def test_to_networkx_digraph():
H = DirectedHypergraph()
H.read("tests/data/basic_directed_hypergraph.txt")
G = directed_graph_transformations.to_networkx_digraph(H)
H_nodes = H.get_node_set()
G_nodes = G.node.keys()
assert H_nodes == set(G_nodes)
H_nodes_attributes = [H.get_node_attributes(node) for node in H_nodes]
for node in G_nodes:
assert G.node[node] in H_nodes_attributes
for hyperedge_id in H.hyperedge_id_iterator():
tail_set = H.get_hyperedge_tail(hyperedge_id)
head_set = H.get_hyperedge_head(hyperedge_id)
for tail_node in tail_set:
for head_node in head_set:
assert G[tail_node][head_node]
# Try transforming an invalid directed hypergraph
try:
directed_graph_transformations.to_networkx_digraph("invalid H")
assert False
except TypeError:
pass
except BaseException as e:
assert False, e
def test_from_networkx_digraph():
H = DirectedHypergraph()
H.read("tests/data/basic_directed_hypergraph.txt")
nxG = directed_graph_transformations.to_networkx_digraph(H)
G = directed_graph_transformations.from_networkx_digraph(nxG)
nxG_nodes = nxG.node.keys()
G_nodes = G.get_node_set()
assert G_nodes == set(nxG_nodes)
for edge in nxG.edges_iter():
tail_node = edge[0]
head_node = edge[1]
assert G.has_hyperedge(tail_node, head_node)
# Try transforming an invalid directed hypergraph
try:
directed_graph_transformations.from_networkx_digraph("G")
assert False
except TypeError:
pass
except BaseException as e:
assert False, e
def main(inprefix, hedge_connectivity_file, pathway_prefix, infix, run_all):
start = time.time()
H, identifier2id, id2identifier = hgraph_utils.make_hypergraph(
inprefix, keep_singleton_nodes=True)
H = hgraph_utils.add_entity_set_info(H)
G = transform.to_networkx_digraph(H)
nodes = set() ## get proteins and complex members.
node_membership = {}
num_complexes = 0
num_entitysets = 0
for n in H.get_node_set():
attrs = H.get_node_attributes(n)
if attrs['is_hypernode']:
nodes.update(attrs['hypernode_members'])
for m in attrs['hypernode_members']:
if m not in node_membership:
node_membership[m] = set()
node_membership[m].add(n)
num_complexes += 1
if attrs['is_entityset']:
nodes.update(attrs['entityset_members'])
for m in attrs['entityset_members']:
if m not in node_membership:
node_membership[m] = set()
node_membership[m].add(n)
num_entitysets += 1
nodes.add(n)
if n not in node_membership:
node_membership[n] = set([n])
print('%d complexes and %d entity sets' % (num_complexes, num_entitysets))
print('%d nodes including hypernode and entity set members' % (len(nodes)))
# get pathway Identifiers to Uniprot ID
pc2uniprot, uniprot2pc = hgraph_utils.get_id_map(
'../../hypergraph/reactome_hypergraphs/')
## get pathway information
pathway_nodes, all_pathway_nodes = get_pathways(pathway_prefix,
run_all=run_all)
#print('%d pathway nodes (including hypernode members)' % (len(all_pathway_nodes)))
#print(list(all_pathway_nodes)[:10])
## get channels
files = glob.glob('../../data/STRING/processed/*.txt')
print('%d files:' % (len(files)), files)
processed_nodes = {}
files = ['../../data/STRING/processed/cooccurence.txt']
for f in files:
print('FILE %s' % (f))
name = f.replace('../../data/STRING/processed/',
'').replace('.txt', '')
print('NAME %s' % (name))
outfile_name = 'outfiles/%s-%s-positive_sets.txt' % (infix, name)
if os.path.isfile(outfile_name):
print('FILE %s EXISTS! Skipping.' % (outfile_name))
continue
interactions = []
missing = {}
with open(f) as fin:
for line in fin:
row = line.strip().split()
interactions.append([row[2], row[3], int(row[4])])
print(' %d INTERACTIONS' % (len(interactions)))
interactions_in_reactome = []
mismapped = 0
notinreactome = 0
for n1, n2, val in interactions:
if n1 in uniprot2pc and n2 in uniprot2pc:
un1 = uniprot2pc[n1]
un2 = uniprot2pc[n2]
else:
if n1 not in uniprot2pc:
missing[n1] = ('NA', 'NotInPC')
if n2 not in uniprot2pc:
missing[n2] = ('NA', 'NotInPC')
mismapped += 1
continue
if un1 in nodes and un2 in nodes:
interactions_in_reactome.append([un1, un2, val])
else:
if un1 not in nodes:
missing[n1] = (un1, 'NotInHypergraph')
if un2 not in nodes:
missing[n2] = (un2, 'NotInHypergraph')
notinreactome += 1
## FOR TESTING:
##interactions_in_reactome = interactions_in_reactome[:500]
print(
' %d INTERACTIONS HAVE BOTH NODES IN REACTOME\n %d interactions not in PathwayCommons Reactome mapping\n %d interactions are not in this hypergraph'
% (len(interactions_in_reactome), mismapped, notinreactome))
out = open('outfiles/%s-%s-mismapped.txt' % (infix, name), 'w')
out.write('#UniProtID\tPathwayCommonsID\tMismappingReason\n')
for m in missing:
out.write('%s\t%s\t%s\n' % (m, missing[m][0], missing[m][1]))
out.close()
print(' wrote %d mismapped nodes to outfiles/%s-%s-mismapped.txt' %
(len(missing), infix, name))
sys.stdout.flush()
interactions_in_pathways, interactions_in_same_pathway = get_pathway_interactions(
interactions_in_reactome, pathway_nodes, all_pathway_nodes)
print(' %d INTERACTIONS HAVE BOTH NODES IN THE REACTOME PATHWAYS' %
(len(interactions_in_pathways)))
print(' %d INTERACTIONS HAVE BOTH NODES IN SAME REACTOME PATHWAY' %
(len(interactions_in_same_pathway)))
sys.stdout.flush()
## NOTE: to do whole thing replace "intearactions-in_pathways" with "interactions-in_reactome"
b_visit_dict = hgraph_utils.make_b_visit_dict(hedge_connectivity_file,
identifier2id)
brelax_dicts, processed_nodes = preprocess_brelax_dicts(
H, interactions_in_pathways, node_membership, b_visit_dict,
processed_nodes)
interactions_brelax = get_bconn_interactions(brelax_dicts,
interactions_in_pathways,
node_membership)
interactions_bipartite = list(interactions_brelax.keys())
interactions_bconn = [
e for e in interactions_bipartite if interactions_brelax[e] == 0
]
print(' %d INTERACTIONS ARE Bipartite CONNECTED IN REACTOME' %
(len(interactions_bipartite)))
print(' %d INTERACTIONS ARE B-CONNECTED IN REACTOME' %
(len(interactions_bconn)))
sys.stdout.flush()
out = open(outfile_name, 'w')
out.write(
'#Node1\tNode2\tScore\tAnyPathway\tSamePathway\tBipartite\tBRelaxDist\n'
)
for n1, n2, val in interactions_in_reactome:
vals = []
if (n1, n2) in interactions_in_pathways:
vals.append(1)
else:
vals.append(0)
if (n1, n2) in interactions_in_same_pathway:
vals.append(1)
else:
vals.append(0)
if (n1, n2) in interactions_brelax:
vals.append(1)
vals.append(interactions_brelax[(n1, n2)])
else:
vals.append(0)
vals.append(-1)
out.write('%s\t%s\t%s\t%d\t%d\t%d\t%d\n' %
(n1, n2, val, vals[0], vals[1], vals[2], vals[3]))
out.close()
print(' wrote outfile to %s' (outfile_name))
sys.stdout.flush()
end = time.time()
print('FINAL TIME:', end - start)
def to_digraph(H):
## simple function so we convert to graph by calling an hgraph_utils function.
G = transform.to_networkx_digraph(H)
return G
