[Biopython-dev] Google Summer of Code Proposal

[Peter Cock]

On Wed, Apr 13, 2011 at 3:55 AM, Maximiliano David Bustos
<md.bustos90 at gmail.com> wrote:
> Hello everybody,
>
> My name is Maximiliano David Bustos, I am a Computer Science student from La
> Rioja, Argentina. I joined the list some days ago to start collaborating
> with BioPython project and to get feedback in Google Summer of Code (GSoC).
> The proposal I submitted to GSoC is titled *"Variant representation, parser,
> generator, and coordinate
> converter"*<https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=0B1Q10jdy75U_YzE4ZmUzMGEtNjA5Ni00Mjc4LTgwYTQtZTI1MTdkNTJiODc4&hl=en&authkey=CN_Dm8ML>.
> This idea was taken from BioPython wiki.
> The project mentor is Reece Hart, who had been helping me a lot in the
> elaboration of my proposal. Brad Chapman made great contributions too.
>
> Reece recommended me to send my proposal to the mailing list. I would really
> appreciate any feedback from you.
>
> Thanks in advance,
>
> Maxi.

Hi Maxi,

Just a couple of quick initial thoughts on the implementation section,

>> Implementation
>>
>> I will implement the library in Python 2.7, using PLY (Python Lex-Yacc)
>> or Pyparsing. I will follow BioPython coding conventions and abstractions
>> so the project can be integrated from the beginning.

Currently Biopython supports Python 2.5 to 2.7 (and we're working on Python 3).
If you target Python 2.7 specific features it would be a problem for integrating
your work into Biopython. You would ideally also run and test your code on
Python 2.5, and on Python 3.

On the bright side, PLY (Python Lex-Yacc) and Pyparsing are pure python
and *should* work cross platform (we do want to support Windows). On
the other hand, if we can do without them and use the standard Python
library only, I'd be happier as it will keep our dependencies down. This is
important for making Biopython easy to install and use. In this case they
are run time dependencies so it isn't critical.

Peter