Metadata-Version: 1.0
Name: oldowan.fasta
Version: 1.0.2
Summary: Read and write FASTA format.

Home-page: http://www.raaum.org/software/oldowan
Author: Ryan Raaum
Author-email: code@raaum.org
License: MIT
Description: oldowan.fasta is a small bioinformatic utility to read and write sequence data
        in the FASTA_ format. FASTA is the most commonly used simple file format for
        storing multiple DNA, RNA, or protein sequences in a single file. It is a
        text-based, human-readable format.
        
        Installation Instructions
        =========================
        
        This package is pure Python and has no dependencies outside of the standard
        library. The easist way to install is using ``easy_install`` from the
        setuptools_ package.  This usually goes something like this::
        
        $ easy_install oldowan.fasta
        
        or on a unix-like system, assuming you are installing to the main Python
        ``site-packages`` directory as a non-privileged user, this::
        
        $ sudo easy_install oldowan.fasta
        
        You may also use the standard python distutils setup method. Download the
        current source archive from the file list towards the bottom of this page,
        unarchive it, and install. On Mac OS X and many other unix-like systems, having
        downloaded the archive and changed to the directory containing this archive in
        your shell, this might go something like::
        
        $ tar xvzf oldowan.fasta*
        $ cd oldowan.fasta*
        $ python setup.py install
        
        Quick Start
        ===========
        
        oldowan.fasta has an interface based on the standard Python ``file``.  Import
        oldowan.fasta::
        
        >>> from oldowan.fasta import fasta
        
        Read a FASTA format file::
        
        >>> for entry in fasta('sequences.fasta', 'r'):
        ...     print entry['name'], len(entry['sequence'])
        
        A more cumbersome, but equivalent way of doing the above::
        
        >>> fasta_file = fasta('sequences.fasta', 'r')
        >>> for entry in fasta_file:
        ...     print entry['name'], len(entry['sequence'])
        >>> fasta_file.close()
        
        Even more cumbersome, and if the FASTA file is large, potentially
        memory-draining version (the previous two methods only read one entry at a time
        from the file, this reads the whole file into memory at once)::
        
        >>> fasta_file = fasta('sequence.fasta', 'r')
        >>> entries = fasta_file.readentries()
        >>> fasta_file.close()
        >>> for entry in entries:
        ...     print entry['name'], len(entry['sequence'])
        
        Read a string of FASTA format sequences::
        
        >>> fasta_string = open('sequences.fasta', 'r').read()
        >>> for entry in fasta(fasta_string, 's'):
        ...     print entry['name'], len(entry['sequence'])
        
        Read a file object::
        
        >>> fasta_file = open('sequences.fasta', 'r')
        >>> for entry in fasta(fasta_file, 'f'):
        ...     print entry['name'], len(entry['sequence'])
        
        Write to a file::
        
        >>> fasta_file = open('sequences.fasta', 'w')
        >>> fasta_file.write({'name':'Sequence1', 'sequence':'AGCTAGCT'})
        >>> fasta_file.close()
        
        Release History
        ===============
        
        1.0.0 (August 16, 2008)
        initial release of module.
        
        1.0.1 (March 25, 2009)
        bug fix updates
        
        1.0.2 (March 26, 2009)
        update VERSION info
        
        .. _FASTA: http://en.wikipedia.org/wiki/Fasta_format
        .. _setuptools: http://peak.telecommunity.com/DevCenter/EasyInstall
        
Platform: Any
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
