msbuilder ------------ +++++++++++++++++++++ MSBuilder +++++++++++++++++++++ A class that constructs COBRA metabolic models from genomes and model templates: .. code-block:: python 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: .. code-block:: python 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: .. code-block:: python 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: .. code-block:: python 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: .. code-block:: python 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: .. code-block:: python 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: .. code-block:: python 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: .. code-block:: python 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: .. code-block:: python 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: .. code-block:: python 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: .. code-block:: python 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.