如何使用biopython配對來對齊單詞列表

Question

當我運行下面的腳本時，輸出被分成單個字符。任何想法爲什麼？它看起來像第二個參數分成單個字符。

我想對齊單詞序列。

我會有很多單詞，因此無法將它們映射到僅字母。

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)) 

輸出：

['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

你傳遞一個列表localms一個希望將string或Seq對象，也gap_char應該是一個字符串不是列表。

試試下面的代碼片段：

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)) 

輸出

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 

[...]