biggr_models.queries.metabolite_queries

Attributes

LINKOUT_PROPERTY_KEYS
ANNOTATION_TYPES
REFERENCE_COMPOUND_TYPES
REF_ANNOTATIONS_SUBQ
COMP_ANNOTATIONS_SUBQ

Functions

get_universal_metabolites_count(session)
get_universal_metabolites(session[, page, size, ...])	Get universal metabolites.
get_model_metabolites_count(model_bigg_id, session)	Count the model metabolites.
get_model_metabolites(model_bigg_id, session[, page, ...])	Get model metabolites.
process_annotation_for_template(ann)
get_metabolite(met_bigg_id, session)
get_model_list_for_metabolite(metabolite_bigg_id, session)
get_model_comp_metabolite(comp_met_id, model_bigg_id, ...)
get_component_object(→ Dict[str, Any])
get_universal_component_object(session, id[, ...])
get_compartmentalized_component_object(session, id[, ...])
get_model_compartmentalized_component_object(session, ...)
get_any_components_by_identifiers(session, identifiers)

Module Contents

biggr_models.queries.metabolite_queries.LINKOUT_PROPERTY_KEYS

biggr_models.queries.metabolite_queries.ANNOTATION_TYPES

biggr_models.queries.metabolite_queries.REFERENCE_COMPOUND_TYPES

biggr_models.queries.metabolite_queries.get_universal_metabolites_count(session)

biggr_models.queries.metabolite_queries.get_universal_metabolites(session, page=None, size=None, sort_column=None, sort_direction='ascending', **kwargs)

Get universal metabolites.

Parameters:

• session (An ome session object.)

• page (The page, or None for all pages.)

• size (The page length, or None for all pages.)

• sort_column (The name of the column to sort. Must be one of 'bigg_id', 'name'.)

• sort_direction (Either 'ascending' or 'descending'.)

Return type:

A list of objects with keys ‘bigg_id’, ‘name’.

biggr_models.queries.metabolite_queries.get_model_metabolites_count(model_bigg_id, session)

Count the model metabolites.

biggr_models.queries.metabolite_queries.get_model_metabolites(model_bigg_id, session, page=None, size=None, sort_column=None, sort_direction='ascending', **kwargs)

Get model metabolites.

Parameters:

• model_bigg_id (The bigg id of the model to retrieve metabolites.)

• session (An ome session object.)

• page (The page, or None for all pages.)

• size (The page length, or None for all pages.)

• sort_column (The name of the column to sort. Must be one of 'bigg_id',)

• 'name'

• 'model_bigg_id'

• 'organism'. (and)

• sort_direction (Either 'ascending' or 'descending'.)

Returns:

• A list of objects with keys ‘bigg_id’, ‘name’, ‘compartment_bigg_id’,

• ’model_bigg_id’, and ‘organism’.

biggr_models.queries.metabolite_queries.process_annotation_for_template(ann: cobradb.models.Annotation)

biggr_models.queries.metabolite_queries.get_metabolite(met_bigg_id, session)

biggr_models.queries.metabolite_queries.get_model_list_for_metabolite(metabolite_bigg_id, session)

biggr_models.queries.metabolite_queries.get_model_comp_metabolite(comp_met_id, model_bigg_id, session)

biggr_models.queries.metabolite_queries.REF_ANNOTATIONS_SUBQ

biggr_models.queries.metabolite_queries.COMP_ANNOTATIONS_SUBQ

biggr_models.queries.metabolite_queries.get_component_object(session: sqlalchemy.orm.Session, id: biggr_models.queries.utils.IDType, load_annotations: bool = True) → Dict[str, Any]

biggr_models.queries.metabolite_queries.get_universal_component_object(session, id: biggr_models.queries.utils.IDType, load_annotations: bool = True)

biggr_models.queries.metabolite_queries.get_compartmentalized_component_object(session, id: biggr_models.queries.utils.IDType, load_annotations: bool = True)

biggr_models.queries.metabolite_queries.get_model_compartmentalized_component_object(session, id: biggr_models.queries.utils.IDType, model_id: biggr_models.queries.utils.IDType, load_annotations: bool = True)

biggr_models.queries.metabolite_queries.get_any_components_by_identifiers(session: sqlalchemy.orm.Session, identifiers: biggr_models.queries.utils.StrList, model_bigg_id: biggr_models.queries.utils.OptStr = None)