biggr_models.queries.download_queries#

Attributes#

`REACTION_MATCH_FLAGS`
`METABOLITE_MATCH_FLAGS`

Functions#

`extract_reaction_participants`(matrix)
`extract_universal_reaction_participants`(matrix)
`extract_cross_references`(annotation_db, source_type, match)	List the external identifiers linked by one annotation, with provenance.
`unique_cross_references`(cross_references)
`get_match_flags`(mapping_db, flags)
`get_reactions`(session)
`get_metabolites`(session)

Module Contents#

biggr_models.queries.download_queries.extract_reaction_participants(matrix)#

biggr_models.queries.download_queries.extract_universal_reaction_participants(matrix)#

biggr_models.queries.download_queries.extract_cross_references(annotation_db, source_type, match)#

List the external identifiers linked by one annotation, with provenance.

source is the annotation the identifiers come from, and source_type how that annotation is linked to the entity: through its reference (Rhea reaction or ChEBI compound), or through ModelSEED matching. match records how the link was established (see the data access page).

biggr_models.queries.download_queries.unique_cross_references(cross_references)#

biggr_models.queries.download_queries.get_match_flags(mapping_db, flags)#

biggr_models.queries.download_queries.REACTION_MATCH_FLAGS = [('bigg_id_match', 'bigg_id'), ('pattern_match', 'stoichiometry')]#

biggr_models.queries.download_queries.METABOLITE_MATCH_FLAGS = [('bigg_id_match', 'bigg_id'), ('inchi_match', 'inchikey')]#

biggr_models.queries.download_queries.get_reactions(session: sqlalchemy.orm.Session)#

biggr_models.queries.download_queries.get_metabolites(session: sqlalchemy.orm.Session)#