[Biopython] Ace support in Bio.SeqIO and/or Bio.AlignIO?

[David Winter]

Peter wrote:
> How do you picture a contig in an ACE assembly file? As a single
> record with read data annotations (e.g. as a SeqRecord), or as a
> sequence alignment with a consensus (e.g. as an Alignment object)?  I
> suspect the answer is "it depends", and that both are useful
>   
Yup, I usually want to trust the assembler and treat them as sequences 
(and having the option of annotations would be great for these cases) 
but sometimes  I want to pull them apart and look inside. 

> Recently David put together an example on the wiki using
> Bio.Sequencing.Ace to build an alignment, which we could use a basis
> for supporting Ace files in Bio.AlignIO as alignments:
> http://biopython.org/wiki/ACE_contig_to_alignment
>
> What do people think?  I should be able to try out David's code on
> some real world ACE files from Newbler (i.e. 454Contigs.ace files)..
The wiki example is based on a script that I use with newbler and mira 
(http://www.chevreux.org/projects_mira.html) assembled contigs (I 
thought I'd use one everyone with biopython has as the example) so it 
should be OK. I'm sure there are much prettier ways of doing what it 
does (eg, using the new SeqRecord annotations to hold the clipping masks 
?). If people want it to be part of biopython I'm happy to provide what 
help I can with it.