[Biopython-dev] MAF Parser/Writer/Indexer

[Peter Cock]

On Mon, May 16, 2011 at 6:54 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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.

Done on my branch:
https://github.com/peterjc/biopython/commit/746d0c30b85753bb40c140b2b964e3256259414b

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

You'll see I have one example (from BioPerl's unit tests), but more
would still be appreciated.

Peter