3.1. mycoplasma_pneumoniae package

3.1.2. Submodules

3.1.3. mycoplasma_pneumoniae.__main__ module

Command line programs for manipulating model definitions

Author:Jonathan Karr <karr@mssm.edu>
Date:2016-12-07
Copyright:2016, Karr Lab
License:MIT
class mycoplasma_pneumoniae.__main__.AnalyzeController(*args, **kw)[source]

Bases: cement.ext.ext_argparse.ArgparseController

Analyze knowledge base, model, and simulation results and save analyses

class Meta[source]

Bases: object

arguments = [(['--kb-core'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/kb/core.xlsx', 'help': 'Path to knowledge base core'}), (['--kb-seq'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/kb/seq.fna', 'help': 'Path to genome sequence'}), (['--model'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/model/core.xlsx', 'help': 'Path to model'}), (['--sim-results'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/sim_results', 'help': 'Path to simulation results'}), (['--analyses'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/analysis_results', 'help': 'Path to save analysis'}), (['--sloppy'], {'dest': 'strict', 'default': True, 'action': 'store_false', 'help': 'If set, do not validate the format of the model file(s)'})][source]
description = 'Analyze knowledge base, model, and simulation results and save analyses'[source]
label = 'analyze'[source]
stacked_on = 'base'[source]
stacked_type = 'nested'[source]
class mycoplasma_pneumoniae.__main__.App(label=None, **kw)[source]

Bases: cement.core.foundation.App

Command line application

class Meta[source]

Bases: object

base_controller = 'base'[source]
handlers = [<class 'mycoplasma_pneumoniae.__main__.BaseController'>, <class 'mycoplasma_pneumoniae.__main__.GenerateModelController'>, <class 'mycoplasma_pneumoniae.__main__.SimulateModelController'>, <class 'mycoplasma_pneumoniae.__main__.AnalyzeController'>, <class 'mycoplasma_pneumoniae.__main__.RunController'>][source]
label = 'mycoplasma_pneumoniae'[source]
class mycoplasma_pneumoniae.__main__.BaseController(*args, **kw)[source]

Bases: cement.ext.ext_argparse.ArgparseController

Base controller for command line application

class Meta[source]

Bases: object

arguments = [(['-v', '--version'], {'action': 'version', 'version': '0.0.1'})][source]
description = 'Mycoplasma pneumoniae whole-cell model'[source]
label = 'base'[source]
class mycoplasma_pneumoniae.__main__.GenerateModelController(*args, **kw)[source]

Bases: cement.ext.ext_argparse.ArgparseController

Generate model from knowledge base and save model

class Meta[source]

Bases: object

arguments = [(['--kb-core'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/kb/core.xlsx', 'help': 'Path to knowledge base core'}), (['--kb-seq'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/kb/seq.fna', 'help': 'Path to genome sequence'}), (['--model'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/model/core.xlsx', 'help': 'Path to save model'}), (['--ignore-repo-metadata'], {'dest': 'set_repo_metadata_from_path', 'default': True, 'action': 'store_false', 'help': 'If set, do not set the Git repository metadata for the knowledge base from the parent directory of `path`'}), (['--sloppy'], {'dest': 'strict', 'default': True, 'action': 'store_false', 'help': 'If set, do not validate the format of the model file(s)'})][source]
description = 'Generate model from knowledge base and save model'[source]
label = 'gen'[source]
stacked_on = 'base'[source]
stacked_type = 'nested'[source]
class mycoplasma_pneumoniae.__main__.RunController(*args, **kw)[source]

Bases: cement.ext.ext_argparse.ArgparseController

Generate model, save model, simulate model, analyze simulation results, and save analyses

class Meta[source]

Bases: object

arguments = [(['--kb-core'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/kb/core.xlsx', 'help': 'Path to knowledge base core'}), (['--kb-seq'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/kb/seq.fna', 'help': 'Path to genome sequence'}), (['--model'], {'type': <class 'str'>, 'default': None, 'help': 'Path to save model'}), (['--time-max'], {'type': <class 'str'>, 'default': 30000.0, 'help': 'Path to save simulation results'}), (['--time-step'], {'type': <class 'str'>, 'default': 10.0, 'help': 'Path to save simulation results'}), (['--sim-results'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/sim_results', 'help': 'Path to save simulation results'}), (['--analyses'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/analysis_results', 'help': 'Path to save analyses'}), (['--ignore-repo-metadata'], {'dest': 'set_repo_metadata_from_path', 'default': True, 'action': 'store_false', 'help': 'If set, do not set the Git repository metadata for the knowledge base from the parent directory of `path`'}), (['--sloppy'], {'dest': 'strict', 'default': True, 'action': 'store_false', 'help': 'If set, do not validate the format of the model file(s)'})][source]
description = 'Generate model, optionally save model, simulate model, optionally save simulation results, analyze simulation results, and save analyses'[source]
label = 'run'[source]
stacked_on = 'base'[source]
stacked_type = 'nested'[source]
class mycoplasma_pneumoniae.__main__.SimulateModelController(*args, **kw)[source]

Bases: cement.ext.ext_argparse.ArgparseController

Simulate model and save simulation results

class Meta[source]

Bases: object

arguments = [(['--model'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/model/core.xlsx', 'help': 'Path to model file.'}), (['--time-max'], {'type': <class 'float'>, 'default': 30000.0, 'help': 'Simulation run time'}), (['--time-step'], {'type': <class 'float'>, 'default': 10.0, 'help': 'Time step of the simulation.'}), (['--checkpoint-period'], {'type': <class 'int'>, 'default': 60.0, 'help': 'Checkpoint period'}), (['--sim-results'], {'type': <class 'str'>, 'default': '/root/project/mycoplasma_pneumoniae/sim_results', 'help': 'Path to save simulation results'}), (['--sloppy'], {'dest': 'strict', 'default': True, 'action': 'store_false', 'help': 'If set "True", do not validate the format of the model file(s)'})][source]
description = 'Simulate model and save simulation results'[source]
label = 'sim'[source]
stacked_on = 'base'[source]
stacked_type = 'nested'[source]
mycoplasma_pneumoniae.__main__.main()[source]

Entrypoint to application

3.1.4. mycoplasma_pneumoniae.runtime_demo module

3.1.5. Module contents