def test_connected_metabolites__example_graph(self):
qc = {'$text': {'$search': 'albumin'}}
connections = self.qry.getconnectedmetabolites(qc, max_associations=10)
r = self.qry.get_connections_graph(connections, json.dumps(qc))
print(nx.info(r))
from nosqlbiosets.graphutils import save_graph
save_graph(r, EXAMPLES + 'hmdb-ex-graph.json')
assert 49 == len(r)
def savegraph(query, outfile, limit=4000):
"""Save IntEnz reaction connections as graph files
param: qc: MongoDB query clause to select subsets of IntEnz entries,
e.g.: \'{"reactions.label.value": ' '"Chemically balanced"}\'
param: outfile: File name for saving the output graph
Format is selected based on the file extension
of the given output file;
.xml for GraphML, .gml for GML,
.json for Cytoscape.js
param: --limit: Maximum number of enzyme-metabolite connections
"""
qry = QueryIntEnz()
qc = parseinputquery(query)
cgraph = qry.get_connections_graph(qc, int(limit / 2))
print(nx.info(cgraph))
save_graph(cgraph, outfile)
def test_example_graph(self):
qc = {'$text': {'$search': 'methicillin'}}
g1 = self.qry.get_connections_graph(qc, "targets")
self.assertAlmostEqual(82, g1.number_of_edges(), delta=10)
self.assertAlmostEqual(73, g1.number_of_nodes(), delta=10)
g2 = self.qry.get_connections_graph(qc, "enzymes")
self.assertAlmostEqual(16, g2.number_of_edges(), delta=4)
self.assertAlmostEqual(12, g2.number_of_nodes(), delta=4)
g3 = self.qry.get_connections_graph(qc, "transporters")
self.assertAlmostEqual(30, g3.number_of_edges(), delta=14)
self.assertAlmostEqual(22, g3.number_of_nodes(), delta=4)
g4 = self.qry.get_connections_graph(qc, "carriers")
self.assertAlmostEqual(7, g4.number_of_edges(), delta=4)
self.assertAlmostEqual(8, g4.number_of_nodes(), delta=4)
r = nx.compose_all([g1, g2, g3, g4])
self.assertAlmostEqual(125, r.number_of_edges(), delta=20)
self.assertAlmostEqual(94, r.number_of_nodes(), delta=14)
remove_small_subgraphs(r)
save_graph(r, EX_GRAPHS + 'drugbank-methicillin.json')
r = neighbors_graph(r, "Ticarcillin", beamwidth=8, maxnodes=100)
assert 2 == r.number_of_nodes()