def assemble_cx(stmts, save_file):
cxa = CxAssembler(stmts)
cxa.make_model(add_indra_json=False)
cxa.save_model(save_file)
return cxa
if __name__ == '__main__':
# Load NDEx credentials
with open('ndex_cred.json', 'rt') as f:
ndex_cred = json.load(f)
# Get the network
ncp = ndex_cx.process_ndex_network('df1fea48-8cfb-11e7-a10d-0ac135e8bacf',
username=ndex_cred['user'],
password=ndex_cred['password'])
gene_names = [
hgnc_client.get_hgnc_name(ag.db_refs['HGNC'])
for ag in ncp.get_agents()
]
"""
# Get PMIDs for reading
entrez_pmids = get_pmids(gene_names)
network_pmids = ncp.get_pmids()
pmids = list(set(entrez_pmids + network_pmids))
save_pmids_for_reading(pmids, 'dna_damage_pmids.txt')
"""
# Build the model
prior_stmts = build_prior(gene_names, 'prior_stmts.pkl')
text_refs = {
'DOI': '10.1038/s41586-020-2286-9',
'PMID': '32353859',
'PMCID': 'PMC7431030'
}
def reground_stmts(stmts):
for stmt in stmts:
for agent in stmt.agent_list():
if agent is not None and agent.name in mappings:
refs = mappings[agent.name]
agent.db_refs = refs
agent.db_refs['TEXT'] = agent.name
for ev in stmt.evidence:
ev.pmid = text_refs['PMID']
# Just to make a copy here
ev.text_refs = {k: v for k, v in text_refs.items()}
return stmts
if __name__ == '__main__':
cxp = ndex_cx.process_ndex_network('43803262-6d69-11ea-bfdc-0ac135e8bacf',
require_grounding=False)
stmts = reground_stmts(cxp.statements)
stmts_file = join(dirname(abspath(__file__)), '..', 'stmts',
'gordon_ndex_stmts.pkl')
with open(stmts_file, 'wb') as fh:
pickle.dump(stmts, fh)
def assemble_cx(stmts, save_file):
cxa = CxAssembler(stmts)
cxa.make_model(add_indra_json=False)
cxa.save_model(save_file)
return cxa
if __name__ == '__main__':
# Load NDEx credentials
with open('ndex_cred.json', 'rt') as f:
ndex_cred = json.load(f)
# Get the network
ncp = ndex_cx.process_ndex_network('55cfccd4-966e-11e7-a10d-0ac135e8bacf',
username=ndex_cred['user'],
password=ndex_cred['password'],
require_grounding=False)
# Add grounding entries for ungrounded nodes/noncanonical gene names
gnd_map_ext = {
'PALB2_wt_eto': {
'HGNC': 'PALB2'
},
'PALB2_wt': {
'HGNC': 'PALB2'
},
'CSDA': {
'HGNC': 'YBX3'
},
'COBRA1': {
'HGNC': 'NELFB'
},
def test_get_cx_from_ndex_unauth():
# This network should error because unauthorized without username/pwd
ncp = process_ndex_network('df1fea48-8cfb-11e7-a10d-0ac135e8bacf')
def test_get_cx_from_ndex():
# Ras Machine network
ncp = process_ndex_network('fc56fe8d-1b60-11e8-b939-0ac135e8bacf')
def test_get_cx_from_ndex():
# Ras Machine network
ncp = process_ndex_network('50e3dff7-133e-11e6-a039-06603eb7f303')