def simple_kp(self, run=False):
sub_directory = os.getcwd()
for ligand_directory in self.ligand_directories:
if ligand_directory == "Ls":
kp_ligand = KPParameterTest(arguments=self.arguments)
self.self_file_list.append("{0}/".format(ligand_directory))
else:
kp_ligand = KPParameterTest(self_foreign=True,
arguments=self.arguments)
self.foreign_file_list.append("{0}/".format(ligand_directory))
self.file_list = self.foreign_file_list + self.self_file_list
make_and_cd(ligand_directory)
kp_ligand.ligand.add_step_0()
self.add_steps(kp_ligand)
kp_ligand.generate(kp_ligand.ligand.simulation_name,
kp_ligand.set_time_step())
if run:
(stdout,
stderr) = subprocess.Popen(["qsub {0}".format("qsub.sh")],
shell=True,
stdout=subprocess.PIPE,
cwd=os.getcwd()).communicate()
os.chdir(sub_directory)
if run:
self.wait_for_simulations()
self.compute_hopfield_error()
def create_submit(self, count, param_grid):
file_path = "{0}_step_{1}".format(self.steps, count)
self.paths.append(file_path)
print("param_grid " + str(param_grid))
self.parameters.append(str(param_grid))
make_and_cd(file_path)
self.make_launch_simulations(param_grid)
os.chdir(self.home_directory)
def make_launch_simulations(self, set):
home = os.getcwd()
for directory in self.sub_directories:
make_and_cd(directory)
pickle_out = open("parameters.pickle", "wb")
pickle.dump(set, pickle_out)
pickle_out.close()
if directory == "Ls_Lf_{0}".format(self.lf):
self.generate_qsub(self_foreign=True)
else:
self.generate_qsub()
if args.run:
self.launch()
os.chdir(home)
def p_test(self):
# make_and_cd(self.sub_directory)
home_directory = os.getcwd()
for d_zap in self.zap_diffusion:
make_and_cd("d_zap_{0}".format(d_zap))
if self.sub_directory == "Ls":
kp = KpMembraneSpecies(arguments=args)
else:
kp = KpMembraneSpecies(self_foreign=True, arguments=args)
kp.ligand.diffusion_constants.d_zap = d_zap
kp.main_script(run=args.run)
os.chdir(home_directory)
def parameter_testing(self, run=False):
home_directory = os.getcwd()
for i in range(len(self.parameter_list)):
dir_name = "parameter_{0}".format(i)
make_and_cd(dir_name)
sub_directory = os.getcwd()
for ligand_directory in self.ligand_directories:
if ligand_directory == "Ls":
kp_ligand = KPParameterTest(arguments=self.arguments)
self.self_file_list.append("{0}/{1}/".format(
dir_name, ligand_directory))
else:
kp_ligand = KPParameterTest(self_foreign=True,
arguments=self.arguments)
self.foreign_file_list.append("{0}/{1}/".format(
dir_name, ligand_directory))
self.file_list = self.foreign_file_list + self.self_file_list
make_and_cd(ligand_directory)
self.change_parameter(kp_ligand, self.parameter_list[i])
# kp_ligand.ligand.rate_constants.k_lck_off_zap_R = self.parameter_list[i]
kp_ligand.ligand.add_step_0()
self.add_steps(kp_ligand)
kp_ligand.generate(kp_ligand.ligand.simulation_name,
kp_ligand.set_time_step())
if run:
(stdout,
stderr) = subprocess.Popen(["qsub {0}".format("qsub.sh")],
shell=True,
stdout=subprocess.PIPE,
cwd=os.getcwd()).communicate()
os.chdir(sub_directory)
os.chdir(home_directory)
np.savetxt("rates", self.parameter_list, fmt='%f')
if run:
self.wait_for_simulations()
self.compute_hopfield_error(parameter_test=True)
default=0,
help="number of KP steps.")
parser.add_argument('--ls',
action='store_true',
default=False,
help="flag for submitting Ls calculations.")
parser.add_argument('--ls_lf',
dest='ls_lf',
action='store',
type=int,
default=3,
help="number of foreign ligands.")
args = parser.parse_args()
directory_name = "{0}_step".format(args.steps)
make_and_cd(directory_name)
if args.ls:
sub_directory = "Ls"
make_and_cd(sub_directory)
kp = KPRealisticSingleMolecule(arguments=args)
elif args.ls_lf:
sub_directory = "Ls_Lf"
# make_and_cd(sub_directory)
kp = KPRealisticSingleMolecule(self_foreign=True, arguments=args)
else:
raise Exception("Need to specify Ls or Ls_Lf")
kp.main_script(run=args.run)
q.write("python ~/SSC_python_modules/pysb_sos_fb.py --run\n")
q.close()
def launch(self):
(stdout, stderr) = subprocess.Popen(["qsub {0}".format("qsub.sh")],
shell=True,
stdout=subprocess.PIPE,
cwd=os.getcwd()).communicate()
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description="Submitting ode calculations as function of steps",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--run',
action='store_true',
default=False,
help='Flag for submitting simulations.')
args = parser.parse_args()
if not args.run:
make_and_cd("Ras_SoS_Fb_200")
qsub = LaunchQsub()
qsub.generate_qsub()
qsub.launch()
else:
sos = SoSFeedback()
sos.main()
default=False,
help="flag for early positive feedback loop.")
parser.add_argument('--latpp_ext',
dest='latpp_ext',
action='store_true',
default=False,
help="flag for building latpp bound tcr network.")
parser.add_argument('--toy_model',
dest='toy_model',
action='store_true',
default=False,
help="flag for running toy model calculations.")
args = parser.parse_args()
make_and_cd("{0}_step".format(args.steps))
sub_directories = ["Ls", "Ls_Lf_{0}".format(args.lf)]
home_directory = os.getcwd()
for directory in sub_directories:
if directory in os.listdir(".."):
continue
make_and_cd(directory)
if directory == "Ls_Lf_{0}".format(args.lf):
if args.early_pos:
qsub = LaunchQsub(args.steps,
lf=args.lf,
self_foreign=True,
early_pos=True)