AttributeError: module 'Bio.SeqIO' has no attribute 'parse'

Question

导入 Biopython 和解析文件的代码在我的笔记本电脑上运行。现在我有一个非常大的文件，我只能在另一台也安装了 python 和 Biopython 的计算机上解析它。但是在那台电脑上，它给了我错误信息。我已经卸载并重新安装了最新的 python 和 biopython。问题仍然存在。

整个代码为：

from Bio import SeqIO

with open('/Users/yuewang/work/18s_tree/aligned_fungi_rna.fasta', 'w') as output:
    output.write('')

with open('/Users/yuewang/work/18s_tree/SILVA_132_SSURef_tax_silva_full_align_trunc.fasta') as fastafile:
    record_iterator = SeqIO.parse(fastafile, 'fasta')

    fungi = 'Eukaryota;Opisthokonta;Nucletmycea;Fungi;'
        for record in record_iterator:
            if fungi in record.id:
                with open('/Users/yuewang/work/18s_tree/aligned_fungi_rna.fasta', 'a') as output:
                    output.write(record.format('fasta'))

错误信息：

Traceback (most recent call last):
  File "copy.py", line 1, in <module>
    from Bio import SeqIO
  File "/usr/local/Cellar/python/3.7.1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/Bio/SeqIO/__init__.py", line 391, in <module>
    from . import UniprotIO
  File "/usr/local/Cellar/python/3.7.1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/Bio/SeqIO/UniprotIO.py", line 34, in <module>
    from xml.etree import cElementTree as ElementTree
  File "/usr/local/Cellar/python/3.7.1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/xml/etree/cElementTree.py", line 3, in <module>
    from xml.etree.ElementTree import *
  File "/usr/local/Cellar/python/3.7.1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/xml/etree/ElementTree.py", line 1660, in <module>
    from _elementtree import *
  File "/Users/yuewang/work/18s_tree/copy.py", line 7, in <module>
    record_iterator = SeqIO.parse(fastafile, 'fasta')
AttributeError: module 'Bio.SeqIO' has no attribute 'parse'

如果我的问题不够清楚，请告诉我。

Answer 1

您的脚本被命名为 copy.py，这将替换标准库 python copy 模块，从而提供非直观的 AttributeError。将您的脚本重命名为其他名称，例如 my_copy.py，它将起作用。

此代码片段演示了导入 SeqIO 会导入 copy:

>>> import sys
>>> sys.modules['copy']
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
KeyError: 'copy'
>>> from Bio import SeqIO
>>> sys.modules['copy']
<module 'copy' from '/usr/lib64/python3.6/copy.py'>

AttributeError: module 'Bio.SeqIO' has no attribute 'parse'

AttributeError: module 'Bio.SeqIO' has no attribute 'parse'

python

bioinformatics

attributeerror

biopython

python-3.x