[Biopython-dev] Bio/SearchIO/BlastIO/blast_xml.py output under Python 2.7.4

[Peter Cock]

On Mon, Apr 8, 2013 at 6:08 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Mon, Apr 8, 2013 at 6:02 PM, Wibowo Arindrarto <bow at bow.web.id> wrote:
>> Hi Peter, everyone,
>>
>> This is reproducible in my machine (which just happen to update its default
>> Python2.x to 2.7.4 actually). Looks like they changed the underlying SAX XML
>> writer (xml.sax.saxutils.XMLGenerator ~ which the SearchIO blast_xml writer
>> subclasses). The new write() method calls the io.TextIOWrapper.write()
>> function, which expects unicode only.
>>
>> See the comparison here:
>> Python2.7.3
>> (http://hg.python.org/cpython/file/70274d53c1dd/Lib/xml/sax/saxutils.py#l84)
>> vs Python2.7.4
>> (http://hg.python.org/cpython/file/026ee0057e2d/Lib/xml/sax/saxutils.py#l109).
>> Also, here's the io module doc page for reference:
>> http://docs.python.org/2/library/io.html
>>
>> I'll write up a Python <=2.7.3-compatible patch to fix this soon, if
>> everybody's ok with it :).
>>
>> Cheers,
>> Bow
>
> Sounds good - with the combination of TravisCI and the buildbot we should
> have the major platforms covered.
>
> Thanks,
>
> Peter

Pull request merged, thanks Bow
https://github.com/biopython/biopython/pull/176

Peter