uniprot_mapper 0.6

Simple interface for uniprot.org/mapping

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

Clone the git repository

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

Make the script executable and add it to your PATH:

chmod +x uniprot_mapper/uniprot_mapper/uniprot_mapper.py
cd /usr/local/bin
sudo ln -s /path/to/uniprot_mapper.py .

Example

standalone

uniprot_mapper.py 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.py 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')