Question

当我运行下面的脚本时，输出将被拆分为单个字符。知道为什么吗？看起来第二个参数被分成单个字符。

我正在努力调整单词序列。

我会有很多单词因此无法将它们映射到字母。

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))

输出：

['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

您正在将列表传递给需要string或Seq对象的localms，同时gap_char应该是不是列表的字符串。

请尝试以下代码段：

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))

<强>输出

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

[...]

如何使用biopython pairwise2

1 个答案: