keggstand 0.0.7

KEGG API client and parsers for pathway protein-protein interactions

keggstand

KEGG API client and parsers for pathway protein-protein interactions

• Free software: MIT license

Usage

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.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.0.7 (2020-07-19)

• First release on PyPI.