def __get_dna(self, ice_id):
'''Gets the sequence ICE entry.'''
url = self.__url + '/rest/file/' + self.get_ice_number(ice_id) + \
'/sequence/sbol1?sid=' + self.__sid
temp_file = tempfile.NamedTemporaryFile(delete=False)
with codecs.open(temp_file.name, 'w', 'utf-8') as text_file:
text_file.write(net_utils.get(url))
return sbol_utils.read(temp_file.name)
def get_genbank(self, ice_id, out=None):
'''Get Genbank file.'''
url = self.__url + '/rest/file/' + self.get_ice_number(ice_id) + \
'/sequence/genbank'
genbank = net_utils.get(url, self.__headers)
if out:
with open(out, 'w') as out_file:
out_file.write(genbank)
return genbank
def __get_meta_data(self, ice_id):
'''Returns an ICE entry metadata.'''
return _read_resp(
net_utils.get(
self.__url + '/rest/parts/' + self.get_ice_number(ice_id),
self.__headers))
def search(self, term, limit=5):
'''Searches ICE.'''
url = self.__url + '/rest/search?offset=0&limit=' + str(limit) + \
'&sort=relevance&q="' + term + '"'
return _read_resp(net_utils.get(url, self.__headers))
def search_groups(self, term):
'''Gets groups from search terms.'''
url = self.__url + '/rest/groups/autocomplete?token=' + term
return _read_resp(net_utils.get(url, headers=self.__headers))
def get_groups(self):
'''Gets a group name to id map.'''
url = self.__url + '/rest/groups?offset=0&limit=4096'
groups = _read_resp(net_utils.get(url, headers=self.__headers))
return {group['label']: group['id'] for group in groups['data']}