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')])