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Simple interface for uniprot.org

Project Description

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 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'])
Release History

Release History

This version
History Node

0.4.1

History Node

0.4

History Node

0.3

History Node

0.2

History Node

0.1

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
uniprot_tools-0.4.1.tar.gz (3.3 kB) Copy SHA256 Checksum SHA256 Source May 11, 2014

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