[Biopython] Entrez.read(handle) for Bio._py3k.EvilHandleHack throws error with python 3.2
Richard Llewellyn
llewelr at gmail.com
Tue Jul 24 02:24:06 UTC 2012
With python 3.2 and biopython 1.60 after getting a handle using
Entrez.esummary (and esearch, others?) I get a TypeError:
>>> from Bio import Entrez
>>> Entrez.email = "Your.Name.Here at example.org"
>>> handle = Entrez.esummary(db="journals", id="30367")
>>> record = Entrez.read(handle)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.2/site-packages/Bio/Entrez/__init__.py",
line 351, in read
record = handler.read(handle)
File "/usr/local/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)
>>> handle
<Bio._py3k.EvilHandleHack object at 0xb737a34c>
Ah, it is evil!
I realize py3k not yet officially supported.
Thanks for the great work.
More information about the Biopython
mailing list