Native Python library for generic sequence alignment
Python
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alignment
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CHANGES.txt
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README.rst Bump the version, again. May 2, 2013
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setup.py

README.rst

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.

Installation

You can install the most recent release using pip:

pip install alignment

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.