1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
import os
from cogent.util.unit_test import TestCase, main
from cogent.db.ensembl.host import HostAccount, get_ensembl_account
from cogent.db.ensembl.database import Database
__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 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, 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(['apparent_ortholog_one2one', 'ortholog_many2many',
'ortholog_one2many', 'ortholog_one2one', 'within_species_paralog'])
self.assertEquals(len(got&expected), len(expected))
def test_get_table_row_counts(self):
"""should return correct row counts for some tables"""
expect = {'homo_sapiens_core_68_37.analysis': 61L,
'homo_sapiens_core_68_37.seq_region': 55616L,
'homo_sapiens_core_68_37.assembly': 102090L,
'homo_sapiens_core_68_37.qtl': 0L}
human = Database(account=account, release=Release,
species='human', db_type='core')
table_names = [n.split('.')[1] for n in expect]
got = dict(human.getTablesRowCount(table_names).getRawData())
for dbname in expect:
self.assertTrue(got[dbname] >= expect[dbname])
def test_table_has_column(self):
"""return correct values for whether a Table has a column"""
account = get_ensembl_account(release=Release)
var61 = Database(account=account, release=61, species='human',
db_type='variation')
var62 = Database(account=account, release=62, species='human',
db_type='variation')
self.assertTrue(var61.tableHasColumn('transcript_variation',
'peptide_allele_string'))
self.assertFalse(var61.tableHasColumn('transcript_variation',
'pep_allele_string'))
self.assertTrue(var62.tableHasColumn('transcript_variation',
'pep_allele_string'))
self.assertFalse(var62.tableHasColumn('transcript_variation',
'peptide_allele_string'))
if __name__ == "__main__":
main()
|
