[Biopython-dev] Newbler ACE file to SAM?

[Peter]

On Wed, Aug 4, 2010 at 3:48 PM, Nick Loman <n.j.loman at bham.ac.uk> wrote:
> Hi biopython-developers,
>
> Has anyone written any code to convert ACE files (Newbler ACE, in
> particular) to SAM format?
>
> I've seen a little bit of discussion on this subject in various places:
> http://seqanswers.com/forums/showthread.php?t=5138
> http://biostar.stackexchange.com/questions/1828/how-to-convert-newbler-output-or-ace-to-sam-format
>
> It seems that a quick way of doing this would involve Biopython's support
> for reading ACE and (perhaps) PySam's support for writing SAM files
> (http://wwwfgu.anat.ox.ac.uk/~andreas/documentation/samtools/contents.html)
>
> The reason I would prefer to convert ACE files to the 454PairAlign.txt file
> as this would mean support for both de novo assemblies as well as mapping
> projects. I am not particularly au fait with the SAM format but can't see
> why that shouldn't work.
>
> If no-one has started writing something I would be happy to give it a go but
> equally if someone has I'd be more than happy to try it out :)
>
> Cheers
>
> Nick

I've done ACE to SAM as an experiment, but haven't given the paired end
stuff much testing (my usual assembly viewer Tablet doesn't support paired
reads yet). Would you like the script? As you suggested it uses Biopython's
ACE parser but write SAM output directly since it is very simple.

Peter