[Biopython-dev] MAF Parser/Writer/Indexer

[Andrew Sczesnak]

On 05/16/2011 09:53 AM, Peter Cock wrote:
> On Mon, May 16, 2011 at 12:14 PM, Peter Cock<p.j.a.cock at googlemail.com>  wrote:
>
> Do you think it makes sense to automatically promote any dots
> (periods) in the sequence to the letter of that position in the first
> sequence? This is something I'd been thinking we should do in
> the PHYLIP parser as well. See the MAF/humor.maf example.
>
> Peter

Yeah, that sounds right to me.  The issue again is going to be the lack 
of an explicitly defined reference sequence.  Are we going to make the 
assumption that the sequence appearing first in an alignment bundle is 
the reference?


Andrew