[Biopython-dev] json formatting of SeqRecord objects

Peter Cock p.j.a.cock at googlemail.com
Thu May 24 11:32:53 UTC 2012

On Thu, May 24, 2012 at 12:24 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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.

e.g. Consider this two protein example for UniProt:


Or with GenBank,


Currently TogoWS' JSON output is essentially the raw record
(here plain text "swiss" format or plain text GenBank), using a
JSON list to make the division into the records explicit.


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