/pystringdb-client

Simple python client for the STRING db api (string-db.org)

Primary LanguagePython

PySTRINGDB-client

STRING (string-db.org) is a database of Known and Predicted Protein-Protein Interactions. This Python library enables simple queries of the STRING api.

What it do

Currently this library only works for fetching interaction networks and their images, because that's what I needed. Potential future plans to cover the whole API some day maybe.

Installation

AFTER I POST THIS:

pip install pystringdb-client

Use

from pystringdb_client import stringdb
Resolve protein names to unique identifiers
matches = stringdb.resolve('ALK', species=9606)

Python requirements

Tested on Python 2.7.10 and 3.5.0.

Dependencies

  • pandas
  • requests
  • six

Contributing

Feel free to report bugs, request features, or send pull requests!

Released under the GPLv2 license.

@jonathanronen, Berlin Institute of Medical Systems Biology, 9/2015