Updated version of nwalign with Python 3.x compatibility.
pip install nwalign3
Usage is essentially the same as the original nwalign package, with a few minor exceptions. As with the original package, a standard alignment can be accomplished with:
$ nwalign3 alphabet alpet
alphabet
alp---et
Scoring matrices can be specified in one of two ways. First, by providing the full path to a matrix file:
$ nwalign3 --matrix /path/to/matrices/BLOSUM62 EEAEE EEEEG
EEAEE-
EE-EEG
You can also provide the name of a built-in matrix (currently just PAM250 and BLOSUM62):
$ nwalign3 --matrix BLOSUM62 EEAEE EEEG
EEAEE-
EE-EEG
As with the original package, match, gap_open and gap_extend scores can be provided:
$ nwalign3 --gap_open -10 --gap_extend -4 --match 12 ASDFF ASFF
ASDFF
AS-FF
nwalign3 serves as essentially a drop-in replacement for nwalign:
>>> 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--')
As with command-line usage, matrix may be either the full path to a matrix file or the name of a built-in matrix.
To get the score of an alignment (where the first two arguments are a pair of aligned sequences):
>>> 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