[Biopython-dev] json formatting of SeqRecord objects

Peter Cock p.j.a.cock at googlemail.com
Thu May 24 11:24:27 UTC 2012

On Thu, May 24, 2012 at 12:06 PM, Alex Leach <albl500 at york.ac.uk> wrote:
> Dear all,
> I've written a fairly simple SeqRecord formatter to convert sequences to/from
> JSON objects, and wondered if it might be useful enough to be included in
> BioPython.

That does look interesting, but from scanning the code the JSON
representation is extremely Biopython specific. I take it there is no
existing JSON representation in wide usage that you know of? It
strikes me that something common between the Bio* projects would
be much more valuable.

I know that TogoWS (which uses both BioRuby and BioPerl internally)
has some JSON support, but it looks more like a dump of the raw
file from a quick look.

How are you using this now? Do you pass JSON encoded SeqRecord
objects over the network for something?

> It currently injects 'json' into SeqIO and AlignIO's _FormatToIterator and
> _FormatToWriter dictionaries, so can be used like any other SeqRecord format.
> I'm not sure where exactly I should submit it, but I thought here might do as
> an initial proposal..
> I attach the source code. If you'd be interested in using it, let me know and
> I'll tidy it up to standards.
> Kind regards,
> Alex

If you are happy with git, we'd suggest you make a fork on github
(i.e. make a copy of the repository), then develop the new code on
a new branch.


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