def test_host_comparison(self):
"""instances with same host, account, database, port are equal"""
h1 = HostAccount("ensembldb.ensembl.org", "anonymous", "", port=5306)
h2 = HostAccount("ensembldb.ensembl.org", "anonymous", "", port=5306)
self.assertNotEqual(id(h1), id(h2))
self.assertEqual(h1, h2)
# hashes are also equal
self.assertEqual(hash(h1), hash(h2))
h3 = HostAccount("ensembldb.ensembl.org", "anonymous", "", port=5300)
self.assertNotEqual(h1, h3)
self.assertNotEqual(hash(h1), hash(h3))
from cogent.db.ensembl.database import Database
__author__ = "Gavin Huttley, Hua Ying"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Gavin Huttley", "hua Ying"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Gavin Huttley"
__email__ = "*****@*****.**"
__status__ = "alpha"
Release = 56
if 'ENSEMBL_ACCOUNT' in os.environ:
username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount('127.0.0.1', username, password)
else:
account = get_ensembl_account(release=Release)
class TestDatabase(TestCase):
def test_connect(self):
human = Database(account=account,
release=Release,
species='human',
db_type='core')
gene = human.getTable('gene')
def test_get_distinct(self):
"""should return list of strings"""
db = Database(account=account,
__credits__ = ["Gavin Huttley", "hua Ying"]
__license__ = "GPL"
__version__ = "1.5.3-dev"
__maintainer__ = "Gavin Huttley"
__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)
class TestEnsemblDbName(TestCase):
def test_cmp_name(self):
"""should validly compare names by attributes"""
n1 = EnsemblDbName('homo_sapiens_core_46_36h')
n2 = EnsemblDbName('homo_sapiens_core_46_36h')
self.assertEqual(n1, n2)
def test_name_without_build(self):
"""should correctly handle a db name without a build"""
n = EnsemblDbName("pongo_pygmaeus_core_49_1")
self.assertEqual(n.Prefix, "pongo_pygmaeus")
from cogent.db.ensembl.host import HostAccount, get_ensembl_account
from cogent.db.ensembl.compara import Compara, Genome
from cogent.util.unit_test import TestCase, main
__author__ = "Jason Merkin"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley", "Hua Ying"]
__license__ = "GPL"
__version__ = "1.5.3-dev"
__maintainer__ = "Gavin Huttley"
__email__ = "*****@*****.**"
__status__ = "alpha"
Release = 12
account = HostAccount('mysql.ebi.ac.uk','anonymous', '', port=4157)
class MZ_ComparaTestBase(TestCase):
comp = Compara(['D.grimshawi', 'D.melanogaster'], Release=Release,
account=account, division='metazoa')
class MZ_TestCompara(MZ_ComparaTestBase):
def test_query_genome(self):
"""compara should attach valid genome attributes by common name"""
brca2 = self.comp.Dmelanogaster.getGeneByStableId("FBgn0050169")
self.assertEquals(brca2.Symbol.lower(), 'brca2')
def test_get_related_genes(self):
"""should correctly return the related gene regions from each genome"""
# using sc35, a splicing factor
sc35 = self.comp.Dmelanogaster.getGeneByStableId("FBgn0040286")
Orthologs = self.comp.getRelatedGenes(gene_region=sc35,