.. automodule:: pybel.io
.. autofunction:: pybel.load
.. autofunction:: pybel.dump
The PyBEL parser has several modes that can be enabled and disabled. They are described below.
By default, this is set to False. The parser does not allow identifiers that are not qualified with
namespaces (naked names), like in p(YFG). A proper namespace, like p(HGNC:YFG) must be used. By
setting this to True, the parser becomes permissive to naked names. In general, this is bad practice and this
feature will be removed in the future.
By default, this is set to False. The parser does not allow nested statements is disabled. See overview.
By setting this to True the parser will accept nested statements one level deep.
By default, this is set to True. While the BEL specification clearly states how the language should be used as
a state machine, many BEL documents do not conform to the strict SET/UNSET rules. To guard against
annotations accidentally carried from one set of statements to the next, the parser has two modes. By default, in
citation clearing mode, when a SET CITATION command is reached, it will clear all other annotations (except
the STATEMENT_GROUP, which has higher priority). This behavior can be disabled by setting this to False
to re-enable strict parsing.
.. autofunction:: pybel.from_bel_script
.. autofunction:: pybel.from_bel_script_url
.. autofunction:: pybel.to_bel_script
.. automodule:: pybel.io.hetionet
.. autofunction:: pybel.from_hetionet_json
.. autofunction:: pybel.from_hetionet_file
.. autofunction:: pybel.from_hetionet_gz
.. autofunction:: pybel.get_hetionet
All transport pairs are reflective and data-preserving.
.. automodule:: pybel.io.gpickle
.. autofunction:: pybel.from_bytes
.. autofunction:: pybel.to_bytes
.. autofunction:: pybel.from_bytes_gz
.. autofunction:: pybel.to_bytes_gz
.. autofunction:: pybel.from_pickle
.. autofunction:: pybel.to_pickle
.. autofunction:: pybel.from_pickle_gz
.. autofunction:: pybel.to_pickle_gz
.. automodule:: pybel.io.nodelink
.. autofunction:: pybel.from_nodelink
.. autofunction:: pybel.to_nodelink
.. autofunction:: pybel.from_nodelink_jsons
.. autofunction:: pybel.to_nodelink_jsons
.. autofunction:: pybel.from_nodelink_file
.. autofunction:: pybel.to_nodelink_file
.. autofunction:: pybel.from_nodelink_gz
.. autofunction:: pybel.to_nodelink_gz
.. automodule:: pybel.io.sbel
.. autofunction:: pybel.from_sbel
.. autofunction:: pybel.to_sbel
.. autofunction:: pybel.from_sbel_file
.. autofunction:: pybel.to_sbel_file
.. autofunction:: pybel.from_sbel_gz
.. autofunction:: pybel.to_sbel_gz
.. automodule:: pybel.io.cx
.. autofunction:: pybel.from_cx
.. autofunction:: pybel.to_cx
.. autofunction:: pybel.from_cx_jsons
.. autofunction:: pybel.to_cx_jsons
.. autofunction:: pybel.from_cx_file
.. autofunction:: pybel.to_cx_file
.. autofunction:: pybel.from_cx_gz
.. autofunction:: pybel.to_cx_gz
.. automodule:: pybel.io.jgif
.. autofunction:: pybel.from_jgif
.. autofunction:: pybel.to_jgif
.. autofunction:: pybel.from_jgif_jsons
.. autofunction:: pybel.to_jgif_jsons
.. autofunction:: pybel.from_jgif_file
.. autofunction:: pybel.to_jgif_file
.. autofunction:: pybel.from_jgif_gz
.. autofunction:: pybel.to_jgif_gz
.. autofunction:: pybel.post_jgif
.. autofunction:: pybel.from_cbn_jgif
.. autofunction:: pybel.from_cbn_jgif_file
.. automodule:: pybel.io.graphdati
.. autofunction:: pybel.to_graphdati
.. autofunction:: pybel.from_graphdati
.. autofunction:: pybel.to_graphdati_file
.. autofunction:: pybel.from_graphdati_file
.. autofunction:: pybel.to_graphdati_gz
.. autofunction:: pybel.from_graphdati_gz
.. autofunction:: pybel.to_graphdati_jsons
.. autofunction:: pybel.from_graphdati_jsons
.. autofunction:: pybel.to_graphdati_jsonl
.. autofunction:: pybel.to_graphdati_jsonl_gz
.. automodule:: pybel.io.indra
.. autofunction:: pybel.from_indra_statements
.. autofunction:: pybel.from_indra_statements_json
.. autofunction:: pybel.from_indra_statements_json_file
.. autofunction:: pybel.to_indra_statements
.. autofunction:: pybel.to_indra_statements_json
.. autofunction:: pybel.to_indra_statements_json_file
.. autofunction:: pybel.from_biopax
.. automodule:: pybel.io.jupyter
.. autofunction:: pybel.to_jupyter
.. automodule:: pybel.io.pynpa
.. autofunction:: pybel.to_npa_directory
.. autofunction:: pybel.to_npa_dfs
.. automodule:: pybel.io.hipathia
.. autofunction:: pybel.to_hipathia
.. autofunction:: pybel.to_hipathia_dfs
.. autofunction:: pybel.from_hipathia_paths
.. autofunction:: pybel.from_hipathia_dfs
.. automodule:: pybel.io.spia
.. autofunction:: pybel.to_spia_dfs
.. autofunction:: pybel.to_spia_excel
.. autofunction:: pybel.to_spia_tsvs
.. automodule:: pybel.io.pykeen
.. autofunction:: pybel.io.pykeen.get_triples_from_bel
.. autofunction:: pybel.io.pykeen.get_triples_from_bel_nodelink
.. autofunction:: pybel.io.pykeen.get_triples_from_bel_pickle
.. autofunction:: pybel.io.pykeen.get_triples_from_bel_commons
.. automodule:: pybel.io.triples
.. autofunction:: pybel.to_triples
.. autofunction:: pybel.to_triples_file
.. autofunction:: pybel.to_edgelist
.. automodule:: pybel.io.bel_commons_client
.. autofunction:: pybel.from_bel_commons
.. autofunction:: pybel.to_bel_commons
.. automodule:: pybel.io.aws
.. autofunction:: pybel.to_s3
.. autofunction:: pybel.from_s3
.. automodule:: pybel.io.biodati_client
.. autofunction:: pybel.to_biodati
.. autofunction:: pybel.from_biodati
.. automodule:: pybel.io.fraunhofer_orientdb
.. autofunction:: pybel.from_fraunhofer_orientdb
.. automodule:: pybel.io.emmaa
.. autofunction:: pybel.from_emmaa
.. automodule:: pybel.manager.database_io
.. autofunction:: pybel.from_database
.. autofunction:: pybel.to_database
.. automodule:: pybel.io.neo4j
.. autofunction:: pybel.to_neo4j
.. automodule:: pybel.io.umbrella_nodelink
.. autofunction:: pybel.to_umbrella_nodelink
.. autofunction:: pybel.to_umbrella_nodelink_file
.. autofunction:: pybel.to_umbrella_nodelink_gz
.. automodule:: pybel.io.graphml
.. autofunction:: pybel.to_graphml
.. automodule:: pybel.io.extras
.. autofunction:: pybel.to_csv
.. autofunction:: pybel.to_sif
.. autofunction:: pybel.to_gsea