[Biopython-dev] MAF Parser/Writer/Indexer

[Andrew Sczesnak]

On 05/16/2011 01:58 PM, Peter Cock wrote:
> That is a subtlety I missed - maybe it is simpler to ignore speciesOrder
> after all. I presume it is intended a graphical output directive really.

Fine by me.  If need be we can add this later.

>> This is interesting.  I wonder if it makes sense to preserve this
>> information if a SeqRecord is going to be maniuplated outside a
>> MultipleSeqAlignment object.  Could this be accomplished by
>> migrating the annotation information to a SeqFeature?
>
> I'm not sure how using a SeqFeature would work here.

Hmm, well, strand is manipulated in a SeqFeature when 
.reverse_complement() is run, right?  I thought that might take care of 
that.  Though truthfully I haven't looked too much at that code.

> Also consider that someone might manipulate the alignment
> directly, e.g. alignment[:,10:60] to pull out fifty columns. That
> seems like a use case where the start/end co-ordinates should
> be updated nicely. Note that internally this calls record[10:60]
> for each row of the alignment, so using SeqRecord objects.

That's true.  Is there a more general way to implement this?  By 
dragging the coordinate information out of .annotations and into fields 
that aren't MAF-specific or something.


Andrew