This sounds like a great idea, James. I suspect Titus Brown will have some
thoughts on this very nice approach to visualization (i.e. marrying an NCList
based GUI with an NCList based backend (pygr)).
Regarding the simple problem of getting JSON output from a Pygr NLMSA, it's
really straightforward. Note that pygr already has an XMLRPC service that
accepts an interval query to an NLMSA and sends results back through XMLRPC.
See the NLMSAServer class in xnestedlist.py -- it's very little code. I guess
you could just copy this class and modify the getSlice() method to return JSON
format, for which Python support exists. Note that in addition to interval
data NLMSAServer also returns some extra index data needed by the NLMSAClient,
which would be unnecessary in your case. Note also that the NCList data get
"flattened" in this process (converted to a single list of intervals, rather
than a tree of nested lists), but presumably jbrowse doesn't care about that.
If you implement the JSON part, the rest is trivial, something like (assuming
your JsonNLMSAServer class exists):
from SimpleXMLRPCServer import SimpleXMLRPCServer
server = SimpleXMLRPCServer((host, port))
nlmsa = JsonNLMSAServer('/path/to/mynlmsa') # the usual NLMSA args
server.register_instance(nlmsa)
server.run_forever()
You would now use xmlrpc calls from JavaScript to run the getSlice() method on
your JsonNLMSAServer, and get back JSON data.
-- Chris
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