how to align lists of words using biopython pairwise2 - biopython

Question

When I run the script below, output is getting split into single chars. Any idea why? It looks like the second argument gets split into single chars.
I am trying to align the word sequences.
I will have many words hence cannot map them to letters only.
from Bio.Seq import Seq
from Bio.pairwise2 import format_alignment
fruits = ["orange","pear", "apple","pear","orange"]
fruits1 = ["pear","apple"]
from Bio import pairwise2
alignments = pairwise2.align.localms(fruits,fruits1,2,-1,-0.5,-0.1, gap_char=["-"])
for a in alignments:
print(format_alignment(*a))
Output:
['orange', 'r', 'a', 'e', 'p', 'e', 'l', 'p', 'p', 'a', 'pear', 'orange']
|||||||||
['-', 'r', 'a', 'e', 'p', 'e', 'l', 'p', 'p', 'a', '-', '-']
Score=4

Answer 1

You are passing a list to localms which expects a string or a Seq object, also gap_char should be a string not a list.
Try the following snippet:
import Bio.pairwise2 as pairwise2
fruits = ["orange", "pear", "apple", "pear", "orange"]
fruits1 = ["pear", "apple"]
for f0 in fruits:
for f1 in fruits1:
print('Aligning {0} and {1}'.format(f0, f1))
alignments = pairwise2.align.localms(f0, f1, 2, -1, -0.5, -0.1, gap_char="-")
for a in alignments:
print(pairwise2.format_alignment(*a))
Output
Aligning orange and pear
orange
|
pear--
Score=2
Aligning orange and apple
orange
|
-apple
Score=2
orange-
|
--apple
Score=2
Aligning pear and pear
pear
||||
pear
Score=8
[...]