def get_compound_infos(compound_id):
baseUrl = 'http://rest.kegg.jp/get/' + compound_id
req = urllib2.Request(baseUrl)
response = urllib2.urlopen(req)
infolines = response.read().split('\n')
current_info_type = ''
compound_info = dict()
for line in infolines:
infos = line.split(' ')
if not line.startswith(' ') and not line.startswith('/'):
current_info_type = infos[0]
infos = infos[1:]
for info_item in infos:
if info_item.endswith('\n'):
info_item = info_item[:-1]
if info_item == 'Compound' and current_info_type == 'ENTRY':
continue
try:
compound_info[current_info_type] += info_item
except:
compound_info[current_info_type] = info_item
try:
names = compound_info['NAME'].split(';')
compound_info['NAME'] = names[0]
compound_info['NICKNAME'] = ''
for i in range(1, len(names)):
compound_info['NICKNAME'] += names[i] + '_'
new_compound = compound(compound_id=compound_info['ENTRY'])
new_compound.name = compound_info['NAME']
new_compound.nicknames = compound_info['NICKNAME']
new_compound.formula = compound_info['FORMULA']
new_compound.exact_mass = compound_info['EXACT_MASS']
new_compound.mol_mass = compound_info['MOL_WEIGHT']
try:
new_compound.save()
return new_compound
except:
traceback.print_exc()
print '%s can not be saved' % compound_info['NAME']
return None
except:
pass
return None
def saveCompoundDataToDB(compound_file):
current_info_type = ''
compound_info = dict()
for line in compound_file.readlines():
if line.endswith('\n'):
line = line[:-1]
infos = line.split(' ')
if not line.startswith(' ') and not line.startswith('/'):
current_info_type = infos[0]
infos = infos[1:]
for info_item in infos:
if info_item.endswith('\n'):
info_item = info_item[:-1]
if info_item == 'Compound' and current_info_type == 'ENTRY':
continue
try:
compound_info[current_info_type] += info_item
except:
compound_info[current_info_type] = info_item
#gene nick names
try:
names = compound_info['NAME'].split(';')
compound_info['NAME'] = names[0]
compound_info['NICKNAME'] = ''
for i in range(1, len(names)):
compound_info['NICKNAME'] += names[i] + '_'
new_compound = compound(compound_id=compound_info['ENTRY'])
new_compound.name = compound_info['NAME']
new_compound.nicknames = compound_info['NICKNAME']
new_compound.formula = compound_info['FORMULA']
new_compound.exact_mass = compound_info['EXACT_MASS']
new_compound.mol_mass = compound_info['MOL_WEIGHT']
try:
new_compound.save()
except:
traceback.print_exc()
print '%s can not be saved' % compound_info['NAME']
except:
pass
