def test_get_distinct(self):
"""should return list of strings"""
db = Database(account=account,
release=Release,
species='human',
db_type='variation')
tn, tc = 'variation_feature', 'consequence_type'
expected = set((('3PRIME_UTR', 'ESSENTIAL_SPLICE_SITE'),
('3PRIME_UTR', 'SPLICE_SITE'),
('5PRIME_UTR', 'ESSENTIAL_SPLICE_SITE')))
self.assertNotEquals(set(db.getDistinct(tn, tc)) & expected, set())
db = Database(account=account,
release=Release,
species='human',
db_type='core')
tn, tc = 'gene', 'biotype'
expected = set([
'protein_coding', 'pseudogene', 'processed_transcript', 'Mt_tRNA',
'Mt_rRNA', 'IG_V_gene', 'IG_J_gene', 'IG_C_gene', 'IG_D_gene',
'miRNA', 'misc_RNA', 'snoRNA', 'snRNA', 'rRNA'
])
got = set(db.getDistinct(tn, tc))
self.assertEquals(len(got & expected), len(expected))
db = Database(account=account, release=Release, db_type='compara')
got = set(db.getDistinct('homology', 'description'))
expected = set([
'apparent_ortholog_one2one', 'between_species_paralog',
'ortholog_many2many', 'ortholog_one2many', 'ortholog_one2one',
'within_species_paralog'
])
self.assertEquals(len(got & expected), len(expected))
def test_get_distinct(self):
"""should return list of strings"""
db = Database(account=account, release=Release,
species='human', db_type='variation')
tn, tc = 'variation_feature', 'consequence_types'
expected = set(('3_prime_UTR_variant', 'splice_acceptor_variant',
'5_prime_UTR_variant'))
got = db.getDistinct(tn, tc)
self.assertNotEquals(set(got) & expected, set())
db = Database(account=account, release=Release,
species='human', db_type='core')
tn, tc = 'gene', 'biotype'
expected = set(['protein_coding', 'pseudogene', 'processed_transcript',
'Mt_tRNA', 'Mt_rRNA', 'IG_V_gene', 'IG_J_gene',
'IG_C_gene', 'IG_D_gene', 'miRNA', 'misc_RNA', 'snoRNA', 'snRNA', 'rRNA'])
got = set(db.getDistinct(tn, tc))
self.assertNotEquals(set(got) & expected, set())
db = Database(account=account, release=Release, db_type='compara')
got = set(db.getDistinct('homology', 'description'))
expected = set([u'gene_split', u'alt_allele', u'other_paralog',
u'ortholog_one2many', u'ortholog_one2one',
u'within_species_paralog', u'ortholog_many2many'])
self.assertEquals(len(got&expected), len(expected))
def test_get_distinct(self):
"""should return list of strings"""
db = Database(account=account,
release=Release,
species='human',
db_type='variation')
tn, tc = 'variation_feature', 'consequence_types'
expected = set(('3_prime_UTR_variant', 'splice_acceptor_variant',
'5_prime_UTR_variant'))
got = db.getDistinct(tn, tc)
self.assertNotEqual(set(got) & expected, set())
db = Database(account=account,
release=Release,
species='human',
db_type='core')
tn, tc = 'gene', 'biotype'
expected = set([
'protein_coding', 'pseudogene', 'processed_transcript', 'Mt_tRNA',
'Mt_rRNA', 'IG_V_gene', 'IG_J_gene', 'IG_C_gene', 'IG_D_gene',
'miRNA', 'misc_RNA', 'snoRNA', 'snRNA', 'rRNA'
])
got = set(db.getDistinct(tn, tc))
self.assertNotEqual(set(got) & expected, set())
db = Database(account=account, release=Release, db_type='compara')
got = set(db.getDistinct('homology', 'description'))
expected = set([
'gene_split', 'alt_allele', 'other_paralog', 'ortholog_one2many',
'ortholog_one2one', 'within_species_paralog', 'ortholog_many2many'
])
self.assertEqual(len(got & expected), len(expected))
def test_get_distinct(self):
"""should return list of strings"""
db = Database(account=account, release=Release, species="human", db_type="variation")
tn, tc = "variation_feature", "consequence_type"
expected = set(
(
("3PRIME_UTR", "ESSENTIAL_SPLICE_SITE"),
("3PRIME_UTR", "SPLICE_SITE"),
("5PRIME_UTR", "ESSENTIAL_SPLICE_SITE"),
)
)
self.assertNotEquals(set(db.getDistinct(tn, tc)) & expected, set())
db = Database(account=account, release=Release, species="human", db_type="core")
tn, tc = "gene", "biotype"
expected = set(
[
"protein_coding",
"pseudogene",
"processed_transcript",
"Mt_tRNA",
"Mt_rRNA",
"IG_V_gene",
"IG_J_gene",
"IG_C_gene",
"IG_D_gene",
"miRNA",
"misc_RNA",
"snoRNA",
"snRNA",
"rRNA",
]
)
got = set(db.getDistinct(tn, tc))
self.assertEquals(len(got & expected), len(expected))
db = Database(account=account, release=Release, db_type="compara")
got = set(db.getDistinct("homology", "description"))
expected = set(
[
"apparent_ortholog_one2one",
"between_species_paralog",
"ortholog_many2many",
"ortholog_one2many",
"ortholog_one2one",
"within_species_paralog",
]
)
self.assertEquals(len(got & expected), len(expected))