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import os
from cogent import DNA
from cogent.util.unit_test import TestCase, main
from cogent.db.ensembl.host import HostAccount, get_ensembl_account
from cogent.db.ensembl.genome import Genome
from cogent.db.ensembl.assembly import CoordSystem, Coordinate, get_coord_conversion
from cogent.db.ensembl.feature_level import FeatureCoordLevels
__author__ = "Gavin Huttley, Hua Ying"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley", "hua Ying"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "alpha"
Release = 68
if 'ENSEMBL_ACCOUNT' in os.environ:
args = os.environ['ENSEMBL_ACCOUNT'].split()
host, username, password = args[0:3]
kwargs = {}
if len(args) > 3:
kwargs['port'] = int(args[3])
account = HostAccount(host, username, password, **kwargs)
else:
account = get_ensembl_account(release=Release)
class TestFeatureCoordLevels(TestCase):
def setUp(self):
self.chicken = Genome(Species='chicken', Release=Release,
account=account)
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']))
def test_repeat(self):
# use chicken genome as it need to do conversion
# chicken coordinate correspondent toRefSeq human IL2A region
coord = dict(CoordName=9, Start=23817146, End=23818935)
region = self.chicken.getRegion(**coord)
# repeat is recorded at contig level, strand is 0
repeats = region.getFeatures(feature_types = 'repeat')
expect = [("9", 23817293, 23817321), ("9", 23817803, 23817812),
("9", 23817963, 23817972)]
obs = []
for repeat in repeats:
loc = repeat.Location
obs.append((loc.CoordName, loc.Start, loc.End))
self.assertEquals(set(obs), set(expect))
def test_cpg(self):
# contain 3 CpG island recorded at chromosome level
coord1 = dict(CoordName=26, Start=110000, End=190000)
cpgs1 = self.chicken.getFeatures(feature_types = 'cpg', **coord1)
exp = [("26", 116969, 117955), ("26", 139769, 140694),
("26", 184546, 185881)]
obs = []
for cpg in cpgs1:
loc = cpg.Location
obs.append((loc.CoordName, loc.Start, loc.End))
self.assertEquals(set(exp), set(obs))
# test cpg features record at supercontig level:
coord2 = dict(CoordName='Un_random', Start=29434117, End=29439117)
cpgs2 = self.chicken.getFeatures(feature_types='cpg', **coord2)
self.assertEquals(len(list(cpgs2)), 1)
if __name__ == '__main__':
main()
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