webng package

Subpackages

• webng.analysis package
  • Submodules
  • webng.analysis.analysis module
    • weAnalysis
      • weAnalysis.set_names()
  • webng.analysis.average module
    • weAverage
      • weAverage.get_mapper()
      • weAverage.open_pdist_file()
      • weAverage.run()
      • weAverage.save_fig()
      • weAverage.set_dims()
      • weAverage.set_iter_range()
      • weAverage.set_names()
      • weAverage.setup_figure()
  • webng.analysis.cluster module
    • weCluster
      • weCluster.cluster()
      • weCluster.get_mstable_assignments()
      • weCluster.load_bin_arrays()
      • weCluster.preprocess_tm()
      • weCluster.print_mstable_states()
      • weCluster.print_pcca_results()
      • weCluster.row_normalize()
      • weCluster.run()
      • weCluster.save_full_mstabs()
      • weCluster.save_mstable_assignments()
      • weCluster.save_pcca()
  • webng.analysis.evolution module
    • weEvolution
      • weEvolution.open_pdist_file()
      • weEvolution.run()
      • weEvolution.save_fig()
      • weEvolution.set_dims()
      • weEvolution.set_names()
      • weEvolution.setup_figure()
  • webng.analysis.network module
    • weNetwork
      • weNetwork.get_coarse_network()
      • weNetwork.get_full_network()
      • weNetwork.run()
      • weNetwork.save_network()
  • webng.analysis.utils module
    • assign_cluster()
    • assign_pcca()
    • assign_voronoi()
    • avg()
    • circumcircle()
    • load_mapper()
    • pull_all_data()
    • pull_data()
    • pull_weight()
    • voronoi()
    • wrapped_clusterer
      • wrapped_clusterer.assign()
    • wrapped_mapper
      • wrapped_mapper.assign()
      • wrapped_mapper.load_pcca_labels()
  • Module contents
• webng.controllers package
  • Submodules
  • webng.controllers.base module
    • Base
      • Base.Meta
        • Base.Meta.arguments
        • Base.Meta.description
        • Base.Meta.epilog
        • Base.Meta.label
      • Base.command1()
  • Module contents
• webng.core package
  • Submodules
  • webng.core.exc module
    • weBNGError
  • webng.core.version module
    • get_version()
  • webng.core.weAnalysis module
    • weAnalysis
      • weAnalysis.run()
  • webng.core.weConvert module
    • weConvert
      • weConvert.copy_run_network()
      • weConvert.make_sim_folders()
      • weConvert.run()
      • weConvert.run_BNGL_on_file()
      • weConvert.write_dynamic_files()
      • weConvert.write_static_files()
  • webng.core.weTemplater module
    • weTemplater
      • weTemplater.run()
  • Module contents

Submodules

webng.main module

webng.main.main()

class webng.main.weBNG(label=None, **kw)

Bases: App

weBNG primary application.

class Meta

Bases: object

config_defaults = {'webng': {'foo': 'bar'}}

config_file_suffix = '.yml'

config_handler = 'yaml'

description = 'A command line tool to setup WESTPA simulations from BNGL models.'

exit_on_close = True

extensions = ['yaml', 'colorlog']

handlers = [<class 'webng.main.weBNGBase'>]

help = 'weBNG'

label = 'webng'

log_handler = 'colorlog'

class webng.main.weBNGBase(*args, **kw)

Bases: ArgparseController

webng is a simple command line tool to simplify WESTPA simulations of BioNetGen models. It can generate a template options file and using the options file you can generate a WESTPA folder ready to run using the model file given.

setup

creates a WESTPA folder ready to run form a given options YAML file

template

generates a simple template YAML file to pass to setup subcommand

analysis

runs the analyses set in the YAML config file

class Meta

Bases: object

description = 'webng'

help = 'webng'

label = 'webng'

analysis()

The analysis subcommand

setup()

This sub command sets up a WESTPA folder from a given options YAML file.

See “webng template -h” for more information on the options YAML file.

template()

This sub command is used to write a template options file

class webng.main.weBNGTest(label=None, **kw)

Bases: TestApp, weBNG

A sub-class of weBNG that is better suited for testing.

class Meta

Bases: object

label = 'webng'

Module contents