def report_paths(scored_paths, model, stmts, cell_line):
"""Report paths for a specific cell line."""
citations = {}
citation_count = 1
ab_name = 'Total c-Jun'
if cell_line == 'C32':
pol = 'decreased'
else:
pol = 'increased'
for drug in scored_paths.keys():
paths = scored_paths[drug]
for path, score in paths[:1]:
title = 'How does %s treatment result in %s %s' % \
(drug, pol, ab_name)
title += ' in %s cells?' % cell_line
print(title)
print('=' * len(title))
path_stmts = stmts_from_path(path, model, stmts)
sentences = []
for i, stmt in enumerate(path_stmts):
if i == 0:
target = stmt.agent_list()[0].name
sentences.append('%s is a target of %s.' %
(target, drug))
# Make citations
pmids = [ev.pmid for ev in stmt.evidence if ev.pmid]
cit_nums = []
for pmid in pmids:
cit_num = citations.get(pmid)
if cit_num is None:
citations[pmid] = citation_count
cit_num = citation_count
citation_count += 1
cit_nums.append(cit_num)
if cit_nums:
cit_nums = sorted(list(set(cit_nums)))
cit_str = ' [%s]' % (','.join([str(c) for c
in cit_nums]))
else:
cit_str = ''
ea = EnglishAssembler([stmt])
sentence = ea.make_model()
sentence = sentence[:-1] + cit_str + '.'
sentences.append(sentence)
sentences[-1] = sentences[-1][:-1] + \
', which is measured by %s.' % ab_name
print(' '.join(sentences))
print()
references = 'References\n==========\n'
for k, v in sorted(citations.items(), key=lambda x: x[1]):
references += '[%d] https://www.ncbi.nlm.nih.gov/pubmed/%s\n' % (v, k)
print(references)
def export_paths(scored_paths, model, stmts):
"""Export paths for pathway map in JSON-like format."""
conc = 1.0
time = 10
paths = {}
for cell_line in scored_paths.keys():
for drug in scored_paths[cell_line].keys():
scpaths = scored_paths[cell_line][drug]
path, score = scpaths[0]
label = '%s_%s_%s_%s' % (drug, time, conc, cell_line)
paths[label] = {'meta': [], 'path': []}
path_stmts = stmts_from_path(path, model, stmts)
uuids = [stmt.uuid for stmt in path_stmts]
paths[label]['path'] = uuids
return paths
def path_to_english(path, model, stmts):
path_stmts = stmts_from_path(path, model, stmts)
ea = EnglishAssembler(path_stmts)
return ea.make_model()