[gt-users] New feature announcement

[Sascha Steinbiss]

Brent Pedersen wrote:
> thanks! is the z_index going into the main repo soon?

Yes, this may happen quite soon.

> also, a couple stylistic questions.
> 1) would you accept a patch that switches the use of e.g.
> Feature.create() and Feature.__init__() i think it's more idiomatic to
> be able to do
>>>> f = FeatureNode(seqid, "gene", 100, 900, "+")
> and then
>>>> f = FeatureNode.create(ptr)
> than vice-versa and it could rename to FeatureNode.create_from_ptr()

I agree. What does Gordon think of this? This is an interface change, so 
I would rather not decide this alone.

> 2) would you accept a patch that implements python descriptors so one can use:
>>>> fnode.strand
> '+'
>>>> fnode.strand = '-'
> instead of fnode.get/set_strand() ?

I think it would be best if both methods were available so the interface 
is not too divergent from the C "get/set" method names. Otherwise, this 
sounds more Python-like, of course.

> if either both of those seem reasonable, i'll upload a patch to the tracker.

Thanks! I have already pulles your changes from github and keep them in 
a separate branch, ready to merge if everything is ok. I did some minor 
cleanup though (the old FeatureNode constructor was also called in the 
RecMap, FeatureIndex and Block classes,so I adapted them).

> -brent

Have a nice weekend,
Sascha

-- 
Sascha Steinbiss
Center for Bioinformatics
University of Hamburg
Bundesstr. 43
20146 Hamburg
Germany

Email:  steinbiss at zbh.uni-hamburg.de
URL:    http://www.zbh.uni-hamburg.de/steinbiss
Phone:  +49 (40) 42838 7322
FAX:    +49 (40) 42838 7312