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')