[Biopython-dev] Newbler ACE file to SAM?

[Nick Loman]

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