[Biopython-dev] MUMmer

[Marcin Swiatek]

Bartek, Brad,

Thank you for the suggestions. I will set myself up as proposed and see
what I can do to align my code with local customs and traditions. If
questions arise, I will post again. 

As for the use of alignment object, I have actually chosen to represent
'candidate' matches by my own simplistic class. Nucmer, the way I use
it, generates lots of spurious matches, which I always need to somehow
filter. Thus, it seemed perfectly reasonable at the time to create the
proper representation of alignment later on, in a separate function
call. Following your suggestion I will probably change it to return an
alignment object, rather than a pair of sequences. But details are best
discussed once the code is available, so I think we will return to this
matter later. 

Regards,

Marcin


-----Original Message-----
From: barwil at gmail.com [mailto:barwil at gmail.com] On Behalf Of Bartek
Wilczynski
Sent: Thursday, April 30, 2009 12:51 PM
To: Marcin Swiatek
Cc: biopython-dev at biopython.org
Subject: Re: [Biopython-dev] MUMmer

Hi Marcin,

On Thu, Apr 30, 2009 at 5:23 PM, Marcin Swiatek
<marcin.swiatek at mail.mcgill.ca> wrote:
> Hello,
>
>
>
> I use this stuff only myself, in work on bacterial genomes, but I
would
> be more than willing to contribute it to the project. It may be rough
> around the edges at the moment, but I think I could easily give it the
> necessary polish if there is interest in having it included.
>
Contributions are always welome

>
>
> Should that be the case, could one of the project leads point me in
the
> right direction, please? How should I go about the submission?
>
>
I don't think I qualify as a lead, but nonetheless I think I can help
here.

I think that the best way to submit your code currently is to create a
branch (fork) of
biopython on github and submit your changes there and then notify
people on biopython-dev
that there is new code to review. You can also submit an enhancement
bug to bugzilla.

There are a couple of wiki pages which might be of interest  to you:
- http://biopython.org/wiki/Contributing
- http://biopython.org/wiki/GitUsage

If you have any questions or problems during the process, ask on the
list.

As for the code, I'm not sure, but maybe instead of returning a pair
of sequences, an alignment object might be a better choice?

You might want to also check out a recent code on application wrappers:
http://lists.open-bio.org/pipermail/biopython-dev/2009-April/005766.html

cheers
  Bartek