def test_init_tables(self):
connection = sqlite_init._connect(self.test_db_name)
with connection:
c = connection.cursor()
c.execute("SELECT name FROM sqlite_master WHERE type='table';")
db_descr = c.fetchall()
self.assertEqual(db_descr, [('Pfam', ), ('GO', ), ('PfamGORelation', ),
('UniProt', ), ('PfamUniProtRelation', )])
def test_init_insert_pfam(self):
connection = sqlite_init._connect(self.test_db_name)
with connection:
c = connection.cursor()
c.execute("SELECT * FROM Pfam")
pfam_table = c.fetchall()
self.assertEqual(pfam_table,
[('PF00001', '7tm_1'), ('PF00002', '7tm_2'),
('PF00003', '7tm_3')])
def test_init_insert_go(self):
connection = sqlite_init._connect(self.test_db_name)
with connection:
c = connection.cursor()
c.execute("SELECT * FROM GO")
go_table = c.fetchall()
self.assertEqual(
go_table,
[('GO:0004930', 'G protein-coupled receptor activity'),
('GO:0007186', 'G protein-coupled receptor signaling pathway'),
('GO:0016021', 'integral component of membrane')])
def test_init_insert_pfam_go_relations(self):
connection = sqlite_init._connect(self.test_db_name)
with connection:
c = connection.cursor()
c.execute("SELECT * FROM PfamGORelation")
rel_table = c.fetchall()
self.assertEqual(rel_table, [('PF00001', 'GO:0004930'),
('PF00001', 'GO:0007186'),
('PF00001', 'GO:0016021'),
('PF00002', 'GO:0004930'),
('PF00002', 'GO:0007186'),
('PF00002', 'GO:0016021'),
('PF00003', 'GO:0004930'),
('PF00003', 'GO:0007186'),
('PF00003', 'GO:0016021')])
def test_uniprot_match_to_go_query(self):
connection = sqlite_init._connect(self.test_db_name)
with connection:
c = connection.cursor()
c.execute("""
SELECT GO_id
FROM PfamGORelation pg
INNER JOIN PfamUniProtRelation pu
ON pg.Pfam_accession = pu.Pfam_accession
WHERE pu.UniProt_accession = 'A0A1Y3N5N1'
AND pu.position = '320-559';
""")
res = c.fetchall()
self.assertEqual(res, [('GO:0004930', ), ('GO:0007186', ),
('GO:0016021', )])
def test_init_insert_pfam_uniprot_relations(self):
connection = sqlite_init._connect(self.test_db_name)
with connection:
c = connection.cursor()
c.execute("SELECT * FROM PfamUniProtRelation")
rel_table = c.fetchall()
self.assertEqual(rel_table, [('PF00001', 'A0A1S3GR90', '54-327'),
('PF00001', 'H9JMZ1', '45-143'),
('PF00001', 'W5NMM9', '44-295'),
('PF00001', 'A0A498M701', '58-314'),
('PF00001', 'C3Z4K9', '144-229'),
('PF00001', 'A0A369RQL1', '50-274'),
('PF00001', 'H3BCE7', '40-292'),
('PF00003', 'F7BBL0', '596-841'),
('PF00003', 'A0A1Y3N5N1', '320-559'),
('PF00003', 'A0A493T6H5', '488-719'),
('PF00003', 'A0A1L8GCA2', '499-734'),
('PF00003', 'A0A3P8PJJ8', '520-719'),
('PF00003', 'A0A3B1JRC8', '60-287'),
('PF00003', 'A0A158PBE8', '363-598'),
('PF00003', 'A0A482VPN5', '481-733')])
def test_init_insert_uniprot(self):
connection = sqlite_init._connect(self.test_db_name)
with connection:
c = connection.cursor()
c.execute("SELECT * FROM UniProt")
uniprot_table = c.fetchall()
self.assertEqual(uniprot_table, [('A0A1S3GR90', 'DIPOR'),
('H9JMZ1', 'BOMMO'),
('W5NMM9', 'LEPOC'),
('A0A498M701', 'LABRO'),
('C3Z4K9', 'BRAFL'),
('A0A369RQL1', '9METZ'),
('H3BCE7', 'LATCH'),
('F7BBL0', 'ORNAN'),
('A0A1Y3N5N1', 'PIRSE'),
('A0A493T6H5', 'ANAPP'),
('A0A1L8GCA2', 'XENLA'),
('A0A3P8PJJ8', 'ASTCA'),
('A0A3B1JRC8', 'ASTMX'),
('A0A158PBE8', 'ANGCA'),
('A0A482VPN5', '9CUCU')])