Metadata-Version: 1.1
Name: uniprot_tools
Version: 0.4.1
Summary: Simple interface for uniprot.org
Home-page: https://github.com/jdrudolph/uniprot
Author: Jan Rudolph
Author-email: jan.daniel.rudolph@gmail.com
License: MIT license
Description: 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'])
        
        
Platform: UNKNOWN
Requires: requests
Requires: argparse
