def test_load():
G = NdexGraph()
toolbox.load(G,
'loadexample.txt',
edge_attributes=['strength'],
header=True)
print G.node
print G.edge
def test_st_layout_full():
G = NdexGraph()
toolbox.load(G, 'st_layout_network2.txt', header=True)
toolbox.annotate(G, 'st_layout_annotate2.txt')
toolbox.apply_source_target_layout(G)
template_id = 'd1856d17-4937-11e6-a5c7-06603eb7f303'
toolbox.apply_template(G, template_id, 'http://public.ndexbio.org', 'scratch', 'scratch')
G.set_name('test_st_layout_wtf1')
# G.write_to('temp.cx')
G.upload_to('http://dev2.ndexbio.org', 'scratch', 'scratch')
def test_st_layout_full():
G = NdexGraph()
toolbox.load(G, 'st_layout_network2.txt', header=True)
toolbox.annotate(G, 'st_layout_annotate2.txt')
toolbox.apply_source_target_layout(G)
template_id = 'd1856d17-4937-11e6-a5c7-06603eb7f303'
toolbox.apply_template(G, template_id, 'http://public.ndexbio.org',
'scratch', 'scratch')
G.set_name('test_st_layout_wtf1')
# G.write_to('temp.cx')
G.upload_to('http://dev2.ndexbio.org', 'scratch', 'scratch')
def test_load():
G = NdexGraph()
toolbox.load(G, 'loadexample.txt', edge_attributes=['strength'], header=True)
print(G.node)
print(G.edge)
#select regulators
top_regulators=select_top_n_in_column_by_magnitude(trns_regs)
#build edge networks
fh_stem=opts.network_directory+'transition_network_'
files=build_networks_from_dict_and_mat(top_regulators, connections_matrix,fh_stem=fh_stem)
#push edge network to NDEx
uuids={}
for f in files:
net=netn.NdexGraph()
netb.load(net,f,edge_attributes=['strength'],header=True)
net_name=f.replace(opts.network_directory,'')
net.set_name(net_name)
uuids[net_name]=net.upload_to('http://public.ndexbio.org','decarlin','perfect6')
#retrieve edge networks uuids
ndex=nc.Ndex(host='http://public.ndexbio.org', username='******', password='******')
id_dict={}
for nn in uuids.keys():
ndex.make_network_public(uuids[nn])
#assign uuids to development edges