[Biopython-dev] json formatting of SeqRecord objects

[Peter Cock]

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:

http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN,A1AG1_MOUSE
http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN,A1AG1_MOUSE.fasta
http://togows.dbcls.jp/entry/uniprot/A1AG1_HUMAN,A1AG1_MOUSE.json

Or with GenBank,

http://togows.dbcls.jp/entry/protein/117606345,117606345
http://togows.dbcls.jp/entry/protein/117606345,117606345.fasta
http://togows.dbcls.jp/entry/protein/117606345,117606345.json

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.

Peter