[Biopython-dev] [Biopython] Bio.Sequencing.Ace

[Jose Blanca]

> What I was thinking of was a contig class as an alignment subclass,
> holding a list of SeqRecord objects and offsets. The consensus might
> just be one element of this list - but could be handled specially. This
> sounds simpler than having to introduce a whole new object system,
> related to but different to SeqFeature objects. However, I don't yet
> have a sample implementation to demonstrate this.
I thought about that implementation and I created some code. The problem I 
found with that approach is that the contig class code got too messy.  Take 
into account that besides the offset you also need the masks and that some 
sequences could be reversed. That's why I decided to split the part that 
calculates the offset and the mask into a separate class.

> One important thing I think we should do BEFORE adding any contig
> class to Biopython, is get it working with at least one other contig file
> format in addition to Ace. I don't want to end up with a class which
> is too specialised for how ace contigs work.
>
> Peter

Well, In fact my contig class is modeled after the caf file format. The ace 
parsing was just an afterthought, my primary interest was the caf format.

-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)