[Biopython-dev] MAF Parser/Writer/Indexer

[Peter Cock]

On Mon, May 16, 2011 at 6:03 PM, Andrew Sczesnak wrote:
> On 05/16/2011 09:53 AM, Peter Cock 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?

That is my assumption for how dots have been used in alignment
formats.

If you have some MAF examples using dots, that would be great.

Regarding PHYLIP, I looked at this and dots/periods have been
explicitly forbidden since the very earliest versions of PHYLIP, so
I've made them raise an error instead:
https://github.com/biopython/biopython/commit/b41975bb8363171add80d19903861f3d8cffe405

Peter