def bng_simulate(model, times, method='ode', output_dir='/tmp', cleanup=True):
"""
Simulate a model with BNG's simulator and return the trajectories.
Adapted from pysb.bng.run_ssa.
Parameters
----------
model : pysb.Model or string
Model to simulate. Can be either a pysb.Model or a string representing
BNGL model.
times: list of floats
Sample times.
method: string
'ode' or 'ssa'
output_dir : string, optional
Location for temporary files generated by BNG. Defaults to '/tmp'.
cleanup : bool, optional
If True (default), delete the temporary files after the simulation is
finished. If False, leave them in place (in `output_dir`). Useful for
debugging.
"""
times = list(times)
run_ssa_code = """
begin actions
generate_network({overwrite=>1});
simulate_%s({sample_times=>%s});\n
end actions
""" % (method, times)
if not isinstance(model, str):
model = BngGenerator(model).get_content()
bng_filename = '%d_%d_temp.bngl' % (
os.getpid(), random.randint(0, 10000))
gdat_filename = bng_filename.replace('.bngl', '.gdat')
cdat_filename = bng_filename.replace('.bngl', '.cdat')
net_filename = bng_filename.replace('.bngl', '.net')
try:
working_dir = os.getcwd()
os.chdir(output_dir)
bng_file = open(bng_filename, 'w')
bng_file.write(model)
bng_file.write(run_ssa_code)
bng_file.close()
p = subprocess.Popen(['perl', _get_bng_path(), bng_filename],
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(p_out, p_err) = p.communicate()
if p.returncode:
raise GenerateNetworkError(p_out.rstrip("at line") + "\n" +
p_err.rstrip())
output_arr = _parse_bng_outfile(gdat_filename)
finally:
if cleanup:
for filename in [bng_filename, gdat_filename,
cdat_filename, net_filename]:
if os.access(filename, os.F_OK):
os.unlink(filename)
os.chdir(working_dir)
return output_arr
def sbml_translator(input_file,
output_file=None,
convention_file=None,
naming_conventions=None,
user_structures=None,
molecule_id=False,
atomize=False,
pathway_commons=False,
verbose=False):
"""
Runs the BioNetGen sbmlTranslator binary.
For more descriptions of the arguments, see the `sbmlTranslator
documentation <http://bionetgen.org/index.php/SBML2BNGL>`_.
Parameters
----------
input_file : string
SBML input filename
output_file : string, optional
BNGL output filename
convention_file : string, optional
Conventions filename
naming_conventions : string, optional
Naming conventions filename
user_structures : string, optional
User structures filename
molecule_id : bool, optional
Use SBML molecule IDs (True) or names (False).
IDs are less descriptive but more BNGL friendly. Use only if the
generated BNGL has syntactic errors
atomize : bool, optional
Atomize the model, i.e. attempt to infer molecular structure and
build rules from the model (True) or just perform a flat import (False)
pathway_commons : bool, optional
Use pathway commons to infer molecule binding. This
setting requires an internet connection and will query the pathway
commons web service.
verbose : bool, optional
Print the SBML conversion output to the console if True
Returns
-------
string
BNGL output filename
"""
sbmltrans_bin = os.path.join(os.path.dirname(_get_bng_path()),
'bin/sbmlTranslator')
sbmltrans_args = [sbmltrans_bin, '-i', input_file]
if output_file is None:
output_file = os.path.splitext(input_file)[0] + '.bngl'
sbmltrans_args.extend(['-o', output_file])
if convention_file:
sbmltrans_args.extend(['-c', convention_file])
if naming_conventions:
sbmltrans_args.extend(['-n', naming_conventions])
if user_structures:
sbmltrans_args.extend(['-u', user_structures])
if molecule_id:
sbmltrans_args.append('-id')
if atomize:
sbmltrans_args.append('-a')
if pathway_commons:
sbmltrans_args.append('-p')
if verbose:
print("sbmlTranslator command:")
print(" ".join(sbmltrans_args))
p = subprocess.Popen(sbmltrans_args,
cwd=os.getcwd(),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
if verbose:
for line in iter(p.stdout.readline, b''):
print(line, end="")
(p_out, p_err) = p.communicate()
if p.returncode:
raise SbmlTranslationError(p_out.decode('utf-8') + "\n" +
p_err.decode('utf-8'))
return output_file
