Manager¶
Manager for Bio2BEL KEGG.
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class
bio2bel_kegg.manager.
Manager
(*args, **kwargs)[source]¶ Protein-pathway memberships.
Doesn’t let this class get instantiated if the pathway_model.
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namespace_model
¶ alias of
bio2bel_kegg.models.Pathway
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pathway_model
¶ alias of
bio2bel_kegg.models.Pathway
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protein_model
¶ alias of
bio2bel_kegg.models.Protein
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pathway_model_identifier_column
¶ KEGG id of the pathway
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get_or_create_pathway
(kegg_id: str, name: Optional[str] = None) → bio2bel_kegg.models.Pathway[source]¶ Get an pathway from the database or creates it.
- Parameters
kegg_id – A KEGG pathway identifier
name – name of the pathway
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get_protein_by_kegg_id
(kegg_id: str) → Optional[bio2bel_kegg.models.Protein][source]¶ Get a protein by its kegg id.
- Parameters
kegg_id – A KEGG identifier
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get_protein_by_hgnc_id
(hgnc_id: str) → Optional[bio2bel_kegg.models.Protein][source]¶ Get a protein by its hgnc_id.
- Parameters
hgnc_id – hgnc_id
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get_protein_by_hgnc_symbol
(hgnc_symbol: str) → Optional[bio2bel_kegg.models.Protein][source]¶ Get a protein by its hgnc symbol.
- Parameters
hgnc_id – hgnc identifier
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populate
(pathways_url=None, protein_pathway_url=None, metadata_existing=False)[source]¶ Populate all tables.
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get_pathway_graph
(kegg_id: str) → Optional[pybel.struct.graph.BELGraph][source]¶ Return a new graph corresponding to the pathway.
- Parameters
kegg_id – A KEGG pathway identifier (prefixed by “path:”)
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