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‎.gitignore‎

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*.pyc

‎build/lib/stochpy/__init__.py‎

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#! /usr/bin/env python
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"""
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StochPy - Stochastic modeling in Python (http://stochpy.sourceforge.net)
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Copyright (C) 2010-2015 T.R Maarlveld, B.G. Olivier, F.J. Bruggeman all rights reserved.
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Timo R. Maarleveld ([email protected])
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Centrum Wiskunde & Informatica, Amsterdam, Netherlands
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VU University, Amsterdam, Netherlands
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Permission to use, modify, and distribute this software is given under the
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terms of the StochPy (BSD style) license.
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NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
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"""
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from __future__ import division, print_function, absolute_import
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__doc__ = """
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StochPy: Stochastic Modeling in Python
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=====================================
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StochPy (Stochastic modeling in Python) is a flexible software tool for stochastic simulation in cell biology. It provides various stochastic
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simulation algorithms, SBML support, analyses of the probability distributions of molecule copy numbers and event waiting times, analyses of stochastic time
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series, and a range of additional statistical functions and plotting facilities for stochastic simulations.
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Options:
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--------
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- Stochastic Simulations
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- Variety of stochastic simulation output analysis:
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--> Time Simulation
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--> Distribution
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--> Waiting times
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--> Propensities
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- Cell Division simulations
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- SBML and PSC MDL input format.
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StochPy can be used in an interactive Python shell:
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Usage
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-----
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>>> import stochpy
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>>> utils = stochpy.Utils()
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>>> utils.doExample1()
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>>> utils.doExample2()
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>>> smod = stochpy.SSA() # stochastic simulation algorithm module
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>>> help(smod)
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>>> help(stochpy.SSA) # (some windows versions)
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>>> stochpy?
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>>> smod.DoStochSim()
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>>> smod.PlotSpeciesTimeSeries()
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>>> converter = stochpy.SBML2PSC()
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>>> converter??
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>>> help(stochpy.SBML2PSC)
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"""
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from .core2.version import __version__
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import os,shutil,sys
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try:
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import readline
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_IsReadline = True
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except:
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_IsReadline = False
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try:
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from numpy.distutils.core import setup, Extension
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_IsNumPy = True
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except Exception as ex:
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_IsNumPy = False
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print(ex)
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print("StochPy requires NumPy")
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print("See http://numpy.scipy.org/ for more information about NumPy")
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os.sys.exit(-1)
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try:
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import matplotlib
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_IsMPL = True
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except:
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_IsMPL = False
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print("Warning: The Matplotlib module is not available, so plotting is not possible")
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print("Info: See http://matplotlib.sourceforge.net/ for more information about Matplotlib.")
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_IsPlotting = False
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try:
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import matplotlib.pyplot as plt
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_IsPlotting = True
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except Exception as er:
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print(er)
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def InitiateModels(directory):
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"""
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Build several models written in PSC MDL and SBML
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Input:
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- *directory* (string)
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"""
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from .pscmodels import Burstmodel
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from .pscmodels import BirthDeath
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from .pscmodels import ImmigrationDeath
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from .pscmodels import DecayingDimerizing
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from .pscmodels import Autoreg
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from .pscmodels import CellDivision as celldivision
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from .pscmodels import GeneDuplication
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from .pscmodels import dsmts_001_01
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from .pscmodels import dsmts_001_11
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from .pscmodels import dsmts_001_19
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from .pscmodels import dsmts_002_10
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from .pscmodels import dsmts_003_03
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from .pscmodels import dsmts_003_04
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from .pscmodels import chain5
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from .pscmodels import chain50
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from .pscmodels import chain500
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from .pscmodels import chain1500
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from .pscmodels import Isomerization
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from .pscmodels import Polymerase
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from .pscmodels import TranscriptionIntermediate
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from .pscmodels import Schlogl
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from .pscmodels import SignalingTimeVaryingL
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from .pscmodels import Signaling3cCD
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models = {}
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models['Signaling3cCD.psc'] = Signaling3cCD.model
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models['SignalingTimeVaryingL.psc'] = SignalingTimeVaryingL.model
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models['Schlogl.psc'] = Schlogl.model
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models['Burstmodel.psc'] = Burstmodel.model
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models['ImmigrationDeath.psc'] = ImmigrationDeath.model
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models['BirthDeath.psc'] = BirthDeath.model
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models['DecayingDimerizing.psc'] = DecayingDimerizing.model
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models['Autoreg.psc'] = Autoreg.model
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models['Autoreg.xml'] = Autoreg.xml_model
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models['CellDivision.psc'] = celldivision.model
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models['GeneDuplication.psc'] = GeneDuplication.model
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models['Isomerization.psc'] = Isomerization.model
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models['Polymerase.psc'] = Polymerase.model
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models['TranscriptionIntermediate.psc'] = TranscriptionIntermediate.model
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models['dsmts-001-01.xml.psc'] = dsmts_001_01.model
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models['dsmts-001-01.xml'] = dsmts_001_01.xml_model
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models['dsmts-001-11.xml.psc'] = dsmts_001_11.model
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models['dsmts-001-11.xml'] = dsmts_001_11.xml_model
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models['dsmts-001-19.xml.psc'] = dsmts_001_19.model
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models['dsmts-001-19.xml'] = dsmts_001_19.xml_model
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models['dsmts-002-10.xml.psc'] = dsmts_002_10.model
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models['dsmts-002-10.xml'] = dsmts_002_10.xml_model
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models['dsmts-003-03.xml.psc'] = dsmts_003_03.model
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models['dsmts-003-03.xml'] = dsmts_003_03.xml_model
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models['dsmts-003-04.xml.psc'] = dsmts_003_04.model
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models['dsmts-003-04.xml'] = dsmts_003_04.xml_model
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models['chain5.psc'] = chain5.model
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models['chain50.psc'] = chain50.model
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models['chain500.psc'] = chain500.model
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models['chain1500.psc'] = chain1500.model
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model_names = list(models)
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dir_models = os.listdir(directory)
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for mod_name in model_names:
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if mod_name not in dir_models:
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print("Info: Model {0:s} copied to {1:s}".format(mod_name ,directory) )
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file_out = open(os.path.join(directory,mod_name),'w')
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file_out.write(models[mod_name])
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file_out.close()
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output_dir = None
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model_dir = None
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if os.sys.platform != 'win32':
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if not os.path.exists(os.path.join(os.path.expanduser('~'),'Stochpy')):
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os.makedirs(os.path.join(os.path.expanduser('~'),'Stochpy'))
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if not os.path.exists(os.path.join(os.path.expanduser('~'),'Stochpy', 'pscmodels')):
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os.makedirs(os.path.join(os.path.expanduser('~'),'Stochpy','pscmodels'))
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if not os.path.exists(os.path.join(os.path.expanduser('~'),'Stochpy', 'temp')):
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os.makedirs(os.path.join(os.path.expanduser('~'),'Stochpy','temp'))
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output_dir = os.path.join(os.path.expanduser('~'),'Stochpy')
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model_dir = os.path.join(os.path.expanduser('~'),'Stochpy','pscmodels')
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temp_dir = os.path.join(os.path.expanduser('~'),'Stochpy','temp')
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InitiateModels(model_dir)
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else:
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if not os.path.exists(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Stochpy')):
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os.makedirs(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Stochpy'))
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if not os.path.exists(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Stochpy','pscmodels')):
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os.makedirs(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Stochpy','pscmodels'))
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if not os.path.exists(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Stochpy','temp')):
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os.makedirs(os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Stochpy','temp'))
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output_dir = os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Stochpy',)
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model_dir = os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Stochpy','pscmodels')
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temp_dir = os.path.join(os.getenv('HOMEDRIVE')+os.path.sep,'Stochpy','temp')
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InitiateModels(model_dir)
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from .modules.SBML2PSC import SBML2PSC
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from .modules.StochSim import SSA
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from .modules.StochPyUtils import Utils
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from .modules.StochPyCellDivision import CellDivision
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from .modules.StochPyDemo import Demo
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from .modules import Analysis as Analysis
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try:
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from .modules.NucleosomeTool import NucleosomeModelBuilder
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from .modules.NucleosomeTool import NucleosomeSimulator
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except Exception as er:
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pass # ignore
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def DeletePreviousOutput(path,type):
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"""
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Delete output of earlier simulations
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Input:
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- *path* (string)
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- *type* (string)
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"""
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for filename in os.listdir(path):
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if filename.endswith(type):
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filename_path = os.path.join(path,filename)
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os.remove(filename_path)
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def DeleteExistingData(path):
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"""
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Delete all existing StochKit simulation data
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Input:
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- *path* (string)
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"""
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if os.path.exists(path):
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for maps in os.listdir(path):
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dir2delete = os.path.join(path,maps)
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shutil.rmtree(dir2delete, ignore_errors=True)
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def SaveInteractiveSession(filename='interactiveSession.py',path=output_dir):
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"""
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Save the interactive session
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Input:
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- *filename*: [default = interactiveSession.py'] (string)
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- *path*: (string)
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"""
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if not _IsReadline:
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print("Error: install 'readline' first")
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elif _IsReadline:
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historyPath = os.path.join(path,filename)
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if not os.path.exists(path):
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os.makedirs(directory)
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readline.write_history_file(historyPath)
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file_in = open(historyPath,'r')
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history_list = file_in.readlines()
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n_import_statement = 0
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for command in history_list:
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if 'import' in command and 'stochpy' in command:
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n_import_statement +=1
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n=0
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file_out = open(historyPath,'w')
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for command in history_list:
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if 'import' in command and 'stochpy' in command:
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n+=1
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if n==n_import_statement:
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file_out.write(command)
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file_out.close()
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print("Info: Interactive session successfully saved at {0:s}".format(historyPath) )
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print("Info: use 'ipython {0:s} to restart modeling with this interactive session".format(filename) )
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DeletePreviousOutput(temp_dir,'.dat')
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DeletePreviousOutput(temp_dir,'.xml')
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DeletePreviousOutput(temp_dir,'.txt')
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DeletePreviousOutput(temp_dir,'temp_parse_module')
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DeleteExistingData(temp_dir)
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#readline.clear_history()
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print("""
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#######################################################################
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# #
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# Welcome to the interactive StochPy environment #
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# #
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#######################################################################
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# StochPy: Stochastic modeling in Python #
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# http://stochpy.sourceforge.net #
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# Copyright(C) T.R Maarleveld, B.G. Olivier, F.J Bruggeman 2010-2015 #
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# DOI: 10.1371/journal.pone.0079345 #
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# Email: [email protected] #
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# VU University, Amsterdam, Netherlands #
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# Centrum Wiskunde Informatica, Amsterdam, Netherlands #
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# StochPy is distributed under the BSD licence. #
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#######################################################################
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""")
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print("Version {0:s}".format(__version__) )
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print("Output Directory: {0:s}".format(output_dir) )
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print("Model Directory: {0:s}".format(model_dir) )
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#print("Warning: Figure freezing? Try a different matplotlib backend (stochpy.plt.switch_backend) and/or set IsInteractive to False (see user guide)")

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