[Biopython-dev] MafIO

[Peter Cock]

On Fri, Jun 22, 2012 at 12:21 AM, Elizabeth Skippington
<e.skippington at imb.uq.edu.au> wrote:
> Hi
>
> I have written software which requires MafIO. Ideally, I would like to use a stable version.
>
> I was just wondering if there is any update on integrating MafIO into the core biopython
> branch? There was an ongoing conversation about this that stopped about 3 months ago:
> https://github.com/biopython/biopython/pull/5
>
> thanks
> Elizabeth

Hi Elizabeth,

I want to get Biopython 1.60 release by early next week, and then look at
merging the MAF support: http://biopython.org/wiki/Multiple_Alignment_Format

Which bits of MafIO are you using - having some non-trivial examples
would be great for documentation and benchmarking, or even unit tests.
In particular are you using the indexing?

I'm curious because GSoC student Clayton Wheeler  is working on this
for our sister project BioRuby, and he is exploring alternative indexes -
it sounds like there is scope for further speedup in the Biopython code.
http://csw.github.com/bioruby-maf/blog/2012/06/04/indexed_maf_access/

The other issue is a general way to hold start/end/strand information
in the SeqRecord or alignment objects, and this overlaps with Bow's
GSoC project on Biopython SearchIO - see also:
http://biopython.org/wiki/SearchIO
http://lists.open-bio.org/pipermail/biopython-dev/2012-May/009646.html

Peter