PKG-INFO

Metadata-Version: 1.0
Name: nwalign3
Version: 0.1.0
Summary: Needleman-Wunsch global sequence alignment
Home-page: https://gitub.com/briney/nwalign3
Author: Bryan Briney
Author-email: briney@scripps.edu
License: BSD
Description: 
        ------------------------------------------------------------------------------
        nwalign3: fast `cython`_  - `Needleman-Wunsch`_ alignment
        ------------------------------------------------------------------------------
        
        .. _`Needleman-Wunsch`: http://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm
        .. _`scoring matrix`: http://en.wikipedia.org/wiki/Substitution_matrix
        .. _`cython`: http://cython.org
        
        This module provides a python module and a command-line interface to do global-
        sequence alignment using the `Needleman-Wunsch` algorithm. It uses `cython`_
        and numpy for speed.
        
        Command-Line Usage
        ==================
        the nwalign3 executable is installed to the PATH by setuptools
        ::
        
        $ nwalign3 alphabet alpet
        alphabet
        alp---et
        
        specify an alignment `scoring matrix`_
        ::
        
        $ nwalign3 --matrix /usr/share/ncbi/data/BLOSUM62 EEAEE EEEEG
        EEAEE-
        EE-EEG
        
        with specified penalties
        ::
        
        $ nwalign3 --gap_open -10 --gap_extend -4 --match 12 ASDFF ASFF
        ASDFF
        AS-FF
        
        
        Python Usage
        ============
        Alignment
        ---------
        ::
        
        >>> import nwalign3 as nw
        >>> nw.global_align("CEELECANTH", "PELICAN", matrix='PAM250')
        ('CEELE-CANTH', '-PEL-ICAN--')
        
        # with a specified penalty for open and extend.
        >>> nw.global_align("CEELECANTH", "PELICAN", gap_open=-10, gap_extend=-4, matrix='PAM250')
        ('CEELECANTH', '-PELICAN--')
        
        
        the `matrix` is specified as the full path to an `scoring matrix`_ as
        is distributed with the NCBI toolset.
        
        Scoring
        -------
        get the score of an alignment. (the first 2 args are from an alignment
        and must have the same length.
        ::
        
        >>> nw.score_alignment('CEELECANTH', '-PELICAN--', gap_open=-5,
        ...                     gap_extend=-2, matrix='PAM250')
        11
        
        >>> nw.score_alignment('CEELE-CANTH', '-PEL-ICAN--', gap_open=-5,
        ...                     gap_extend=-2, matrix='PAM250')
        6
        
        
        
Keywords: sequence bioinformatics alignment needleman-wunsch
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Text Processing