def test_example_notebook(self):
my_network_uuid = 'd3c5ca09-bb42-11e7-94d3-0ac135e8bacf'
my_account = "drh"
my_password = "******"
print("downloading network and buiding NiceCX...")
my_network = ndex2.create_nice_cx_from_server(
server='public.ndexbio.org', uuid=my_network_uuid)
print("done")
my_network.print_summary()
# (for clarity, this example code is rather verbose)
source_attribute1 = "TYPEA"
source_attribute2 = "TYPEB"
target_attribute = "TYPE"
for node_id, node in my_network.nodes.items():
value1 = my_network.get_node_attribute(node, source_attribute1)
value2 = my_network.get_node_attribute(node, source_attribute2)
merged_value = value1 or value2
if merged_value:
my_network.set_node_attribute(node, target_attribute,
merged_value)
my_network.remove_node_attribute(node, source_attribute1)
my_network.remove_node_attribute(node, source_attribute2)
my_network.print_summary()
def test_data_types_with_special_chars2(self):
niceCx = ndex2.create_empty_nice_cx()
fox_node_id = niceCx.create_node(node_name='A#"')
mouse_node_id = niceCx.create_node(node_name='B!@#$%')
bird_node_id = niceCx.create_node(node_name='*&^%^$')
fox_bird_edge = niceCx.create_edge(edge_source=fox_node_id,
edge_target=bird_node_id,
edge_interaction='&"""""""')
fox_mouse_edge = niceCx.create_edge(edge_source=fox_node_id,
edge_target=mouse_node_id,
edge_interaction='//////\\\\\\')
niceCx.add_node_attribute(property_of=fox_node_id,
name='Color',
values='Red')
niceCx.add_node_attribute(property_of=mouse_node_id,
name='Color',
values='Gray')
niceCx.add_node_attribute(property_of=bird_node_id,
name='Color',
values='Blue')
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
spec_char_network_uuid = upload_message.split('\\')[-1]
niceCx = ndex2.create_nice_cx_from_server(
server='public.ndexbio.org',
uuid='fc63173e-df66-11e7-adc1-0ac135e8bacf'
) #NiceCXNetwork(server='dev2.ndexbio.org', username='******', password='******', uuid='9433a84d-6196-11e5-8ac5-06603eb7f303')
self.assertTrue(upload_message)
def test_create_from_server(self):
print('Testing: Create from server with 548970 edges (uuid:75bf1e85-1bc7-11e6-a298-06603eb7f303)')
#niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='72ef5c3a-caff-11e7-ad58-0ac135e8bacf') #NiceCXNetwork(server='dev2.ndexbio.org', username='******', password='******', uuid='9433a84d-6196-11e5-8ac5-06603eb7f303')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', username='******', password='******', uuid='75bf1e85-1bc7-11e6-a298-06603eb7f303') #NiceCXNetwork(server='dev2.ndexbio.org', username='******', password='******', uuid='9433a84d-6196-11e5-8ac5-06603eb7f303')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_from_server(self):
print('public network')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='72ef5c3a-caff-11e7-ad58-0ac135e8bacf') #NiceCXNetwork(server='dev2.ndexbio.org', username='******', password='******', uuid='9433a84d-6196-11e5-8ac5-06603eb7f303')
#niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', username='******', password='******', uuid='75bf1e85-1bc7-11e6-a298-06603eb7f303') #NiceCXNetwork(server='dev2.ndexbio.org', username='******', password='******', uuid='9433a84d-6196-11e5-8ac5-06603eb7f303')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_example_notebook(self):
my_network_uuid = 'd3c5ca09-bb42-11e7-94d3-0ac135e8bacf'
my_account = "drh"
my_password = "******"
print("downloading network and buiding NiceCX...")
my_network = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid=my_network_uuid)
print("done")
my_network.print_summary()
# (for clarity, this example code is rather verbose)
source_attribute1 = "TYPEA"
source_attribute2 = "TYPEB"
target_attribute = "TYPE"
for node_id, node in my_network.nodes.items():
value1 = my_network.get_node_attribute(node, source_attribute1)
value2 = my_network.get_node_attribute(node, source_attribute2)
merged_value = value1 or value2
if merged_value:
my_network.set_node_attribute(node, target_attribute, merged_value)
my_network.remove_node_attribute(node, source_attribute1)
my_network.remove_node_attribute(node, source_attribute2)
my_network.print_summary()
def test_create_nice_cx_from_server_cocanet2_network(self):
net = ndex2.create_nice_cx_from_server(
'public.ndexbio.org', uuid='f1dd6cc3-0007-11e6-b550-06603eb7f303')
self.assertEqual(
'CoCaNet2', net.get_name(), "Probably failing due to this error: "
"https://ndexbio.atlassian.net/browse/UD-2222")
def test_create_from_server_1(self):
#====================================
# BUILD NICECX FROM SERVER
#====================================
niceCx = ndex2.create_nice_cx_from_server(server='dev.ndexbio.org', username='******', password='******', uuid='b7190ca4-aec2-11e7-9b0a-06832d634f41') #NiceCXNetwork(server='dev.ndexbio.org', username='******', password='******', uuid='b7190ca4-aec2-11e7-9b0a-06832d634f41')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_to_netx(self):
niceCx_from_server = ndex2.create_nice_cx_from_server(server='public.ndexbio.org',
uuid='3f08d557-1e5f-11e8-b939-0ac135e8bacf')
niceCx_from_server_to_netx = niceCx_from_server.to_networkx()
print(niceCx_from_server_to_netx)
self.assertTrue(niceCx_from_server_to_netx)
def test_to_netx(self):
niceCx_from_server = ndex2.create_nice_cx_from_server(server='public.ndexbio.org',
uuid='3f08d557-1e5f-11e8-b939-0ac135e8bacf')
niceCx_from_server_to_netx = niceCx_from_server.to_networkx()
print(niceCx_from_server_to_netx)
self.assertTrue(niceCx_from_server_to_netx)
def test_create_from_server_1(self):
print('Testing: Create from serve (uuid:b7190ca4-aec2-11e7-9b0a-06832d634f41)')
#====================================
# BUILD NICECX FROM SERVER
#====================================
niceCx = ndex2.create_nice_cx_from_server(server='dev.ndexbio.org', username='******', password='******', uuid='b7190ca4-aec2-11e7-9b0a-06832d634f41') #NiceCXNetwork(server='dev.ndexbio.org', username='******', password='******', uuid='b7190ca4-aec2-11e7-9b0a-06832d634f41')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_to_pandas(self):
niceCx_from_server = ndex2.create_nice_cx_from_server(server='public.ndexbio.org',
uuid='3f08d557-1e5f-11e8-b939-0ac135e8bacf')
niceCx_from_server_df = niceCx_from_server.to_pandas_dataframe()
upload_message = niceCx_from_server_df
print(upload_message)
self.assertFalse(upload_message.empty)
def test_to_pandas(self):
niceCx_from_server = ndex2.create_nice_cx_from_server(server='public.ndexbio.org',
uuid='3f08d557-1e5f-11e8-b939-0ac135e8bacf')
niceCx_from_server_df = niceCx_from_server.to_pandas_dataframe()
upload_message = niceCx_from_server_df
print(upload_message)
self.assertFalse(upload_message.empty)
def test_ndex_load_cx_model(self):
niceCxBuilder = NiceCXBuilder()
#nice_cx_from_builder = niceCxBuilder.create_from_server('http://dev2.ndexbio.org', 'scratch', 'scratch', '94766028-934d-11e7-9743-0660b7976219')
nice_cx = ndex2.create_nice_cx_from_server(
server='dev2.ndexbio.org',
username='******',
password='******',
uuid='94766028-934d-11e7-9743-0660b7976219')
print(nice_cx)
def add_pathway_info(network, network_id, cytoscape_visual_properties_template_id):
"""
Adds network
:param network:
:param network_id:
:param cytoscape_visual_properties_template_id: UUID of NDEx network to
extract various network attributes such as description, rightsHolder,
reference, rights
:return:
"""
dataframe = get_signor_pathway_description_df(network_id)
if dataframe is not None:
template_network = ndex2.create_nice_cx_from_server(server=my_server,
uuid=cytoscape_visual_properties_template_id,
username=my_username, password=my_password)
if not pd.isnull(dataframe.iat[0, 1]):
network.set_name(dataframe.iat[0, 1])
if not pd.isnull(dataframe.iat[0, 0]):
network.set_network_attribute("labels", [dataframe.iat[0, 0]], type='list_of_string')
if not pd.isnull(dataframe.iat[0, 3]):
network.set_network_attribute("author", dataframe.iat[0, 3])
if not pd.isnull(dataframe.iat[0, 2]):
network.set_network_attribute("description",
'%s %s' % (dataframe.iat[0, 2],
template_network.get_network_attribute('description')['v']))
network.set_network_attribute('rightsHolder',
template_network.get_network_attribute('rightsHolder')['v'])
network.set_network_attribute("rights", template_network.get_network_attribute('rights')['v'])
network.set_network_attribute("reference", template_network.get_network_attribute('reference')['v'])
network.set_network_attribute('dataSource',
'https://signor.uniroma2.it/pathway_browser.php?organism=&pathway_list=' + str(
network_id))
network.set_network_attribute("version", f"{datetime.now():%d-%b-%Y}")
disease_pathways = ['ALZHAIMER DISEASE', 'FSGS', 'NOONAN SYNDROME', 'PARKINSON DISEASE']
cancer_pathways = ['ACUTE MYELOID LEUKEMIA', 'COLORECTAL CARCINOMA', 'GLIOBLASTOMA MULTIFORME',
'LUMINAL BREAST CANCER', 'MALIGNANT MELANOMA', 'PROSTATE CANCER',
'RHABDOMYOSARCOMA', 'THYROID CANCER']
network.set_network_attribute("organism", "Human, 9606, H**o sapiens")
if signor_id_name_mapping.get(network_id).upper() in disease_pathways:
network.set_network_attribute("networkType", "Disease Pathway")
elif signor_id_name_mapping.get(network_id).upper() in cancer_pathways:
network.set_network_attribute("networkType", "Cancer Pathway")
else:
network.set_network_attribute("networkType", "Signalling Pathway")
# TODO: set “networkType” property depending on network
# a. Signalling Pathway
# b. Disease Pathway
# c. Cancer Pathway
else:
print('skipping ' + network_id)
def test_add_int_attr(self):
niceCx = NiceCXNetwork()
int_node = niceCx.create_node(node_name="testint")
niceCx.add_node_attribute(property_of=int_node, name='Size', values=1, type="integer")
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(server='dev.ndexbio.org', uuid=UUID, username=upload_username, password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "integer")
def test_get_set2(self):
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='192ce948-1e5f-11e8-b939-0ac135e8bacf')
context = [{'ncbigene': 'http://identifiers.org/ncbigene/',
'hgnc.symbol': 'http://identifiers.org/hgnc.symbol/',
'uniprot': 'http://identifiers.org/uniprot/'}]
niceCx.set_context(context)
niceCx.set_name('Testing Context')
upload_message = niceCx.upload_to('public.ndexbio.org', 'scratch', 'scratch')
print(niceCx.__str__())
def test_node_data_types(self):
self.assertFalse(upload_username == 'username')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='f1dd6cc3-0007-11e6-b550-06603eb7f303')
my_aspect = []
my_aspect.append({'node': '1', 'value': 'test1'})
my_aspect.append({'node': '2', 'value': 'test2'})
my_aspect.append({'node': '3', 'value': 'test3'})
my_aspect.append({'node': '4', 'value': 'test4'})
my_aspect.append({'node': '5', 'value': 'test5'})
my_aspect.append({'node': '6', 'value': 'test6'})
niceCx.add_opaque_aspect('fakeAspect', my_aspect)
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(True)
def test_add_lst_flt(self):
niceCx = NiceCXNetwork()
list_float_node = niceCx.create_node(node_name="testlstflt")
niceCx.add_node_attribute(property_of=list_float_node, name='Too many scores', values=[15.3,43.6,-34.0,43.3], type="list_of_float")
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(server='dev.ndexbio.org', uuid=UUID, username=upload_username,
password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "list_of_double")
def test_node_data_types(self):
self.assertFalse(upload_username == 'username')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='f1dd6cc3-0007-11e6-b550-06603eb7f303')
my_aspect = []
my_aspect.append({'node': '1', 'value': 'test1'})
my_aspect.append({'node': '2', 'value': 'test2'})
my_aspect.append({'node': '3', 'value': 'test3'})
my_aspect.append({'node': '4', 'value': 'test4'})
my_aspect.append({'node': '5', 'value': 'test5'})
my_aspect.append({'node': '6', 'value': 'test6'})
niceCx.add_opaque_aspect('fakeAspect', my_aspect)
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(True)
def get_networkx_object(self, ndex_uuid):
"""
Given a NDEx uuid, this method returns
the network as a networkx object
:param ndex_uuid: NDEx uuid to get
:return: networkx object upon success or None if unable to load
"""
if ndex_uuid is None:
logger.error('UUID passed in is None')
return None
logger.info('Retreiving network with uuid: ' + ndex_uuid)
cxnet = create_nice_cx_from_server(server=self._ndex_server,
uuid=ndex_uuid)
return cxnet.to_networkx()
def _get_network_from_server(self):
"""
"""
self._network = ndex2.create_nice_cx_from_server(
server=self._server, uuid=self._uuid, username=self._user, password=self._pass)
#import json
#print('edges:\n {}'.format(json.dumps(self._network.edges, indent=4)))
#print('\nedgeAttributes:\n {}'.format(json.dumps(self._network.edgeAttributes, indent=4)))
#print(json.dumps(self._network.edgeAttributes, indent=4))
#logger.info('Found {:,} unique Ensembl Ids in {}\n'.format(len(ensembl_ids), self._full_file_name))
return 0
def test_create_from_server_manipulate_and_save(self):
print('Testing: Create from server and manupulate (uuid:51247435-1e5f-11e8-b939-0ac135e8bacf)')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='51247435-1e5f-11e8-b939-0ac135e8bacf')
nice_networkx = niceCx.to_networkx()
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
# Restore template
niceCx_from_netx.apply_template('public.ndexbio.org', '51247435-1e5f-11e8-b939-0ac135e8bacf')
niceCx_from_netx.set_name('Round trip from server to networkx to NDEx')
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_from_server_manipulate_and_save2(self):
print('public network')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='21106ea7-cbba-11e7-ad58-0ac135e8bacf')
nice_networkx = niceCx.to_networkx()
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
# Restore template
niceCx_from_netx.apply_template('public.ndexbio.org', '72ef5c3a-caff-11e7-ad58-0ac135e8bacf')
niceCx_from_netx.set_name('Round trip from server to networkx to NDEx')
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def _get_style_network_from_uuid(self):
try:
self._style_network = ndex2.create_nice_cx_from_server(
self._style_server
if self._style_server is not None else self._server,
username=self._style_user
if self._style_user is not None else self._user,
password=self._style_pass
if self._style_pass is not None else self._pass,
uuid=self._style_uuid)
except Exception as e:
print(e)
print("Error while loading style network from NDEx. "
"Default style will be used instead.")
self._style_file = _get_default_style_file_name()
self._get_style_network_from_file()
def test_node_data_types2(self):
self.assertFalse(upload_username == 'username')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='a18fd45e-68d5-11e7-961c-0ac135e8bacf') #NiceCXNetwork(server='dev2.ndexbio.org', username='******', password='******', uuid='9433a84d-6196-11e5-8ac5-06603eb7f303')
found_double_type = False
for id, node in niceCx.get_nodes():
abc_node_attrs = niceCx.get_node_attributes(node)
if abc_node_attrs is not None:
for node_attr in abc_node_attrs:
if node_attr.get('d') == 'double':
found_double_type = True
break
self.assertTrue(found_double_type)
print(niceCx.__str__())
def test_node_data_types2(self):
self.assertFalse(upload_username == 'username')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='a18fd45e-68d5-11e7-961c-0ac135e8bacf') #NiceCXNetwork(server='dev2.ndexbio.org', username='******', password='******', uuid='9433a84d-6196-11e5-8ac5-06603eb7f303')
found_double_type = False
for id, node in niceCx.get_nodes():
abc_node_attrs = niceCx.get_node_attributes(node)
if abc_node_attrs is not None:
for node_attr in abc_node_attrs:
if node_attr.get('d') == 'double':
found_double_type = True
break
self.assertTrue(found_double_type)
print(niceCx.__str__())
def from_ndex(
self,
uuid="f93f402c-86d4-11e7-a10d-0ac135e8bacf", #PCNet
node_name="name",
):
del self.__dict__
network_niceCx = ndex2.create_nice_cx_from_server(
server='public.ndexbio.org', uuid=uuid)
network = network_niceCx.to_networkx()
self.__init__(network=network, node_name=node_name)
return self
def test_update_style(self):
print('!!!!! WARNING !!!!!')
print('This test will load a network with 63 Million edges. It will take a while to run and consume a lot of RAM')
test_uuid = '83013c93-75ca-11e8-8b82-525400c25d22'
test_user = '******'
test_pass = '******'
test_server = 'dev.ndexbio.org'
print('loading network to nice cx')
niceCx = ndex2.create_nice_cx_from_server(server=test_server, uuid=test_uuid, username=test_user, password=test_pass)
print('done loading network to nice cx')
print('applying template')
niceCx.apply_template('public.ndexbio.org', '2ccec370-6689-11e7-a03e-0ac135e8bacf')
print('done applying template')
print('uploading to server')
message = niceCx.update_to(test_uuid, test_server, test_user, test_pass)
print('FINISHED')
def test_node_data_types(self):
niceCx = ndex2.create_nice_cx_from_server(
server='public.ndexbio.org',
uuid='fc63173e-df66-11e7-adc1-0ac135e8bacf'
) #NiceCXNetwork(server='dev2.ndexbio.org', username='******', password='******', uuid='9433a84d-6196-11e5-8ac5-06603eb7f303')
found_int_type = False
for id, node in niceCx.get_nodes():
abc_node_attrs = niceCx.get_node_attributes(node)
if abc_node_attrs is not None:
for node_attr in abc_node_attrs:
if node_attr.get_data_type(
) == ATTRIBUTE_DATA_TYPE.INTEGER:
found_int_type = True
self.assertTrue(found_int_type)
print(niceCx.__str__())
def _process_network_by_id(self, networkid):
"""
Processes network by id
:param networkid:
:return:
"""
if networkid is None:
logger.error('network id is None')
return
network = ndex2.create_nice_cx_from_server(self._sourceserver, username=self._sourceuser,
password=self._sourcepass,
uuid=networkid)
logger.info('NETWORK: ' + network.get_name())
for id, node in network.get_nodes():
raw_type = network.get_node_attribute(id, 'WP.type')
if raw_type is None:
continue
raw_type = raw_type['v']
# some nodes have empty string for name which currently screws up enrichment
# so going to just set the type to something else for these right now
if 'n' not in node or node['n'] is None or len(node['n']) == 0:
node['n'] = 'unset'
network.add_node_attribute(property_of=id, name='type', values='unsetname' + raw_type, overwrite=True)
else:
network.add_node_attribute(property_of=id, name='type',
values=self._remap_raw_type_new_normalized_type(raw_type),
overwrite=True)
# apply style to network
network.apply_style_from_network(self._template)
network_update_key = self._net_summaries.get(network.get_name().upper())
if network_update_key is not None:
return network.update_to(network_update_key, self._server, self._user, self._pass,
user_agent=self._get_user_agent())
else:
upload_message = network.upload_to(self._server, self._user,
self._pass,
user_agent=self._get_user_agent())
return upload_message
def test_create_from_server_manipulate_and_save2(self):
print('Testing: Create from server and generate networkx (uuid:51247435-1e5f-11e8-b939-0ac135e8bacf)')
niceCx = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='51247435-1e5f-11e8-b939-0ac135e8bacf')
#serialized = pickle.dumps(niceCx.to_cx(), protocol=0)
#print('Serialized memory:', sys.getsizeof(serialized))
nice_networkx = niceCx.to_networkx()
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
# Restore template
niceCx_from_netx.apply_template('public.ndexbio.org', '51247435-1e5f-11e8-b939-0ac135e8bacf')
niceCx_from_netx.set_name('Round trip from server to networkx to NDEx')
print(niceCx_from_netx)
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_add_lst_int(self):
niceCx = NiceCXNetwork()
list_int_node = niceCx.create_node(node_name="testlstint")
niceCx.add_node_attribute(property_of=list_int_node,
name='Too many sizes',
values=[1, 2, 3, 4, 5],
type="list_of_integer")
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(
server='dev.ndexbio.org',
uuid=UUID,
username=upload_username,
password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "list_of_integer")
def test_add_flt(self):
niceCx = NiceCXNetwork()
float_node = niceCx.create_node(node_name="testflt")
niceCx.add_node_attribute(property_of=float_node,
name='Score',
values=1.0,
type="float")
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(
server='dev.ndexbio.org',
uuid=UUID,
username=upload_username,
password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "double")
def from_ndex(
self,
uuid="f93f402c-86d4-11e7-a10d-0ac135e8bacf", #PCNet
node_name="name",
ndex_username=None,
ndex_password=None,
ndex_server="http://public.ndexbio.org",
):
del self.__dict__
network_niceCx = ndex2.create_nice_cx_from_server(
server=ndex_server,
username=ndex_username,
password=ndex_password,
uuid=uuid)
network = network_niceCx.to_networkx()
self.__init__(network=network, node_name=node_name)
return self
def get_full_signor_network(load_plan, species):
url = "https://signor.uniroma2.it/getData.php?organism=" + species # Human 9606 # mouse 10090 - Rat 10116
df = get_full_signor_pathway_relations_df(species)
# filter dataframe to remove rows that are not human
human_dataframe = df[(df["entitya"] != "") & (df["entityb"] != "") & (df["ida"] != "") & (df["idb"] != "")]
# upcase column names
rename = {}
for column_name in human_dataframe.columns:
rename[column_name] = column_name.upper()
human_dataframe = human_dataframe.rename(columns=rename)
network = t2n.convert_pandas_to_nice_cx_with_load_plan(human_dataframe, load_plan)
# Fix values for "DIRECT"
for edge_id, edge in network.get_edges():
direct = network.get_edge_attribute_value(edge_id, "DIRECT")
# print(direct)
if direct:
if direct == "t":
network.set_edge_attribute(edge, "DIRECT", "YES")
else:
network.set_edge_attribute(edge, "DIRECT", "NO")
# Set prefixes for represents based on the "DATABASE" attribute
#
# Note that this is a good example of a situation that calls
# for custom code and does not justify an extension to the load_plan
# Cases of this type are too variable. Custom code is easier.
#
for node_id, node in network.get_nodes():
database = network.get_node_attribute_value(node_id, "DATABASE")
represents = node.get('r')
if database == "UNIPROT":
represents = "uniprot:" + represents
node['r'] = represents
if database == "SIGNOR":
represents = "signor:" + represents
node['r'] = represents
# in all other cases, the identifier is already prefixed
network.remove_node_attribute(node_id, "DATABASE")
template_network = ndex2.create_nice_cx_from_server(server=my_server,
uuid=cytoscape_visual_properties_template_id,
username=my_username, password=my_password)
network.set_network_attribute("labels", template_network.get_network_attribute('labels'))
network.set_network_attribute("author", template_network.get_network_attribute('author'))
full_desc = ('This network contains all the ' +
species_mapping.get(species) +
' interactions currently available in SIGNOR' +
template_network.get_network_attribute('description')['v'])
network.set_network_attribute('description', full_desc)
network.set_network_attribute("version", f"{datetime.now():%d-%b-%Y}") # "0.0.1")
network.set_network_attribute('rightsHolder', template_network.get_network_attribute('rightsHolder')['v'])
network.set_network_attribute('rights', template_network.get_network_attribute('rights')['v'])
network.set_network_attribute("reference",
template_network.get_network_attribute('reference')['v'])
return network
def test_creating_from_server(self):
niceCx_from_server = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='3f08d557-1e5f-11e8-b939-0ac135e8bacf')
upload_message = niceCx_from_server.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
nice_cx_from_networkx = ndex2.create_nice_cx_from_networkx(G)
# #### *ndex2.create_nice_cx_from_pandas(dataframe)
# In[ ]:
#create an Empty Pandas Dataframe
df = pd.DataFrame()
nice_cx_from_pandas = ndex2.create_nice_cx_from_pandas(df)
# #### *ndex2.create_nice_cx_from_server(server, username=None, password=None, uuid=None)
# In[ ]:
uuid = "1c69beff-1229-11e6-a039-06603eb7f303"
nice_cx_from_server = ndex2.create_nice_cx_from_server(
server='http://public.ndexbio.org', uuid=uuid)
nice_cx_from_server.print_summary()
# #### create_node(name, represents=None)
# In[ ]:
#Starting with an Empty Network
NiceCX_creatures = NiceCXNetwork()
node_id_list = []
#create_node() method returns the new node id. IDs are always assigned in an ascending order.
#add 10 nodes to the network
for i in range(10):
node_name = "new node" + str(i)
node_id = NiceCX_creatures.create_node(node_name)
def test_creating_from_server(self):
niceCx_from_server = ndex2.create_nice_cx_from_server(server='public.ndexbio.org', uuid='3f08d557-1e5f-11e8-b939-0ac135e8bacf')
upload_message = niceCx_from_server.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def netprop_zscore(seed_gene_file,
seed_gene_file_delimiter=None,
num_reps=10,
alpha=0.5,
interactome_file=None,
interactome_uuid='f93f402c-86d4-11e7-a10d-0ac135e8bacf',
ndex_server='public.ndexbio.org',
ndex_user=None,
ndex_password=None,
out_name='out',
save_final_heat=False,
save_random_final_heats=False):
'''Performs network heat propagation on the given interactome with the given
seed genes, then returns the z-scores of the final heat values of each node
in the interactome.
The z-scores are calculated based on a null model, which is built by running
the network propagation multiple times using randomly selected seed genes
with similar degree distributions to the original seed gene set.
Args:
seed_gene_file (str): Location of file containing a delimited list of
seed genes.
seed_gene_file_delimiter (str): Delimiter used to separate genes in seed
gene file. (Default: any whitespace)
num_reps (int): Number of times the network propagation algorithm should
be run using random seed genes in order to build the null model.
(Default: 10)
alpha (float): Number between 0 and 1. Denotes the importance of the
propagation step in the network propagation, as opposed to the step
where heat is added to seed genes only. Recommended to be 0.5 or
greater. (Default: 0.5)
interactome_file (str): Location of file containing the interactome in
NetworkX gpickle format. Either the interactome_file argument or the
interactome_uuid argument must be defined.
interactome_uuid (str): UUID of the interactome on NDEx. Either the
interactome_file argument or the interactome_uuid argument must be
defined. (Default: The UUID of PCNet, the Parsimonious Composite
Network: f93f402c-86d4-11e7-a10d-0ac135e8bacf)
ndex_server (str): The NDEx server on which the interactome is stored.
Only needs to be defined if interactome_uuid is defined. (Default:
ndexbio.org)
ndex_user (str): The NDEx user that the interactome belongs to. Only
needs to be defined if interactome_uuid is defined, and the
interactome is private.
ndex_password (str): The password of the NDEx user's account. Only needs
to be defined if interactome_uuid is defined, and the interactome is
private.
out_name (str): Prefix for saving output files. (Default: out)
save_final_heat (bool): If this is set to true, then the raw network
propagation heat scores for the original seed gene set will be saved
in the form of a csv file in the current directory. (Default: False)
save_random_final_heats (bool): If this is set to true, then the raw
network propagation heat scores for every repetition of the
algorithm using random seed genes will be saved in the form of a csv
file in the current directory. (Beware: This can be a large file if
num_reps is large.) (Default: False)
'''
# TODO: INTEGRATE OUTPUT WITH network_localization.py, and network_colocalization.py
# TODO: IMPROVE COMMENTS
# Process arguments
# seed_gene_file
seed_gene_file = os.path.abspath(seed_gene_file)
#num_reps
try:
num_reps = int(num_reps)
except:
raise TypeError("The num_reps argument should be an integer")
#int_file and int_uuid
if interactome_file is None and interactome_uuid is None:
raise TypeError(
"Either interactome_file or interactome_uuid argument must be provided"
)
# Load interactome
if interactome_file is not None:
interactome_file = os.path.abspath(interactome_file)
interactome = nx.Graph()
interactome = nx.read_gpickle(interactome_file)
else:
interactome = ndex2.create_nice_cx_from_server(
ndex_server,
username=ndex_user,
password=ndex_password,
uuid=interactome_uuid).to_networkx()
if 'None' in interactome.nodes():
interactome.remove_node('None')
nodes = list(interactome.nodes)
# print out interactome num nodes and edges for diagnostic purposes
print('number of nodes:')
print(len(interactome.nodes))
print('\nnumber of edges:')
print(len(interactome.edges))
# Load seed genes
seed_file = open(seed_gene_file, 'r')
seed_genes = list(
np.intersect1d(nodes,
seed_file.read().split(seed_gene_file_delimiter)))
print('\nnumber of seed genes in interactome:')
print(len(seed_genes))
# Calculate individual_heats_matrix from interactome
print('\ncalculating w_prime')
w_prime = get_normalized_adjacency_matrix(interactome, conserve_heat=True)
print('\ncalculating individual_heats_matrix')
individual_heats_matrix = get_individual_heats_matrix(w_prime, alpha)
# Calculate the z-score
print('\nCalculating z-scores: ' + seed_gene_file)
z_scores, final_heat, random_final_heats = calc_zscore_heat(
individual_heats_matrix,
nodes,
dict(interactome.degree),
seed_genes,
num_reps=num_reps)
# Save z-score results
z_scores.to_csv('z_' + out_name + '_' + str(num_reps) + '_reps_.tsv',
sep='\t')
# If save_final_heat is true, save out the final heat vectore
if save_final_heat == 'True':
final_heat.to_csv('final_heat_' + out_name + '_' + str(num_reps) +
'_reps_.tsv',
sep='\t')
# If save_random_final_heats is true, save out the vector of randoms (this can be a large file)
if save_random_final_heats == 'True':
pd.DataFrame(random_final_heats).to_csv('Fnew_' + out_name + '_rand' +
str(num_reps) + '_reps_.tsv',
sep='\t')
return z_scores, random_final_heats
import pandas as pd
import igraph
from ndex2.nice_cx_network import NiceCXNetwork
import ndex2.client as nc
import ndex2
import networkx as nx
from fa2 import ForceAtlas2
from . import utils
SERVER = 'public.ndexbio.org'
UUID = '0dcb39d6-43b6-11e6-a5c7-06603eb7f303'
if __name__ == '__main__':
nice_cx_network = ndex2.create_nice_cx_from_server(
server=SEVER, uuid=UUID)
# show the graph detail
nice_cx_network.print_summary()
# convert nice_cx -> pandas
nice_cx_from_server_df = nice_cx_network.to_pandas_dataframe()
# convert pandas -> igraph
edgelist = nice_cx_from_server_df.iloc[:, [0, 2]]
tuples = [tuple(x) for x in edgelist.values]
g_original = igraph.Graph.TupleList(tuples, directed=False)
# Pick largest subgraph
subgraphs = g_original.decompose()
tmp = [i.vcount() for i in subgraphs]
largeset_subgraph = subgraphs[tmp.index(max(tmp))]
