nwalign 0.3.0

Needleman-Wunsch global sequence alignment

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 nwalign executable is installed to the PATH by setuptools

$ nwalign alphabet alpet
alphabet
alp---et

specify an alignment scoring matrix

$ nwalign --matrix /usr/share/ncbi/data/BLOSUM62 EEAEE EEEEG
EEAEE-
EE-EEG

with specified penalties

$ nwalign --gap_open -10 --gap_extend -4 --match 12 ASDFF ASFF
ASDFF
AS-FF

Python Usage

Alignment

>>> import nwalign 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