uniprot mapper

map a string of whitespace seperated entries from one format onto another using uniprots mapping api

Args:
	query: to be mapped
	f: from ACC | P_ENTREZGENEID | ...
	t: to ...
	format: tab by default

Help:
	for a list of all possible mappings visit
	'http://www.uniprot.org/faq/28'

Installation

From pypi (recommended)

pip install uniprot_mapper

From source (UNIX) as standalone only

Clone the git repository

git clone https://github.com/jdrudolph/uniprot_mapper.git

Use `distutils to install the package

cd uniprot_mapper
sudo python setup.py install

Example

standalone

uniprot_mapper ACC P_ENTREZGENEID acc_file map_file

This will read UniprotIDs seperated by whitespaces from acc_file and store them to map_file.

Using a pipe:

echo P31749 | uniprot_mapper ACC P_ENTREZGENEID

will print the result to stdout which can be redirected further

inside a python script

import uniprot_mapper as mapper
print mapper.map('P31749', f='ACC', t='P_ENTREZGENEID')