def run(self): e = Environment(url=self.options.api_url, key_id=self.options.key_id, key=self.options.key, env_id = self.options.env_id, api_version = '2.3.0') e.write(self.config.base_path) e = Environment.from_ini(self.config.base_path) print e
def run(self): e = Environment( url=self.options.api_url, ldap_login=self.options.login, env_id = self.options.env_id, api_version = '2.3.0', auth_type='ldap') e.write(self.config.base_path) e = Environment.from_ini(self.config.base_path) print e
def run(self):
e = Environment(
url=self.options.api_url,
key_id=self.options.key_id,
key=self.options.key,
env_id=self.options.env_id,
api_version="2.3.0",
auth_type="password",
)
e.write(self.config.base_path)
e = Environment.from_ini(self.config.base_path)
print e
def __init__(self, args):
# The query sequences
self.ids = args.f
# The output file
self.output = args.o
# The evalue
self.eval = args.e
# Create the Ensembl interface
self.En = Ensembl()
# Init environment variables (Mainly db paths)
env = Environment()
# Get the database path
self.db = env.getDb(int(args.g[0]))
actual = []
# Split comma separated query values
for i in self.ids:
# Split on the comma
r = i.split(",")
# For each id, clean it and add to list
for e in r:
# Remove whitespaces
e = re.sub(" ", "", e)
# If this is not empty string, include it
if e != "":
actual.append(e)
# Init object with actual sequence ids
self.ids = actual
def run(self):
e = Environment.from_ini(self.config.base_path)
print e