embedded(do_pore_transport=False)
# Set Bid initial condition to be tBid
model.update_initial_condition_pattern(Bid(state='U', bf=None),
Bid(state='T', bf=None))
# Get rid of CytoC and Smac
model.parameters['Smac_0'].value = 0
model.parameters['CytoC_0'].value = 0
# Put some Noxa at the membrane
Initial(Noxa(state='M', bf=None), Parameter('mNoxa_0', 1))
Initial(Bad(state='M', bf=None), Parameter('mBad_0', 1))
# Generate the contact map
output_dir = os.path.abspath(os.path.dirname(__file__))
contact_map(model, output_dir, 'fig5d')
try:
# Remove the extra output files we don't need
os.unlink('fig5d.ka')
os.unlink('fig5d_cm.jpg')
except OSError:
pass
print()
print("Generated fig5d_cm.dot in", output_dir)
