[Biopython-dev] Gsoc 2014 aspirant

[Fields, Christopher J]

On Mar 4, 2014, at 6:32 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Tue, Mar 4, 2014 at 10:40 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>> I would suggest to implement this in C, with a thin wrapper in Python.
>> Using 3rd-party libraries would increase the compile-time dependencies of Biopython.
>> Anyway I expect that the tricky part will be the design of the module, rather than the algorithms themselves, so using 3rd-party libraries wouldn't help us so much.
>> Best,
>> -Michiel.
> 
> I would also consider a pure Python implementation on top,
> both for cross-testing, but also for use under Jython or PyPy
> where using the C code wouldn't be possible (or at least,
> becomes more complicated).
> 
> (This is what the existing Bio.pairwise2 module does)

Ah, so it’s pure python.  Makes sense to have it for that purpose.  You could simply repurpose the existing code. 

> Adding third party C libraries would also make life hard for
> cross platform testing (Linux, Mac, Windows).
> 
> Peter

This is a problem with bioinformatics tools in general; they simply aren’t Windows-friendly.  However, one can write code with portability in mind (even C/C++).

chris