class GenomeTestBase(TestCase):
human = Genome(Species="human", Release=Release, account=account)
mouse = Genome(Species="mouse", Release=Release, account=account)
rat = Genome(Species="rat", Release=Release, account=account)
macaq = Genome(Species="macaque", Release=Release, account=account)
gorilla = Genome(Species="gorilla", Release=Release, account=account)
brca2 = human.getGeneByStableId(StableId="ENSG00000139618")
def test_gorilla(self):
"""should correctly return a gorilla gene"""
self.gorilla = Genome(Species="gorilla",
Release=Release,
account=account)
gene = self.gorilla.getGeneByStableId('ENSGGOG00000005730')
self.assertEquals(str(gene.Seq[:10]), 'TGGGAGTCCA')
def _attach_genomes(self):
for species in self.Species:
attr_name = _Species.getComparaName(species)
genome = Genome(Species=species,
Release=self.Release,
account=self._account)
self._genomes[species] = genome
setattr(self, attr_name, genome)
def test_no_assembly(self):
"""return N's for coordinates with no assembly"""
krat = Genome('Kangaroo rat', Release=58)
Start = 24385
End = Start + 100
region = krat.getRegion(CoordName='scaffold_13754',
Start=Start,
End=End)
self.assertEquals(str(region.Seq), 'N' * (End - Start))
__email__ = "*****@*****.**"
__status__ = "alpha"
Release = 76
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)
human = Genome(Species='human', Release=Release, account=account)
platypus = Genome(Species='platypus', Release=Release, account=account)
class TestLocation(TestCase):
def test_init(self):
human_loc = Coordinate(CoordName='x',
Start=1000,
End=10000,
Strand=-1,
genome=human)
# TODO: complete test for platpus
self.assertEqual(human_loc.CoordType, 'chromosome')
self.assertEqual(human_loc.CoordName, 'x')
self.assertEqual(human_loc.Start, 1000)
self.assertEqual(human_loc.End, 10000)
def setUp(self):
self.chicken = Genome(Species='chicken', Release=Release,
account=account)
def test_genome_comparison(self):
"""different genome instances with same CoreDb connection are equal"""
h2 = Genome(Species='human', Release=Release, account=account)
self.assertEquals(self.human, h2)
def test_pool_connection(self):
"""excercising ability to specify pool connection"""
dog = Genome(Species="dog",
Release=Release,
account=account,
pool_recycle=1000)
class GenomeTestBase(TestCase):
human = Genome(Species="human", Release=Release, account=account)
mouse = Genome(Species="mouse", Release=Release, account=account)
rat = Genome(Species="rat", Release=Release, account=account)
macaq = Genome(Species="macaque", Release=Release, account=account)
brca2 = list(human.getGenesMatching(StableId="ENSG00000139618"))[0]
