def assign_formula(self, features, for_adducts, with_tol_ppm=10.0):
"""
assign molecular formula to features using multiprocessing module
:param for_adducts: string adducts list
:param features: list or set ? of features
:param with_tol_ppm: mz tolerance in order to perform the look up
:return: dictionary with key: feature, value: list of metabolites
"""
m_count, not_found = 0, 0
for for_adduct in for_adducts:
formula = Formula.from_str(for_adduct)
logging.info("searching for adducts: {}".format(str(formula)))
# pool = billiard.Pool(processes=billiard.cpu_count())
# args = [(self.HMDB_FILE, f, formula, with_tol_ppm) for f in features]
# metabs = pool.map(search_metabolites_for, args, chunksize=20)
# pool.close()
#DEBUG CODE
metabolites = []
for f in features:
metabolites.append(search_metabolites_for((self.HMDB_FILE, f, formula, with_tol_ppm)))
# create Annotation objects
for f, metabs in izip(features, metabolites):
if not metabs:
not_found += 1
else:
m_count += len(metabs)
for_adducts_str = '[M{}{}]='.format('-' if f.polarity > 0 else '+', formula)
f.annotations += [Annotation(m, for_adducts_str) for m in metabs]
return m_count, not_found
