def test_from_sim(self):
"""Test that the run_clixo function can run."""
sim, genes = self.ont.flatten()
genes = list(genes)
print(genes)
sim = pd.DataFrame(sim, columns=genes, index=genes)
ddo = Ontology.run_clixo(
sim,
'test_df_output.txt',
'test_clixo_output.txt',
'test_output.txt',
square=True,
square_names=genes,
)
print('ddo:\n', ddo)
# print(x)
return x
cooc_df = cooc_df.apply(normalize, axis=1)
# print(cooc_df)
namemap_df = pd.read_csv(nnm, sep="|", header=None).set_index(0)
namemap_df.columns = ["Label"]
# print(namemap_df)
ont = Ontology.run_clixo(
cooc_df,
alpha,
beta,
verbose=False,
)
ont.update_node_attr(namemap_df)
# print(ont.to_table(output, clixo_format=True))
# nwx = ont.to_networkx()
# nx.write_graphml(nwx, 'clixotable.graphml')
grph = ont.to_igraph(include_genes=True)
grph.write_graphml(output + '.graphml')
if upload:
ndex_url, ont_ndexgraph = ont.to_ndex(
name="Pitch 15 Asthma Ontology",
def infer_hierarchical_model(
self,
method='clixo-api',
method_kwargs=None,
edge_attr='has_edge',
ddot_api_location=None,
get_ontology_object=False,
):
if method_kwargs is None:
method_kwargs = {}
if method == 'clixo-api':
cols = self.edge_table.columns
table = self.edge_table[[cols[0], cols[1], edge_attr]]
self.ddot_client = DDOT_Client.from_dataframe(
table, ddot_api_location=ddot_api_location)
(self.ddot_client.call(**method_kwargs).wait_for_hiview_url())
self.hiview_url = self.ddot_client.hiview_url
if get_ontology_object:
self.ddot_client.get_output_file(create_object=True)
self.ontology = self.ddot_client.ontology
elif method == 'clixo':
from ddot import Ontology
self.ontology = Ontology.run_clixo(
self.edge_table,
method_kwargs['alpha'],
method_kwargs['beta'],
clixo_cmd=method_kwargs['clixo_path'],
clixo_version=method_kwargs['clixo_version'],
)
if len(self.edge_table.columns) != 3:
#TODO
print("future warning about edge table columns")
if method_kwargs.get("upload_to_ndex", True):
self.upload_ontology_to_ndex(
method_kwargs['ndex_username'],
method_kwargs['ndex_password'],
ndex_server=method_kwargs.get('ndex_server',
"http://test.ndexbio.org"),
main_network=self.edge_table,
main_feature=self.edge_table.columns[-1])
ndex_url, _ = self.ontology.to_ndex(
method_kwargs['ndex_username'],
method_kwargs['ndex_password'],
method_kwargs.get('ndex_server',
'http://test.ndexbio.org'),
network=self.edge_table,
main_feature=self.edge_table.columns[-1])
uuid = ndex_url.split('/')[-1]
self.hiview_url = f"http://hiview-test.ucsd.edu/{uuid}?type=test&server=http://dev2.ndexbio.org"
else:
raise ValueError("Invalid method!")
return self
concept1 = x[0]
concept2 = x[1]
x[0] = x[0].replace(' ', '_')
x[1] = x[1].replace(' ', '_')
x[2] = float(x[2]) / (frequency_dict[concept1] * frequency_dict[concept2])
# print(x)
return x
cooc_df = cooc_df.apply(normalize, axis=1)
print(cooc_df)
print(isinstance(cooc_df, pd.DataFrame))
ont = Ontology.run_clixo(cooc_df, alpha, beta)
print(ont.to_table(output, clixo_format=True))
# nwx = ont.to_networkx()
# nx.write_graphml(nwx, 'clixotable.graphml')
grph = ont.to_igraph(include_genes=True)
grph.write_graphml(output + '.graphml')
if upload:
ndex_url, ont_ndexgraph = ont.to_ndex(
name="Pitch 15 Asthma Ontology",
ndex_server="http://test.ndexbio.org",
ndex_pass='******',
ndex_user='******',
layout='bubble-collect',
def StreamElements(self, element_iterator, context):
try:
params = {
'similarity' : 'Similarity',
'name' : 'Data-Driven Ontology',
'min_dt' : -100000,
'features' : '',
'all_features' : False,
'input_fmt' : 'cx',
'timeout' : 100,
'ndex_uuid' : None
}
params.update(default_params)
G, params, errors = self.read_element_stream(element_iterator, params)
self.format_params(params)
if verbose:
print('Parameters', params)
input_fmt = params['input_fmt'].replace('ndex', 'cx')
G_df, nodes_attr = ndex_to_sim_matrix(
params['ndex_uuid'],
params['ndex_server'],
params['ndex_user'],
params['ndex_pass'],
similarity=params['similarity'],
input_fmt=input_fmt,
output_fmt='sparse')
print 'Similarity'
print G_df.head()
features = [params['similarity']]
if params['all_features']:
features.extend(G_df.columns.values.tolist())
gene_names = np.unique(np.append(
G_df['Gene1'].values,
G_df['Gene2'].values))
if verbose:
print 'Gene names:', gene_names
if params['features']:
to_concat = []
for f in params['features']:
if f in G_df.columns:
in_G.append(f)
else:
tmp = ndex_to_sim_matrix(
params['ndex_uuid'],
params['ndex_server'],
params['ndex_user'],
params['ndex_pass'],
similarity=params['similarity'],
input_fmt=input_fmt,
output_fmt='sparse',
subset=None)
tmp.set_index(['Gene1', 'Gene2'], inplace=True)
to_concat.append(tmp)
to_concat.append(G_df)
G_df = pd.concat(to_concat, axis=1)
if verbose:
print 'Features:', features
errors = [e for e in errors if e.message != "Error decoding token from stream, EOF"]
if len(errors) == 0:
## Run CLIXO
graph = G_df[['Gene1', 'Gene2', params['similarity']]]
ont = Ontology.run_clixo(
graph,
params['alpha'],
params['beta'],
min_dt=params['min_dt'],
timeout=params['timeout']
)
# Create an NDEX network for every term's subnetwork
term_2_uuid = ont.upload_subnets_ndex(
G_df,
features,
params['ndex_server'],
params['ndex_user'],
params['ndex_pass'],
params['name'],
propagate=True
)
if params['output_fmt']=='cx':
# Use CXmate to stream to NDEX
for elt in self.stream_ontology(ont, term_sizes, term_2_uuid, tree_edges):
yield elt
elif params['output_fmt']=='ndex':
description = (
'Data-driven ontology created by CLIXO '
'(parameters: alpha={alpha}, beta={beta}). '
'Created from similarity network '
'at {ndex_server}/{ndex_uuid}').format(**params)
# nx_nodes_to_pandas(G)
ont_ndex = ont.to_NdexGraph(
name=params['name'],
description=description,
term_2_uuid=term_2_uuid,
gene_attr=nodes_attr)
ont_url = ont_ndex.upload_to(
params['ndex_server'],
params['ndex_user'],
params['ndex_pass'])
print 'ontology_url:', ont_url
for elt in yield_ndex(ont_url):
yield elt
else:
for caught_error in errors:
error = self.create_internal_crash_error(caught_error.message, 500)
log_error(error)
yield error
except Exception as e:
message = "Unexpected error: " + str(e)
error = self.create_internal_crash_error(message, 500)
log_error(error)
import traceback
print traceback.print_exc()
yield error
import networkx as nx
import pandas as pd
import ddot
from ddot import Ontology
net = nx.read_edgelist('/home/hsher/secM/string_subnetwork_secM')
df = nx.convert_matrix.to_pandas_dataframe(net, weight='combined_score')
print(df.sum(axis=1))
print(df.shape)
ont = Ontology.run_clixo(df,
alpha=0.2,
beta=0.9,
output='/home/hsher/secM/secM_ontology',
square=True,
square_names=df.index.tolist())
# put to ndex
ndex_server = 'http://public.ndexbio.org'
ndex_user, ndex_pass = '******', '5mY87$747l'
url, _ = ont.to_ndex(ndex_server=ndex_server,
ndex_user=ndex_user,
ndex_pass=ndex_pass)
print(url)