[Biopython-dev] Phylo: support for JSON trees

Peter Cock p.j.a.cock at googlemail.com
Wed Dec 9 21:33:36 UTC 2015

Hi Fabio,

You're right JSON has a lot of advantages (people said this about XML
too), but inventing your own file format is not something to be taken

Are there really no pre-existing tree formats using JSON?


On Wed, Dec 9, 2015 at 9:12 PM, Fabio Zanini <fabio.zanini at fastmail.fm> wrote:
> Hi all,
> I've been working with phylogenetic trees for a few years and found it
> very convenient to convert Bio.Phylo trees to/from JSON, e.g.
> {'name': 'root', 'children': [
>   {'name': 'leaf1', 'branch_length': 0.01, children: []},
>   {'name': 'leaf2', 'branch_length': 0.02, children: []}]
> }
> I would like to implement such import/export functions into Bio.Phylo if
> there is interest. Because Python has a JSON parser already, it's like
> 50 lines of code altogether.
> The main arguments in favour of this are:
> - *JSON is standard for the web*, and the web is where all is moving
> (Jupyter, bokeh, but also specific tree-oriented web apps such as
> http://nextflu.org)
> - embedding metadata is trivial (just add more keys to those dicts!)
> How's that sound, shall I make a github PR?
> Cheers,
> Fabio
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