[Biopython] Problem using Entrez with Python 3.2

Nicolas Joannin nicolas.joannin at gmail.com
Tue Dec 11 01:15:48 UTC 2012


Hello,

I'm having problems when trying to use Bio.Entrez with Python 3.2.
I get the following error message:

>>> from Bio import Entrez
>>> Entrez.email='my at email.address'
>>> handle=Entrez.esearch(db='nuccore',term='36329')
>>> record=Entrez.read(handle)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/Bio/Entrez/__init__.py",
line 351, in read
    record = handler.read(handle)
  File
"/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/Bio/Entrez/Parser.py",
line 169, in read
    self.parser.ParseFile(handle)
TypeError: read() did not return a bytes object (type=str)

Any comment, suggestion or help would be greatly appreciated!
Best regards,

Nicolas



More information about the Biopython mailing list