def test_metabolite_networks_neighbors(self):
qc = {'$text': {'$search': 'glycerol'}}
mn = qry.get_metabolite_network(qc, limit=1440)
assert "Glycerol" in mn.nodes
assert len(mn.edges) == 3219
assert len(mn.nodes) == 906
qc = {'$text': {'$search': 'glycerol'}, 'is_transport': True}
mn = qry.get_metabolite_network(qc)
assert "Glycerol" in mn.nodes
assert len(mn.edges) == 228
assert len(mn.nodes) == 64
qc = {"_id": "rxn36327"}
mn = qry.get_metabolite_network(qc)
assert "(S)-Propane-1,2-diol" in mn.nodes
qc = {"status": "OK", "reversibility": "<"}
mn = qry.get_metabolite_network(qc)
self.assertAlmostEqual(len(mn.edges), 2027, delta=100)
self.assertAlmostEqual(len(mn.nodes), 961, delta=100)
assert 'Phosphate' in mn.nodes
r = neighbors_graph(mn, "Phosphate", beamwidth=8, maxnodes=100)
assert r.number_of_nodes() == 95
r = neighbors_graph(mn, "Phosphate", beamwidth=6, maxnodes=20)
assert r.number_of_nodes() == 20
r = neighbors_graph(mn, "Phosphate", beamwidth=4, maxnodes=20)
assert r.number_of_nodes() == 20
def test_metabolite_network_bigg(self):
qc = {"$or": [{"source.lib": 'bigg'}, {"xrefs.lib": 'bigg'}]}
mn = qrymtntx.get_metabolite_network(qc, max_degree=1400)
cmpnds = {
'carboxyacetyl-[acyl-carrier protein]', 'acetate', 'hexadecanoate',
'xylitol', "L-xylulose", "L-arabinitol"
}
assert len(cmpnds.intersection(mn.nodes())) == 6
assert mn.degree("L-arabinitol") >= 2
assert mn.degree("L-xylulose") >= 5
r = neighbors_graph(mn, "L-arabinitol", beamwidth=5, maxnodes=160)
assert len(r) == 0 # L-arabinitol is product, not reactant
paths = shortest_paths(mn, 'alpha-L-arabinan', 'L-arabinitol', 10)
assert len(paths) == 10
assert paths[0][1] == 'aldehydo-L-arabinose'
set_degree_as_weight(mn)
paths = shortest_paths(mn,
'alpha-L-arabinan',
'L-arabinitol',
10,
weight='weight')
assert len(paths) == 1
assert paths[0][1] == 'aldehydo-L-arabinose'
qc = {"source.lib": "bigg", "xrefs.lib": 'bigg', "balance": "true"}
mn = qrymtntx.get_metabolite_network(qc)
self.assertAlmostEqual(2815, len(mn.nodes()), delta=200)
self.assertAlmostEqual(3741, len(mn.edges()), delta=200)
assert 'L-xylulose' not in mn.nodes()
assert "Zymosterol ester (yeast specific)" in mn.nodes()
assert len(cmpnds.intersection(mn.nodes())) == 2
assert mn.degree("Zymosterol ester (yeast specific)") == 8
r = neighbors_graph(mn, "L-ascorbate", beamwidth=5, maxnodes=100)
self.assertAlmostEqual(7, r.number_of_nodes(), delta=4)
def test_metabolite_network_rhea(self):
qc = {"source.lib": "rhea", "balance": "true"}
mn = qrymtntx.get_metabolite_network(qc, max_degree=660)
paths = shortest_paths(mn, 'L-serine', 'acetyl-CoA', 1600, cutoff=5)
assert 225 == len(paths)
assert ['L-serine', 'phosphate', 'acetyl-CoA'] in paths
set_degree_as_weight(mn)
paths = shortest_paths(mn,
'L-serine',
'acetyl-CoA',
1600,
cutoff=5,
weight='weight')
assert 2 == len(paths)
assert [
'L-serine', '3-(pyrazol-1-yl)-L-alanine', 'O-acetyl-L-serine',
'acetyl-CoA'
] in paths
self.assertAlmostEqual(7806, len(mn.nodes()), delta=400)
self.assertAlmostEqual(17698, len(mn.edges()), delta=1200)
r = neighbors_graph(mn, "L-ascorbate", beamwidth=5, maxnodes=100)
self.assertAlmostEqual(100, r.number_of_nodes(), delta=12)
assert 5 == mn.in_degree('L-ascorbate')
cofactors = [
'FMNH2', 'L-ascorbate', 'Cu(+)', 'Cu(2+)', 'Fe(3+)', 'FMN',
'5,10-methenyltetrahydrofolate', 'NH4(+)', 'Fe(2+)', 'Mn(2+)',
"riboflavin", "heme b", "Zn(2+)", "Mg(2+)"
]
for i in cofactors:
assert i in mn.nodes(), i
def test_example_graph(self):
qc = {'$text': {'$search': 'methicillin'}}
g1 = self.qry.get_connections_graph(qc, "targets")
self.assertAlmostEqual(82, g1.number_of_edges(), delta=10)
self.assertAlmostEqual(73, g1.number_of_nodes(), delta=10)
g2 = self.qry.get_connections_graph(qc, "enzymes")
self.assertAlmostEqual(16, g2.number_of_edges(), delta=4)
self.assertAlmostEqual(12, g2.number_of_nodes(), delta=4)
g3 = self.qry.get_connections_graph(qc, "transporters")
self.assertAlmostEqual(30, g3.number_of_edges(), delta=14)
self.assertAlmostEqual(22, g3.number_of_nodes(), delta=4)
g4 = self.qry.get_connections_graph(qc, "carriers")
self.assertAlmostEqual(7, g4.number_of_edges(), delta=4)
self.assertAlmostEqual(8, g4.number_of_nodes(), delta=4)
r = nx.compose_all([g1, g2, g3, g4])
self.assertAlmostEqual(125, r.number_of_edges(), delta=20)
self.assertAlmostEqual(94, r.number_of_nodes(), delta=14)
remove_small_subgraphs(r)
save_graph(r, EX_GRAPHS + 'drugbank-methicillin.json')
r = neighbors_graph(r, "Ticarcillin", beamwidth=8, maxnodes=100)
assert 2 == r.number_of_nodes()
def test_metabolite_network_reactome(self):
qc = {"source.lib": "reactome", "balance": "true"}
mn = qrymtntx.get_metabolite_network(qc, max_degree=400)
self.assertAlmostEqual(430, len(mn.nodes()), delta=60)
self.assertAlmostEqual(1157, len(mn.edges()), delta=120)
assert "L-serine" in mn.nodes()
r = neighbors_graph(mn, "acetyl-CoA", beamwidth=20, maxnodes=200)
# number of nodes differ based on selected search branches
self.assertAlmostEqual(143, r.number_of_nodes(), delta=30)
paths = shortest_paths(mn, 'L-serine', 'acetyl-CoA', 30)
assert 30 == len(paths)
assert ['L-serine', 'glycine', 'CoA', 'acetyl-CoA'] in paths[:4]
set_degree_as_weight(mn)
paths = shortest_paths(mn,
'L-serine',
'acetyl-CoA',
30,
weight='weight')
assert 30 == len(paths)
assert ['L-serine', 'glycine', 'CoA', 'acetyl-CoA'] == paths[0]
def test_drug_targets_graph(self):
qc = {'$text': {'$search': '\"side effects\"'}}
g = self.qry.get_connections_graph(qc, "targets")
self.assertAlmostEqual(g.number_of_edges(), 580, delta=30)
self.assertAlmostEqual(g.number_of_nodes(), 342, delta=20)
assert "Olanzapine" in g.nodes
assert "CCX915" in g.nodes
r = neighbors_graph(g, "Olanzapine", max_iter=10, tol=1e-2)
assert 5 == r.number_of_nodes()
qc = {'$text': {'$search': 'defensin'}}
gfile = "./docs/example-graphs/defensin-targets.json"
g = self.qry.get_connections_graph(qc, "targets", gfile)
assert g.number_of_edges() == 38
self.assertAlmostEqual(g.number_of_nodes(), 33, 10)
g = self.qry.get_connections_graph(qc, "enzymes")
assert g.number_of_edges() == 1
assert g.number_of_nodes() == 2
g = self.qry.get_connections_graph(qc, "transporters")
assert g.number_of_edges() == 0
assert g.number_of_nodes() == 0
g = self.qry.get_connections_graph(qc, "carriers")
assert g.number_of_edges() == 0
assert g.number_of_nodes() == 0