KEGG API client and parsers for pathway protein-protein interactions
Project description
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.
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