[Biopython] Problem using Entrez with Python 3.2

[Nicolas Joannin]

Hi Bow,

Thanks a million for your answer!
It is very clear and pedagogical; I appreciate that a lot!
Works like a charm ;)

Best regards,
Nicolas



Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan




On Sat, Dec 15, 2012 at 2:58 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com>wrote:

> 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
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>