Metadata-Version: 1.1
Name: tfasta
Version: 0.2.2
Summary: Parses fasta files using templates and creates formatted fasta.
Home-page: http://pypi.python.org/pypi/tfasta/
Author: James C. Stroud
Author-email: xtald00d@gmail.com
License: BSD
Description: ========
         tfasta 
        ========
        
        Introduction
        ------------
        
        The tfasta python package simplifies working
        with fasta, providing functionality
        for both reading and writing fasta files.
        The "t" in "tfasta" represents
        "templated", which means that fasta parsing is
        performed according to pre-defined or user-defined
        templates. Examples are given below.
        
        Installation
        ------------
        
        Install tfasta with `pip`_ (recommended) or `easy_install`_::
        
          sudo pip install tfasta
        
        Optionally, download the source files from
        http://pypi.python.org/pypi/tfasta/
        and run the following commands in the source directory::
        
          python setup.py build
          sudo python setup.py install
        
        Home Page & Repository
        ----------------------
        
          - Home Page: http://pypi.python.org/pypi/tfasta/
          - Documentation: http://pythonhosted.org/radialx/
          - Repository: https://github.com/jcstroud/tfasta/
        
        
        Usage
        -----
        
        Reading Fasta Files
        ~~~~~~~~~~~~~~~~~~~
        
        Reading fasta files is performed with the *fasta_parser()* function.
        The following text is the first 10 lines of the
        file "``short-extended.fas``"::
        
            >gi|32033604|ref|ZP_00133915.1|
            ATGQVIGTFTVRNDNGLHARPSAVLVQTLKPFAAKVTVENLDRGTAPANAKSTMKVVALG
            ASQAHRLRFVAEGEDAQQAIEALAKAFVEGLGESVSFVPAVEDTIEGAAQPQAVESAKNF
            ANPTASEPTVEGQVEGTFVIQNEHGLHARPSAVLVNEVKKYNATIVVQNLDRNTQLVSAK
            SLMKIVALGVVKGHRLHFVATGDDAQKAIDGIGEAIAAGLGE
            >gi|1573424|gb|AAC22107.1|
            VEGAVVGTFTIRNEHGLHARPSANLVNEVKKFTSKITMQNLTRESEVVSAKSLMKIVALG
            VTQGHRLRFVAEGEDAKQAIESLGKAIANGLGENVSAVPPSEPDTIEIMGDQIHTPAVTE
            DDNLPANAIEAVFVIKNEQGLHARPSAILVNEVKKYNASVAVQNLDRNSQLVSAKSLMKI
            VALGVVKGTRLRFVATGEEAQQAIDGIGAVIESGLGE
        
        Any fasta file may be parsed with a single command::
        
            >>> import tfasta
            >>> fast = tfasta.fasta_parser("short-extended.fas")
            >>> f = fast.next()
            >>> print f['name']
            gi|32033604|ref|ZP_00133915.1|
            >>> print f['sequence'][:60]
            ATGQVIGTFTVRNDNGLHARPSAVLVQTLKPFAAKVTVENLDRGTAPANAKSTMKVVALG
            f = fast.next()
            print f['name']
            gi|1573424|gb|AAC22107.1|
        
        In this example, the *fasta_parser()* function returns
        an iterator of dictionaries ("``fast``") with two
        keys: ``name`` and ``sequence``.
        The ``name`` key corresponds to all of the plain text after
        the fasta format marker "``>``" that marks a new sequence.
        
        .. _`pip`: http://www.pip-installer.org/en/latest/
        .. _`easy_install`: http://peak.telecommunity.com/DevCenter/EasyInstall
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
