[Biopython-dev] MAF Parser/Writer/Indexer

[Andrew Sczesnak]

On 05/16/2011 07:14 AM, Peter Cock wrote:
> Do you think we should follow the speciesOrder directive if
> present?

Yeah, why not.  I started working on this and the problem was, as 
defined in the spec, the species is just "hg19" or "mm9," yet the 
records are in species.chromosome format.  Should we enforce that the 
species in a speciesOrder directive must exactly match a sequence 
identifier, or add a split and do some checks to make sure a record 
matches only one species in speciesOrder?

> Also I think we may need to do something rigorous with start/end
> co-ordinates and strand in either the Seq or SeqRecord object.
> They could be updated automatically during slicing and taking
> reverse complement... they might not survive addition though.

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?


Andrew