uniprot_tools

uniprot provides a command-line and python interface to access the uniprot database

available services: map, retrieve

map map a list of ids from one format onto another using uniprots mapping api

Args:
    query: id or list of ids 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'

retrieve request entries by uniprot acc using batch retrieval

Args:
    query: list of ids to retrieve
    format: txt by default

Help:
    possible formats:
    txt, xml, rdf, fasta, gff

Installation

From pypi (recommended)

pip install uniprot_tools

From source (UNIX) as standalone only

Clone the git repository

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

Use distutils to install the package

cd uniprot
sudo python setup.py install

Example

standalone

uniprot map ACC P_ENTREZGENEID acc_file map_file

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

uniprot retrieve acc_file entries.txt

Retrieve textual etries for all uniprot ids in acc_file and save to entries.txt

Using a pipe:

echo P31749 | uniprot map ACC P_ENTREZGENEID

will print the result to stdout which can be redirected further

echo P31749 | uniprot retrieve

will print the result to stdout which can be redirected further

inside a python script

import uniprot as uni
print uni.map('P31749', f='ACC', t='P_ENTREZGENEID') # map single id
print uni.map(['P31749','Q16204'], f='ACC', t='P_ENTREZGENEID') # map list of ids
print uni.retrieve('P31749')
print uni.retrieve(['P31749','Q16204'])