def _precompute_term_frequencies():
print("Start precomputations of term frequencies...")
go_freq_dict = dict()
go_dag = GODag(GO_DAG_FILE_PATH, prt=open(os.devnull, 'w'))
associations = IdToGosReader(UNIPROT_ASSOCIATIONS_FILE_PATH,
godag=go_dag).get_id2gos('all')
term_counts = TermCounts(go_dag, associations)
for i in go_dag.values():
go_freq_dict[i.id] = term_counts.get_count(i.id)
for alt_id in i.alt_ids:
go_freq_dict[alt_id] = term_counts.get_count(i.id)
# write frequency dict to JSON file
with open(FREQUENCY_COUNTS_FILE_PATH, 'w') as json_file:
json.dump(go_freq_dict, json_file)
def intialize_term_counts():
go_freq_dict = dict()
go_dag = GODag(os.path.join(DATA_DIR, "go-basic.obo"))
associations = IdToGosReader(UNIPROT_ASSOCIATIONS_FILE_PATH,
godag=go_dag).get_id2gos('all')
term_counts = TermCounts(go_dag, associations)
for i in go_dag.values():
go_freq_dict[i.id] = term_counts.get_count(i.id)
# write frequency dict to JSON file
with open(JSON_INDEXED_FILE_PATH, 'w') as json_file:
json.dump(go_freq_dict, json_file)