Metadata-Version: 1.1
Name: seqtools
Version: 0.8
Summary: Tools for sequence and alignment manipulation
Home-page: http://github.com/faircloth-lab/seqtools/
Author: Brant Faircloth
Author-email: brant.faircloth+seqtools@gmail.com 
License: http://www.opensource.org/licenses/BSD-3-Clause
Description: Introduction
        ============
        
        *seqtools* is a set of Python_ libraries for manipulating sequence data and 
        generating sequence alignments.  Many of the functions and classes
        within are derived from the excellent galaxy-tools_ libraries 
        (`Blankenberg et al. <http://dx.doi.org/10.1093/bioinformatics/btq281>`_),
        but modified to use numpy_ for storing quality values, etcetera.  There
        are also functions for working with lastz_ and some general functions
        for parsing arguments and validating input.
        
        Generally speaking, this is a utility library that we use in other
        programs on which we work.  Thus, it's commonly a dependency of many of
        these packages.
        
        Installation
        ------------
        
        seqtools_ requires numpy_ (> 1.3).  After installing numpy, to install
        seqtools_:
        
        - from source::
        
            tar -xzvf ~/your/download/location/seqtools-*.tar.gz
            python setup.py install
        
        - using easy_install::
        
            easy_install seqtools
        
        - using pip::
        
            pip install seqtools
        
        
        Tests
        -----
        
        While several of the functions and classes within seqtools_ are not (yet) 
        fully tested, **ALL** of the *sequence-handling* classes, methods, and functions are
        covered by unittests.
        
        Running the tests as below, requires python-nose_.  After installing python-nose_, numpy_, 
        and seqtools_ run the tests using:
        
        >>> from seqtools import sequence
        >>> sequence.test()
        
        
        Alternatively, you can run:::
        
            python setup.py test
        
        Or, after installing numpy_ and seqtools_ you can run the tests using:::
        
            python seqtools/sequence/tests/run.py
        
        
        .. _Python: http://www.python.org/
        .. _galaxy-tools: http://bitbucket.org/galaxy/galaxy-dist/src/
        .. _numpy: http://numpy.scipy.org/
        .. _lastz: http://www.bx.psu.edu/~rsharris/lastz/
        .. _python-nose: http://code.google.com/p/python-nose/
        .. _seqtools: https://github.com/faircloth-lab/seqtools/
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
