[Biopython-dev] More 'fun' with GenBank

[Peter Cock]

On Mon, Jan 21, 2013 at 9:49 AM, Kai Blin
<kai.blin at biotech.uni-tuebingen.de> wrote:
>
>> Kai - would you mind retesting with f_loc5 (the rebased branch)?
>
> The location of the feature that caused trouble for me still looks
> correct. I'm currently running some more sequences, but I'm pretty
> confident that the code will work just fine. The tests I added to the
> genbank parser code for all the problem cases I had pass, after all. :)
>
>> Everyone - does it seem sensible to include this now, ready for the
>> upcoming release (*)? Or perhaps just after the release?
>
> I'd perfer having this in the next release if possible, but of course
> if the release after that is coming up within a reasonable time frame,
> that would work as well.
>
> Cheers,
> Kai

Unless anyone objects, I will apply the (rebased) version of this
f_loc4 / f_loc5 branch later this week (now that Biopython 1.61
is out).

This replaces the SeqFeature use of sub_features with a new
CompoundLocation which I think is a far more natural way to
handle join locations in EMBL/GenBank files.

Also, it means we can offer parsing of GenBank/EMBL style
location lines into (Compound)Location objects directly :)

Regards,

Peter