[Biopython-dev] Biograpy 1.0 beta released

Peter Cock p.j.a.cock at googlemail.com
Thu Sep 8 17:08:50 UTC 2011

On Thursday, September 8, 2011, Andrea Pierleoni <andrea at biocomp.unibo.it>
>> On Thu, Sep 8, 2011 at 3:47 PM, Andrea Pierleoni
>> <andrea at biocomp.unibo.it> wrote:
>>> Hi,
>>> one year ago we were talking about a library I was developing basically
>>> to draw seqrecord in a similar way to the BioPerl Bio::Graphics module.
>>> Today, I'm releasing the public beta version of that software ...
>>> http://apierleoni.github.com/BioGraPy/
>> Are you doing anything with "join" features from GenBank files (or
>> similar compound features)? This is something I'm thinking about
>> changing in the Biopython SeqFeature objects - having a single
>> SeqFeature with a compound location, rather than as now having
>> a parent SeqFeature with child SeqFeatures for the sub parts
>> (which does not make sense with things like GFF3 where there
>> are real parent/child relationships between features).
> Yes, I'm using 'join' features, there is a specific "graphic feature"
> for features with 'join'. I think it can be easily changed accordingly.
> Actually I'm also guessing a hierarchy when plotting directly a gene
> seqrecord/seqfeature with attached joined subfeatures.
> Being able to trace  parent/child relationships would be a big
> improvement, and not just for this library of course.

I'll write more about this later, once my code gets a bit
closer to being ready.

>>> BioGraPy is released under the LGPL license.
>> I'm curious about the license choice - LGPL prevents Biopython
>> adopting it for example.
> Then I think it's time to change the license :)
> Why is it preventing biopython to adopt it?

Adopt in the sense of include into Biopython.

> Which one do you suggest?
> I could also use the biopython license, I don't need a strict control
> on the code, I just want the library to be used by everybody willing to,
> even closed source programs.

As I recall, Biopythin, NumPy, SciPy etc all use a very
Liberal MIT/BSD type licence, while LGPL tends to
scare commercial users ;)


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