[Biopython-dev] test_AlignIO to python 3

[Peter Cock]

>>>> 3. The big one: No sgmllib in p3.
>>>>   The obvious solution is to include it (I suppose the licenses are
>>>> compatible?). The alternative (using htmllib) might be more long-term,
>>>> in my opinion
>>>
>>> A lot of the things using sgmllib are already deprecated (e.g.
>>> Bio.NetCatch and Bio.Prosite). I think that leaves just Bio.UniGene
>>> and Bio.InterPro - which isn't such a big issue.
>>
>> I know very little about those parts of the code, but there was an
>> import required for sgmllib in test_AlignIO.
>
> This is due to Bio/File.py trying to import sgmllib, and Bio.File is used
> by several of the SeqIO/AlignIO parsers (e.g. Bio.GenBank). That
> code needing sgmllib was deprecated in Biopython 1.52 (Sept 2009),
> and so we should be keeping it until Sept 2010... I think making it a
> lazy import will do the trick.

How's this?

http://github.com/biopython/biopython/commit/e9ab0b353ae4a914db20a53f2377a34bc56c30a6

Peter