def __init__(self, Species, Release, account=None, pool_recycle=None):
super(Genome, self).__init__()
assert Release, 'invalid release specified'
if account is None:
account = get_ensembl_account(release=Release)
self._account = account
self._pool_recycle = pool_recycle
# TODO: check Release may not be necessary because: assert Release above
if Release is None:
Release = get_latest_release(account=account)
self._gen_release = None
# TODO make name and release immutable properties
self.Species = _Species.getSpeciesName(Species)
self.Release = str(Release)
# the db connections
self._core_db = None
self._var_db = None
self._other_db = None
self._feature_type_ids = FeatureTypeCache(self)
self._feature_coord_levels = FeatureCoordLevels(self.Species)
def test_feature_levels(self):
ChickenFeatureLevels = FeatureCoordLevels('chicken')
chicken_feature_levels = ChickenFeatureLevels(
feature_types=['gene', 'cpg', 'est'],
core_db=self.chicken.CoreDb,
otherfeature_db=self.chicken.OtherFeaturesDb)
self.assertEquals(chicken_feature_levels['repeat'].levels, ['contig'])
self.assertEquals(set(chicken_feature_levels['cpg'].levels),\
set(['contig', 'supercontig', 'chromosome']))