KEGG API client and parsers for pathway protein-protein interactions
- Free software: MIT license
To use the API client, instantiate a new instance:
client = Kegg(cache=True)
To list organism codes in KEGG:
client.organisms()
To list available pathway accessions and names for a given organism:
accessions = client.list_pathways(organism='hsa')
To parse a particular pathway into a dataframe of protein-protein interactions, pass a KEGG pathway accession to the method below:
pathway = client.get_pathway(pathway='path:hsa01521') # Inspect individual protein/genes parsed from XML file pathway.entries # Inspect relations between entries parsed from XML file pathway.relations # Pandas DataFrame of interactions with annotated post-translational modifications pathway.interactions
To make a call to the accession mapping service you can convert a source database to a destination database:
client.convert(source='hsa', destination='uniprot')
This will create a mapping from KEGG hsa identifiers to uniprot swissprot identifiers.
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.