[Biopython] Problem using Entrez with Python 3.2

[Wibowo Arindrarto]

Hi Nicolas,

AFAIK, the Entrez XML parser requires bytes instead of strings. The
distinction matters in Python 3, so what you need to do is to convert
your string stream into a byte stream. To do so, you need to add a new
import:

from io import BytesIO

and replace the last line with these:

bytehandle = BytesIO(bytes(handle.read(), 'utf-8'))  # utf-8 or any
other encoding you want
record = Entrez.read(bytehandle)

We're basically reading the string, convert it to bytes, and create a
buffered bytes I/O that Entrez.read expects.

Alternativey, you can also read the handle into a file first, and open
it in binary mode:

with open('outfile.xml', 'w') as outfile:
    outfile.write(handle.read())

with open('outfile.xml', 'rb') as sourcefile:
    record = Entrez.read(sourcefile)

Hope that helps :),
Bow

On Tue, Dec 11, 2012 at 2:15 AM, Nicolas Joannin
<nicolas.joannin at gmail.com> wrote:
> 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
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython