[Biopython] next-gen sequencing software

[Peter]

On Fri, Jul 24, 2009 at 9:53 AM, Jose Blanca<jblanca at btc.upv.es> wrote:
> Hi:
>
> We have been writting some code that we think that could be interesting to the
> Biopython community. ... Currently the software is not finished but it starts to
> be useful. Everything is written in python. We have used Biopython for some
> things, but for some others we have used a slighty different approach. If the
> Biopython developers think that some of our ideas could be of any use we
> would be willing to incorporate it into Biopython.
> If you want to take a look just go to:
> http://bioinf.comav.upv.es/svn/biolib/biolib/src/

Cool. I already knew you had some interested ideas for contig classes.
I see you also have a parser for EMBOSS water output - where you
actually collect some useful information from the header, which the
Biopython parser ignores. This was a simplification because the current
Biopython alignment object doesn't have a proper annotation system.

Work on improving the Biopython alignment object and introducing a
contig object is something I would like to see for the next release (once
Biopython 1.51 is out).

I'm sure there is other stuff in your code that would also be very useful.

If you want to contribute code to Biopython is will have to be under our
MIT style license, but in the meantime maybe you should stick an
an explicit license on your code?

Peter