"""
Wrapper functions for running the Kappa programs *KaSim* and *KaSa*.
The path to the directory containing the KaSim and KaSa executables can be
specified in one of three ways:
- setting the KAPPAPATH environment variable to the KaSim directory
- setting the path using the :py:func:`set_kappa_path` function at runtime
- adding the path to the KaSim directory to the system PATH environment variable
"""
from __future__ import print_function as _
import pysb
from pysb.generator.kappa import KappaGenerator
import os
import subprocess
import random
import re
import sympy
import numpy as np
import tempfile
import shutil
import warnings
from collections import namedtuple
try:
from future_builtins import zip
except ImportError:
pass
# Cached value of Kappa program paths
_kasim_path = None
_kasa_path = None
def _check_dist_dir(kappa_prog, dist_dir):
kappa_prog_path = os.path.join(dist_dir, kappa_prog)
if os.access(kappa_prog_path, os.F_OK):
return kappa_prog_path
else:
return None
[docs]def set_kappa_path(path):
"""Set the path to the KaSim and KaSa executables.
Parameters
----------
path: string
Directory containing KaSim and Kasa executables.
"""
global _kasim_path
global _kasa_path
# Check locations of both KaSim and KaSa
kasim_path = _check_dist_dir('KaSim', path)
kasa_path = _check_dist_dir('KaSa', path)
# KaSim is required, so raise if we didn't find it.
if kasim_path is None:
raise Exception('Could not find KaSim in %s.' % os.path.abspath(path))
# KaSa is optional, so only warn if we didn't find it.
if kasa_path is None:
warnings.warn('Could not find KaSa in %s; install KaSa for static '
'analysis features.' % os.path.abspath(path))
_kasim_path = kasim_path
_kasa_path = kasa_path
def _get_kappa_path(kappa_prog):
"""
Return the path to the KaSim or KaSa executable.
Looks for a KaSim/KaSa distribution at the path stored in the KAPPAPATH
environment variable if that's set, or else in a few hard-coded standard
locations.
"""
if kappa_prog not in ['KaSim', 'KaSa']:
raise ValueError("kappa_prog must be one of 'KaSim', 'KaSa'.")
global _kasim_path
global _kasa_path
# Just return cached value if it's available
if kappa_prog == 'KaSim' and _kasim_path is not None:
return _kasim_path
elif kappa_prog == 'KaSa' and _kasa_path is not None:
return _kasa_path
path_var = 'KAPPAPATH'
dist_dirs = [
'/usr/local/share/KaSim',
'c:/Program Files/KaSim',
]
# First check the environment variable, which has the highest precedence
if path_var in os.environ:
kappapath = os.environ[path_var]
kappa_prog_path = _check_dist_dir(kappa_prog, kappapath)
if not kappa_prog_path:
raise Exception('Environment variable %s is set to "%s" but %s '
'could not be found there.' %
(path_var, kappapath, kappa_prog))
# If the environment variable isn't set, check the standard locations
else:
for dist_dir in dist_dirs:
kappa_prog_path = _check_dist_dir(kappa_prog, dist_dir)
if kappa_prog_path:
break
else:
raise Exception('Could not find %s installed in one of the '
'following locations:' % kappa_prog +
''.join('\n ' + d for d in dist_dirs) +
'\nSet the environment variable %s to the '
'directory containing KaSim and KaSa.' % path_var)
# Cache path for future use
if kappa_prog == 'KaSim':
_kasim_path = kappa_prog_path
elif kappa_prog == 'KaSa':
_kasa_path = kappa_prog_path
return kappa_prog_path
class KasimInterfaceError(RuntimeError):
pass
class KasaInterfaceError(RuntimeError):
pass
StaticAnalysisResult = namedtuple('StaticAnalysisResult',
['contact_map', 'influence_map'])
SimulationResult = namedtuple('SimulationResult',
['timecourse', 'flux_map'])
[docs]def run_simulation(model, time=10000, points=200, cleanup=True,
output_prefix=None, output_dir=None, flux_map=False,
perturbation=None, verbose=False):
"""Runs the given model using KaSim and returns the parsed results.
Parameters
----------
model : pysb.core.Model
The model to simulate/analyze using KaSim.
time : number
The amount of time (in arbitrary units) to run a simulation.
Identical to the -t argument when using KaSim at the command line.
Default value is 10000. If set to 0, no simulation will be run.
points : integer
The number of data points to collect for plotting.
Identical to the -p argument when using KaSim at the command line.
Default value is 200. Note that the number of points actually returned
by the simulator will be points + 1 (including the 0 point).
cleanup : boolean
Specifies whether output files produced by KaSim should be deleted
after execution is completed. Default value is True.
output_prefix: str
Prefix of the temporary directory name. Default is
'tmpKappa_<model name>_'.
output_dir : string
The directory in which to create the temporary directory for
the .ka and other output files. Defaults to the system temporary file
directory (e.g. /tmp). If the specified directory does not exist,
an Exception is thrown.
flux_map: boolean
Specifies whether or not to produce the flux map (generated over the
full duration of the simulation). Default value is False.
perturbation : string or None
Optional perturbation language syntax to be appended to the Kappa file.
See KaSim manual for more details. Default value is None (no
perturbation).
verbose : boolean
Whether to pass the output of KaSim through to stdout/stderr.
Returns
-------
If flux_map is False, returns the kasim simulation data as a Numpy ndarray.
Data is accessed using the syntax::
results[index_name]
The index 'time' gives the time coordinates of the simulation. Data for the
observables can be accessed by indexing the array with the names of the
observables. Each entry in the ndarray has length points + 1, due to the
inclusion of both the zero point and the final timepoint.
If flux_map is True, returns an instance of SimulationResult, a namedtuple
with two members, `timecourse` and `flux_map`. The `timecourse` field
contains the simulation ndarray, and the `flux_map` field is an instance of
a pygraphviz AGraph containing the flux map. The flux map can be rendered
as a pdf using the dot layout program as follows::
fluxmap.draw('fluxmap.pdf', prog='dot')
"""
gen = KappaGenerator(model)
if output_prefix is None:
output_prefix = 'tmpKappa_%s_' % model.name
base_directory = tempfile.mkdtemp(prefix=output_prefix, dir=output_dir)
base_filename = os.path.join(base_directory, model.name)
kappa_filename = base_filename + '.ka'
fm_filename = base_filename + '_fm.dot'
out_filename = base_filename + '.out'
args = ['-i', kappa_filename, '-t', str(time), '-p', str(points),
'-o', out_filename]
# Generate the Kappa model code from the PySB model and write it to
# the Kappa file:
with open(kappa_filename, 'w') as kappa_file:
kappa_file.write(gen.get_content())
# If desired, add instructions to the kappa file to generate the
# flux map:
if flux_map:
kappa_file.write('%%mod: [true] do $FLUX "%s" [true]\n' %
fm_filename)
# If any perturbation language code has been passed in, add it to
# the Kappa file:
if perturbation:
kappa_file.write('\n%s\n' % perturbation)
# Run KaSim
kasim_path = _get_kappa_path('KaSim')
p = subprocess.Popen([kasim_path] + args,
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 KasimInterfaceError(p_out + '\n' + p_err)
# The simulation data, as a numpy array
data = _parse_kasim_outfile(out_filename)
if flux_map:
try:
import pygraphviz
flux_graph = pygraphviz.AGraph(fm_filename)
except ImportError:
if cleanup:
raise RuntimeError(
"Couldn't import pygraphviz, which is "
"required to return the flux map as a "
"pygraphviz AGraph object. Either install "
"pygraphviz or set cleanup=False to retain "
"dot files.")
else:
warnings.warn(
"pygraphviz could not be imported so no AGraph "
"object returned (returning None); flux map "
"dot file available at %s" % fm_filename)
flux_graph = None
if cleanup:
shutil.rmtree(base_directory)
# If a flux map was generated, return both the simulation output and the
# flux map as a pygraphviz graph
if flux_map:
return SimulationResult(data, flux_graph)
# If no flux map was requested, return only the simulation data
else:
return data
[docs]def run_static_analysis(model, influence_map=False, contact_map=False,
cleanup=True, output_prefix=None, output_dir=None,
verbose=False):
"""Run static analysis (KaSa) on to get the contact and influence maps.
If neither influence_map nor contact_map are set to True, then a ValueError
is raised.
Parameters
----------
model : pysb.core.Model
The model to simulate/analyze using KaSa.
influence_map : boolean
Whether to compute the influence map.
contact_map : boolean
Whether to compute the contact map.
cleanup : boolean
Specifies whether output files produced by KaSa should be deleted
after execution is completed. Default value is True.
output_prefix: str
Prefix of the temporary directory name. Default is
'tmpKappa_<model name>_'.
output_dir : string
The directory in which to create the temporary directory for
the .ka and other output files. Defaults to the system temporary file
directory (e.g. /tmp). If the specified directory does not exist,
an Exception is thrown.
verbose : boolean
Whether to pass the output of KaSa through to stdout/stderr.
Returns
-------
StaticAnalysisResult, a namedtuple with two fields, `contact_map` and
`influence_map`, each containing the respective result as an instance
of a pygraphviz AGraph. If the either the contact_map or influence_map
argument to the function is False, the corresponding entry in the
StaticAnalysisResult returned by the function will be None.
"""
# Make sure the user has asked for an output!
if not influence_map and not contact_map:
raise ValueError('Either contact_map or influence_map (or both) must '
'be set to True in order to perform static analysis.')
gen = KappaGenerator(model, _warn_no_ic=False)
if output_prefix is None:
output_prefix = 'tmpKappa_%s_' % model.name
base_directory = tempfile.mkdtemp(prefix=output_prefix, dir=output_dir)
base_filename = os.path.join(base_directory, model.name)
kappa_filename = base_filename + '.ka'
im_filename = base_filename + '_im.dot'
cm_filename = base_filename + '_cm.dot'
# NOTE: in the args passed to KaSa, the directory for the .dot files is
# specified by the --output_directory option, and the output_contact_map
# and output_influence_map should only be the base filenames (without
# a directory prefix).
# Contact map args:
if contact_map:
cm_args = ['--compute-contact-map', '--output-contact-map',
os.path.basename(cm_filename)]
else:
cm_args = ['--no-compute-contact-map']
# Influence map args:
if influence_map:
im_args = ['--compute-influence-map', '--output-influence-map',
os.path.basename(im_filename)]
else:
im_args = ['--no-compute-influence-map']
# Full arg list
args = [kappa_filename, '--output-directory', base_directory] \
+ cm_args + im_args
# Generate the Kappa model code from the PySB model and write it to
# the Kappa file:
with open(kappa_filename, 'w') as kappa_file:
kappa_file.write(gen.get_content())
# Run KaSa using the given args
kasa_path = _get_kappa_path('KaSa')
p = subprocess.Popen([kasa_path] + args,
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 KasaInterfaceError(p_out + '\n' + p_err)
# Try to create the graphviz objects from the .dot files created
try:
import pygraphviz
# Convert the contact map to a Graph
cmap = pygraphviz.AGraph(cm_filename) if contact_map else None
imap = pygraphviz.AGraph(im_filename) if influence_map else None
except ImportError:
if cleanup:
raise RuntimeError(
"Couldn't import pygraphviz, which is "
"required to return the influence and contact maps "
" as pygraphviz AGraph objects. Either install "
"pygraphviz or set cleanup=False to retain "
"dot files.")
else:
warnings.warn(
"pygraphviz could not be imported so no AGraph "
"objects returned (returning None); "
"contact/influence maps available at %s" %
base_directory)
cmap = None
imap = None
# Clean up the temp directory if desired
if cleanup:
shutil.rmtree(base_directory)
return StaticAnalysisResult(cmap, imap)
[docs]def influence_map(model, **kwargs):
"""Generates the influence map via KaSa.
Parameters
----------
model : pysb.core.Model
The model for generating the influence map.
**kwargs : other keyword arguments
Any other keyword arguments are passed to the function
:py:func:`run_static_analysis`.
Returns
-------
pygraphviz AGraph object containing the influence map.
The influence map can be rendered as a pdf using the dot layout program
as follows::
influence_map.draw('influence_map.pdf', prog='dot')
"""
kasa_result = run_static_analysis(model, influence_map=True,
contact_map=False, **kwargs)
return kasa_result.influence_map
### "PRIVATE" Functions ###############################################
def _parse_kasim_outfile(out_filename):
"""
Parses the KaSim .out file into a Numpy ndarray.
Parameters
----------
out_filename : string
String specifying the location of the .out filename produced by KaSim.
Returns
-------
numpy.ndarray
Returns the KaSim simulation data as a Numpy ndarray. Data is accessed
using the syntax::
results[index_name]
The index 'time' gives the data for the time coordinates of the
simulation. Data for the observables can be accessed by indexing the
array with the names of the observables.
"""
try:
out_file = open(out_filename, 'r')
line = out_file.readline().strip() # Get the first line
out_file.close()
line = line[2:] # strip off opening '# '
raw_names = re.split(' ', line)
column_names = []
# Get rid of the quotes surrounding the observable names
for raw_name in raw_names:
mo = re.match("'(.*)'", raw_name)
if (mo):
column_names.append(mo.group(1))
else:
column_names.append(raw_name)
# Create the dtype argument for the numpy record array
dt = list(zip(column_names, ('float', ) * len(column_names)))
# Load the output file as a numpy record array, skip the name row
arr = np.loadtxt(out_filename, dtype=float, skiprows=1)
recarr = arr.view(dt)
except Exception as e:
raise Exception("problem parsing KaSim outfile: " + str(e))
return recarr