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

Question

The codes which import Biopython and parse the files have worked on my laptop. Now I have a very big file that I can only parse it on another computer which also have installed python and Biopython. But on that computer, it gives me error message. I have uninstalled and reinstalled the latest python and biopython. The problem is still there.

The entire code is:

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'))

Error message:

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'

Please let me know if my question is not clear enough.

score 1 · Accepted Answer · answered Nov 13 '18 at 09:09

Your script is named copy.py this is replacing the standard library python copy module and thus giving the non-intuitive AttributeError. Re-name your script to something else, for example my_copy.py, and it will work.

This code snippet demonstrates that importing SeqIO imports 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'

1 Answers1