msbuilder¶

MSBuilder¶

A class that constructs COBRA metabolic models from genomes and model templates:

new_model = MSBuilder(genome, template=None)

genome modelseedpy.core.msgenome.MSGenome: The genome that will form the COBRA model.
template modelseedpy.core.mstemplate.MSTemplate: The template that will construct the COBRA model.

get_gpr_from_template_reaction()¶

Returns the collection of genes for all roles of all complexes from the template reaction:

gpr_dict = new_model.get_gpr_from_template_reaction(template_reaction, allow_incomplete_complexes=True)

template_reaction modelseedy.core.mstemplate.MSTemplateReaction: The reaction whose GPR relationships will be discerned.
allow_incomplete_complexes bool: specifies whether the complexes will be built regardless of total complex determination.

Returns gpr_dict dict: The collection of genes (values) for all roles of all complexes (keys) of the parameterized reaction.

build_exchanges()¶

Constructs exchange reactions from model reactions whose metabolites exist in the extracellular compartment:

reactions_exchanges = new_model.build_exchanges(model, extra_cell='e0')

model cobra.core.model.Model: The COBRA model that will be expanded with exchange reactions.
extra_cell str: The compartment of the excellular solution.

Returns reactions_exchanges list: The collection of COBRA exchange reactions that were added to the model.

build_biomasses()¶

Constructs biomass reaction(s) for a model with a specified template:

biomass_reactions = new_model.build_biomasses(model, template, index)

model cobra.core.model.Model: The COBRA model that will be expanded with exchange reactions.
template modelseedpy.core.mstemplate.MSTemplate: The template within which the biomass reactions of the model will be constructed.
index str: The compartment index of the respective model.

Returns biomass_reactions list: The collection of biomass reactions that are created and added to the model.

auto_select_template()¶

Returns the predicted class of a genome per the knn_ACNP_RAST_filter filter ID:

genome_class = new_model.auto_select_template()

Returns genome_class Pickle prediction: The genome class that is predicted for the model based upon its genome and a knn_ACNP_RAST_filter filter ID.

build_metabolic_reactions()¶

Returns the collection of reactions that are constructed from the gpr set for each reaction in the template:

reactions = new_model.build_metabolic_reactions(index='0', allow_incomplete_complexes=True)

index str: The compartment index of the respective model.
allow_incomplete_complexes bool: specifies whether the complexes will be built regardless of total complex determination.

Returns reactions list: The collection of formated template reactions that have associated gpr information.

build_non_metabolite_reactions()¶

Returns the collection of reactions that lack gpr information:

reactions_no_gpr = new_model.build_non_metabolite_reactions(cobra_model, index='0', allow_all_non_grp_reactions=False)

model cobra.core.model.Model: The COBRA model that will be expanded with exchange reactions.
index str: The compartment index of the respective model.

Returns reactions_no_gpr list: The collection of formated template reactions that lack associated gpr information.

build()¶

Constructs a COBRA model based upon the genome in the MSBuilder class and the provided model ID:

model = new_model.build(model_id, index='0', annotate_with_rast=True)

model_id str: The ID of the model that will be constructed.
index str: The compartment index of the respective model.
allow_all_non_grp_reactions bool: specifies whether non-metabolite reactions will be added to the model.
annotate_with_rast bool: specifies whether the genome will be ontologically annotated via RAST.

Returns cobra_model cobra.core.model.Model: The COBRA model that is generated from the provided genome and model ID.

build_full_template_model()¶

Constructs a COBRA model from a template:

model = new_model.build_full_template_model(template, model_id=None, index='0')

template modelseedpy.core.mstemplate.MSTemplate: The template that will guide the model construction.
model_id str: The ID of the model that will be constructed.
index str: The compartment index of the respective model.

Returns cobra_model cobra.core.model.Model: The COBRA model that is generated from the provided template and model ID.

build_metabolic_model()¶

A concise function that develops a COBRA metabolic model from a genome and various specifications:

model = new_model.build_full_template_model(model_id, genome, gapfill_media=None, template=None, index='0',
                             allow_all_non_grp_reactions=False, annotate_with_rast=True)

model_id str: The ID of the model that will be constructed.
genome modelseedpy.core.msgenome.MSGenome: The genome that will form the COBRA model.
gapfill_media modelseedpy.core.msgapfill.MSGapfill: The media that will be used to gapfill the model, where None specifies that the model will not be gapfilled.
template modelseedpy.core.mstemplate.MSTemplate: The template that will guide the model construction.
index str: The compartment index of the respective model.
allow_all_non_grp_reactions bool: specifies whether non-metabolite reactions will be added to the model.
annotate_with_rast bool: specifies whether the genome will be ontologically annotated via RAST.

Returns cobra_model cobra.core.model.Model: The COBRA model that is generated from the provided template and model ID.

gapfill_model()¶

A model is gapfilled for a target reaction, extracellular media, and model template:

model = new_model.gapfill_model(original_mdl, target_reaction, template, media)

original_mdl cobra.core.model.Model: The model that will be gapfilled.
target_reaction str: The ID of the reaction that will be defined as the objective during gapfilling.
template modelseedpy.core.mstemplate.MSTemplate: The template that will guide the model gapfilling.
media modelseedpy.core.msgapfill.MSGapfill: The media that will be used to gapfill the model.

Returns cobra_model cobra.core.model.Model: The gapfilled COBRA model.