memote.experimental.config

Provide a YAML parser for experiment configuration files.

Module Contents

Classes

ExperimentConfiguration Represent an experimental configuration.
class memote.experimental.config.ExperimentConfiguration(filename, **kwargs)[source]

Bases: object

Represent an experimental configuration.

load(self, model)[source]

Load all information from an experimental configuration file.

Parameters:
model : cobra.Model

The metabolic model under investigation.

validate(self)[source]

Validate the configuration file.

load_medium(self, model)[source]

Load and validate all media.

load_essentiality(self, model)[source]

Load and validate all data files.

load_growth(self, model)[source]

Load and validate all data files.

get_path(self, obj, default)[source]

Return a relative or absolute path to experimental data.

get_minimal_growth_rate(self, model, threshold=0.1)[source]

Calculate min growth default value or return input value.

This value is used to determine if a model is capable of growth under certain experimental conditions.

Parameters:
model : cobra.Model
threshold : float, optional

If no input is provided by the user the default value is set to a coefficient threshold times the growth under default constraints (default: 0.1).