def main():
'''
Commands are in order of dependencies.
'''
if len(sys.argv) == 2:
this_file, command = sys.argv
if command == 'sentences':
generate_sentences() # generates train_sentences.json
return
elif command == 'clean_chemicals':
clean_chemicals() # generates train_clean_chemicals.json
return
elif command == 'match_name':
match_name() # generates train_match_name.json
return
elif command == 'tag_sentences':
tag_sentences() # generates train_tag_sentences.json
chemtagger.save_map()
return
elif command == 'match_inchi':
match_inchi() # train_match_inchi.json
return
elif command == 'combine':
combine() # generates train_match.json
return
elif command == 'stats':
stats()
return
elif command == 'abstract_stats':
abstract_stats()
return
print 'Wrong number of arguments. Usage: python rapier.py [sentences, clean_chemicals, match_name, tag_sentences, match_inchi, combine, stats, abstract_stats]'
def main():
tests = [
[
0,
[(1, ['serine', 'glycine'])],
'10347152-2',
'As for flux through serine hydroxymethyltransferase and GCS, the conversion of serine to glycine occurred fairly rapidly, followed by GCS-mediated slow decarboxylation of the accumulated glycine',
],
[
1,
[(1, ['3-phosphohydroxypyruvate', 'l-phosphoserine'])],
'10024454-0',
'Phosphoserine aminotransferase (PSAT; EC 2.6.1.52), a member of subgroup IV of the aminotransferases, catalyses the conversion of 3-phosphohydroxypyruvate to l-phosphoserine'
],
[
2,
[(2, ['methionine', 'methanethiol'])],
'10482527-7',
'We therefore propose that in P. putida methionine is converted to methanethiol and then oxidized to methanesulfonate',
],
[
3,
[(2, ['ornithine', 'N-alpha-acetylornithine']),
(5, ['ornithine', 'N-alpha-acetylornithine'])],
'10692366-1',
'Only two exceptions had been reported-the Enterobacteriaceae and Myxococcus xanthus (members of the gamma and delta groups of the class Proteobacteria, respectively)-in which ornithine is produced from N-alpha-acetylornithine by a deacylase, acetylornithinase (AOase) (argE encoded)',
],
[
4,
[(4, ['l-lysine', 'l-beta-lysine'])],
'17944492-3',
'The energetics is here reported for the action of lysine 2,3-aminomutase (LAM), which catalyzes the interconversion of l-lysine and l-beta-lysine',
],
[
5,
[(4, ['estrone', 'estradiol'])],
'8013376-0',
'Estradiol 17 beta-hydroxysteroid dehydrogenase (17 beta HSD) mediates the interconversion of estrone and estradiol in endocrine-responsive tissues such as the breast',
],
[
6,
[(5, ['5-Hydroxymethyltryptophan', '5-hydroxy-4-methyltryptophan', '5-methyltryptophan'])],
'10587452-4',
'5-Hydroxymethyltryptophan and 5-hydroxy-4-methyltryptophan are the products from 5-methyltryptophan',
],
[
7,
[(6, ['maltose', 'trehalose'])],
'18505459-2',
'We show that TreS from Mycobacterium smegmatis, as well as recombinant TreS produced in Escherichia coli, has amylase activity in addition to the maltose <--> trehalose interconverting activity (referred to as MTase)',
],
]
for index, output, sid, sent in tests:
res = extract(sid, sent)
if res == output:
print 'Test %s passed.' % index
else:
print 'TEST %s FAILED!\nResult: %s\n' % (index, res)
chemtagger.save_map()
def main():
'''
Commands are in order of dependencies.
'''
if len(sys.argv) == 2:
this_file, command = sys.argv
if command == 'run':
evaluate()
chemtagger.save_map()
return
elif command == 'stats':
stats()
return
print 'Wrong number of arguments. Usage: python evaluate.py [run, stats]'