2.1. wc_kb_gen package

2.1.2. Submodules

2.1.3. wc_kb_gen._version module

2.1.4. 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, optional

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 (str): id

  • name (str): name

  • version (str): version

  • input_kb (wc_kb.core.KnowledgeBase, optional): knowledge base input if

    one wants to build upon an existing knowledge base

  • component (dict): dictionary of options whose keys are the names

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

component_generators[source]

component generators of the knowledge base

Type

list of KbComponentGenerator

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, optional

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

2.1.5. Module contents