[Biopython-dev] interaction networks in biopython

[Michiel de Hoon]

Jake Feala wrote:
> Here is an example that worked fine for me:
>    from Network import *
>    f = open(<GRID flat file from http://theBioGRID.org>)
>    parser = GRIDIterator(f):
>    net = create_network()
>    net.load(parser)
> 
To be more consistent with recent parsers in Biopython, this would be 
more appropriate:

 >>> import Network
 >>> f = open(<GRID flat file from http://theBioGRID.org>)
 >>> net = Network.parse(f, format="GRID")


Also, assuming that

 >>> net = create_network()

creates a NetworkObject representing an empty network, you could instead 
use the initialization function of Network objects. As in

 >>> import Network
 >>> net = Network.NetworkObject()

For the example above, you might then also consider

 >>> import Network
 >>> f = open(<GRID flat file from http://theBioGRID.org>)
 >>> net = Network.NetworkObject(f, format="GRID")

instead of using "parse".

I'm using "NetworkObject" here only as a placeholder to distinguish it 
from the Network module; there are probably better names.


--Michiel.