[Biopython-dev] Newbler ACE file to SAM?

[Kevin Jacobs <jacobs@bioinformed.com>]

On Wed, Aug 4, 2010 at 1:03 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Wed, Aug 4, 2010 at 6:00 PM, Kevin Jacobs <jacobs at bioinformed.com>
> <bioinformed at gmail.com> wrote:
> > On Wed, Aug 4, 2010 at 12:35 PM, Nick Loman <n.j.loman at bham.ac.uk>
> wrote:
> >> [...]
> >> Not sure if there's scope for tighter integration to Biopython but will
> >> leave that to you experts!
> >>
> >>
> > Unlike much of my other code, there is no dependency on pysam, so there
> is
> > no reason why biopython couldn't adopt my converter -- I'd certainly be
> > happy to donate it.   I'm just not sure if there is a good place for it.
>
> Is it a stand alone script using Biopython to parse ACE and SFF?
> Maybe we can include it in the scripts folder - at the very least you could
> add a link to it on http://www.biopython.org/wiki/Scriptcentral
>
>
The code is here:

http://code.google.com/p/glu-genetics/source/browse/glu/modules/seq/Newbler2SAM.py

There are some fairly simple dependencies on GLU libraries and an optional
Cython accelerator for CIGAR and NM computation, but otherwise it is fairly
easy to make it stand alone.

-Kevin