[Biopython-dev] More 'fun' with GenBank

[Peter Cock]

On Tue, Feb 5, 2013 at 10:38 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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

Applied to master,
https://github.com/biopython/biopython/commit/e5ff9e48e315924d59348c013ab082d6f155d18b

Peter