def __init__(self, cache_folder, genome_build):
""" obtain the sequence for a transcript from ensembl
Args:
cache_folder: path to folder for caching data requested from Ensembl
genome_build: string indicating the genome build ("grch37" or "grch38")
"""
self.cache = EnsemblCache(cache_folder, genome_build)
self.prior_time = time.time() - 1
self.rate_limit = 0.067
server_dict = {"grch37": "grch37.", "grch38": ""}
self.server = "http://{}rest.ensembl.org".format(server_dict[genome_build])
self.check_ensembl_api_version()
def ensembl_cache(folder=None):
''' store/retrive repeated ensembl requests from a persistent sqlite cache
'''
if folder is None:
folder = Path.home() / '.cache' / 'ensembl'
cache = EnsemblCache(str(folder))
def decorator(func):
@functools.wraps(func)
async def wrapper(*args, **kwargs):
url = args[1]
if 'rest.ensembl.org' in url:
cached = cache.get_cached_data(url)
if cached is not None:
return cached
data = await func(*args, **kwargs)
cache.cache_url_data(url, data)
return data
else:
return await func(*args, **kwargs)
return wrapper
return decorator
def setUpClass(self):
self.temp_dir = tempfile.mkdtemp()
self.cache = EnsemblCache(self.temp_dir)
def run(self):
cache = EnsemblCache(cache_dir)
while self.counter > 0:
write(cache)
self.counter -= 1
def setUpClass(self):
self.temp_dir = tempfile.mkdtemp()
self.cache = EnsemblCache(self.temp_dir, "grch37")
self.cache.set_ensembl_api_version("3.0.0")
def run(self):
cache = EnsemblCache(cache_dir, 'grch37')
cache.set_ensembl_api_version('6.0')
while self.counter > 0:
write(cache)
self.counter -= 1
