README

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'])