[Biopython-dev] Biograpy 1.0 beta released

Andrea Pierleoni andrea at biocomp.unibo.it
Thu Sep 8 19:02:50 UTC 2011

>> 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.

ok, let me know.

>>>> 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.

well if you think it is worth it, biograpy can of course
be included in biopython.

the good thing is that it is all sphinx documented, so if biopython is
moving to sphinx too, this part is ready.
Biograpy requires matplotlib (and thus of course numpy), but could be
just an optional installation for those who want to use this graphic
package, as it is reportlab for genomediagram.

Also, now that there is a drawing library it should be easy to complete
the DAS client, and have something very similar to DASTY that given a
protein id is able to fetch all the das annotation and even draw them with
an html4 (image maps) or html5 (svg) friendly result.

>> 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 ;)

it's funny, since I choose the LGPL license not to scare commercial users :)
can you send me a link to the license so that I can include it in biograpy?


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