compath-hgnc 0.0.1

A package that wraps PyHGNC to perform mappings between different gene identifiers

This package support the mapping across different protein/gene identifiers.

Citation

Gray KA, Yates B, Seal RL, Wright MW, Bruford EA. genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015 Jan;43(Database issue):D1079-85. doi: 10.1093/nar/gku1071. http://www.ncbi.nlm.nih.gov/pubmed/25361968

Installation

compath_hgnc can be installed easily from PyPI with the following code in your favorite terminal:

$ python3 -m pip install compath_hgnc

or from the latest code on GitHub with:

$ python3 -m pip install git+https://github.com/compath/compath_hgnc.git@master

Setup

HGNC can be downloaded and populated from either the Python REPL or the automatically installed command line utility.

Python REPL

>>> import compath_hgnc
>>> compath_hgnc_manager = compath_hgnc.Manager()
>>> compath_hgnc_manager.populate()

Command Line Utility

compath_hgnc populate

Acknowledgements

• This package heavily relies on Andrej Konotopez’s package PyHGNC and the Bio2BEL HGNC.