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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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')

