#!/usr/bin/env python

import MetagenomeDB as mdb

### User-modifiable parameters
network_fn = "network.sif"
###

# first, we create the file that will contain our network
# as a list of edge, following the Cytoscape .SIF format
# (see http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/Network_Formats)
network_fh = open(network_fn, 'w')

# edges will be stored at first as keys of a dictionary
# to avoid duplicates
edges = {}

# for each collection in the database,
for collection in mdb.Collection.find():
	# for each sub-collection of this collection (if any),
	for sub_collection in collection.list_sub_collections():
		# we store a directed edge from this sub-collection to the collection
		edges[sub_collection, collection] = True

	# for each super-collection of this collection (if any),
	for super_collection in collection.list_super_collections():
		# we store a directed edge from this collection to the super-collection
		edges[collection, super_collection] = True

# finally, we write those directed edges in the output file
for (collection_a, collection_b) in sorted(edges.keys()):
	print >>network_fh, "%s	part_of	%s" % (collection_a["name"], collection_b["name"])