Python interface for the seq-align C library, written by Isaac Turner (@noporpoise).
I expanded no_start_gap_penalty and no_end_gap_penalty to:
no_start_gap_penalty, no_start_gap_penalty_a, no_start_gap_penalty_b,
no_end_gap_penalty, no_end_gap_penalty_a, no_end_gap_penalty_b.
The feature no_start_gap_penalty_a seems not to work, but no_start_gap_penalty_b works.
The code is 100% symmetric for all these cases, but investigate seq-align/src/alignment.c
where the comments say: // Think carefully about which way round these are
The algorithm may not be symmetric.
pip install pyseq-align
To install directly from GitHub,
git clone https://github.com/Lioscro/pyseq-align.git --recursive
cd pyseq-align
pip install .
Two alignment algorithms are provided: Needleman-Wunsch and Smith-Waterman.
from pyseq_align import NeedlemanWunsch
nw = NeedlemanWunsch()
al = nw.align('ACGT', 'ACGTC')
print(al.result_a) # ACGT-
print(al.result_b) # ACGTC
print(al.score)from pyseq_align import SmithWaterman
sw = SmithWaterman()
als = sw.align('ACGT', 'ACGTC') # unlike above, this is a list of Alignment's
for al in als:
print(al.result_a, al.pos_a) # ACGT, 0
print(al.result_b, al.pos_b) # ACGT, 0
print(al.score)