Metadata-Version: 1.1
Name: alignment
Version: 1.0.4
Summary: Native Python library for generic sequence alignment.
Home-page: https://github.com/eseraygun/python-alignment
Author: Eser Aygün
Author-email: eser.aygun@gmail.com
License: LICENSE.txt
Description: =========
        Alignment
        =========
        
        Alignment is a native Python library for generic sequence alignment. It is
        useful in cases where your alphabet is arbitrarily large and you cannot use
        traditional biological sequence analysis tools. It supports global and local
        pairwise sequence alignment. I also plan to add support for profile-profile
        alignments, but who knows when.
        
        Usage
        =====
        
        Typical usage looks like this::
        
            from alignment.sequence import Sequence
            from alignment.vocabulary import Vocabulary
            from alignment.sequencealigner import SimpleScoring, GlobalSequenceAligner
        
            # Create sequences to be aligned.
            a = Sequence('what a beautiful day'.split())
            b = Sequence('what a disappointingly bad day'.split())
        
            # Create a vocabulary and encode the sequences.
            v = Vocabulary()
            aEncoded = v.encodeSequence(a)
            bEncoded = v.encodeSequence(b)
        
            # Create a scoring and align the sequences using global aligner.
            scoring = SimpleScoring(2, -1)
            aligner = GlobalSequenceAligner(scoring, -2)
            score, encodeds = aligner.align(aEncoded, bEncoded, backtrace=True)
        
            # Iterate over optimal alignments and print them.
            for encoded in encodeds:
                alignment = v.decodeSequenceAlignment(encoded)
                print alignment
                print 'Alignment score:', alignment.score
                print 'Percent identity:', alignment.percentIdentity()
                print
        
        TODO List
        =========
        
        - Profile-profile alignment is not working yet.
        
Platform: UNKNOWN
Requires: numpy
