2.1. wc_kb_gen package

2.1.2. Submodules

2.1.3. wc_kb_gen.core module

Base classes for generating wc_kb-formatted knowledge bases for whole-cell models.

Author:Jonathan Karr <jonrkarr@gmail.com>
Date:2018-05-04
Copyright:2018, Karr Lab
License:MIT
class wc_kb_gen.core.KbComponentGenerator(knowledge_base, options=None)[source]

Bases: object

Base class for knowledge base component generators

knowledge_base[source]

knowledge base

Type:wc_kb.core.KnowledgeBase
options[source]

options

Type:dict
clean_and_validate_options()[source]

Apply default options and validate options

gen_components()[source]

Construct knowledge base components

get_data()[source]

Get data for knowledge base components

process_data()[source]

Process data for knowledge base components

run()[source]

Generate knowledge base components

class wc_kb_gen.core.KbGenerator(component_generators=None, options=None)[source]

Bases: object

Generator for knowledge bases of experimental data for whole-cell models

Options:

  • id
  • name
  • component
component_generators[source]

component generators of the knowledge base

Type:list
options[source]

dictionary of options whose keys are the names of component generator classes and whose values are dictionaries of options for the component generator classes

Type:dict
DEFAULT_COMPONENT_GENERATORS = ()[source]
clean_and_validate_options()[source]

Apply default options and validate options

run()[source]

Generate a knowledge base of experimental data for a whole-cell model

Returns:knowledge base
Return type:wc_kb.core.KnowledgeBase

2.1.4. Module contents