Question

导入Biopython并解析文件的代码已在我的笔记本电脑上运行。现在，我有一个很大的文件，只能在另一台同时安装了python和Biopython的计算机上进行解析。但是在那台计算机上，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。

整个代码是：

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'))

错误消息：

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，它将替换标准库python copy模块，从而提供不直观的AttributeError。将脚本重命名为其他名称，例如my_copy.py，它将起作用。

此代码段演示了导入SeqIO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：模块'Bio.SeqIO'没有属性'parse'

1 个答案: