问题描述
我正在尝试在biopython
中循环运行成对全局对齐方法,以处理大约10000对字符串.每个字符串平均为20个字符长.对一对序列运行该方法效果很好.但是将其循环运行(低至4对)会导致分段错误.该如何解决?
I am trying to run pairwise global alignment method in biopython
in loop for about 10000 pair of strings. Each string on an average is 20 characters long. Running the method for a single pair of sequences works fine. But running this in a loop, for as low as 4 pairs, results in segmentation fault. How can this be solved?
from Bio import pairwise2
def myTrial(source,targ):
if source == targ:
return [source,targ,source]
alignments = pairwise2.align.globalmx(source, targ,1,-0.5)
return alignments
sour = ['najprzytulniejszy', 'sadystyczny', 'wyrzucić', 'świat']
targ = ['najprzytulniejszym', 'sadystycznemu', 'wyrzucisz', 'świat']
for i in range(4):
a = myTrial(sour[i],targ[i])
推荐答案
由于使用循环,所以没有发生分段错误,而是因为您提供非ASCII字符作为采用ASCII字符串的对齐方式的输入仅输入.幸运的是,Bio.pairwise2.align.globalmx
还允许将包含任意ASCII和非ASCII字符字符串的对齐列表作为标记(即,将诸如['ABC', 'ABD']
和['ABC', 'GGG']
之类的字符串列表对齐以产生类似
The segmentation fault isn't happening because you are using a loop, but because you are providing non-ASCII characters as input for an alignment mode that takes ASCII string inputs only. Luckily, Bio.pairwise2.align.globalmx
also permits aligning lists that contain arbitrary strings of ASCII and non-ASCII characters as tokens(i.e. aligning lists of strings, such as ['ABC', 'ABD']
with ['ABC', 'GGG']
to produce alignments like
['ABC', 'ABD', '-' ]
['ABC', '-' , 'GGG']
或者在您的情况下,将非ASCII字符(例如['ś', 'w', 'i', 'a', 't']
和['w', 'y', 'r', 'z', 'u', 'c', 'i', 's', 'z']
)的列表对齐以产生类似的对齐方式
or in your case, aligning lists of non-ASCII characters such as ['ś', 'w', 'i', 'a', 't']
and ['w', 'y', 'r', 'z', 'u', 'c', 'i', 's', 'z']
to produce alignments like
['ś', 'w', '-', '-', '-', '-', '-', 'i', 'a', 't', '-', '-']
['-', 'w', 'y', 'r', 'z', 'u', 'c', 'i', '-', '-', 's', 'z']
要使用Biopython完成此操作,请在您的代码中替换
To accomplish this with Biopython, in your code, replace
alignments = pairwise2.align.globalmx(source, targ,1,-0.5)
与
alignments = pairwise2.align.globalmx(list(source), list(targ), 1, -0.5, gap_char=['-'])
因此输入
source = 'świat'
targ = 'wyrzucisz'
修改后的代码将产生
[(['ś', 'w', '-', '-', '-', '-', '-', 'i', 'a', 't', '-', '-'],
['-', 'w', 'y', 'r', 'z', 'u', 'c', 'i', '-', '-', 's', 'z'],
2.0,
0,
12)]
代替分段错误.
由于列表中的每个标记只有一个字符长,因此您还可以使用以下方法将对齐的列表转换回字符串:
And since each token in the list is only one character long, you can also convert the resulting aligned lists back into strings using:
new_alignment = []
for aln in alignment:
# Convert lists back into strings
a = ''.join(aln[0])
b = ''.join(aln[1])
new_aln = (a, b) + aln[2:]
new_alignment.append(new_aln)
在上面的示例中,new_alignment
将为
[('św-----iat--', '-wyrzuci--sz', 2.0, 0, 12)]
根据需要.
这篇关于Biopython成对对齐在循环中运行时会导致分段错误的文章就介绍到这了,希望我们推荐的答案对大家有所帮助,也希望大家多多支持!