Unfortunately, rpy is one sided in that it only allows access to R
objects in python, not the opposite, which is what interests me right
now.

I was thinking of something of the sort of XMLRPC client for R that is
able to query NLMSA server and push the data management to the server
side. The responses could be as simple as lists of sequence ids,
coordinates (integers) and strings, which are all well supported by
the XMLRPC protocol. This would allow for letting both programs do
what they do best: pygr for data management and R for statistical
analysis. Doing some research today I could not find a sensible
implementation of XMLRPC functionality for R. Does anyone know more
than I do on this?
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